<a href="/tags/swc<!DOCTYPE HTML> Effective Teaching Tips from a Train-the-Trainers Workshop
13 Feb 2015

Effective Teaching Tips from a Train-the-Trainers Workshop

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective?

At the 2014 Society for Neuroscience Annual Meeting, I picked up the November “Focus on Big Data” issue of Nature Neuroscience, a collection of research articles, reviews, and commentaries on Big Data in neuroscience, from epigenomics and connectomics to large behavioral data sets. A common theme is that while large-scale studies are increasingly common, many challenges remain for data collection, analysis, and interpretation. To my surprise, there was no explicit mention of training the next generation of neuroscientists, which is a central focus of NIH’s “Big Data to Knowledge (BD2K) “ initiative.

Biomedical research is rapidly becoming data-intensive…however, the ability to … utilize the data is often limited by the lack of tools, accessibility, and training. From NIH BD2K RFA-14–008.

Cover image of Nature Neuroscience “Focus on Big Data” Issue, November 2014 Volume 17 No 11. Image by: Erin Dewalt

Big Data & Teaching

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective? This question has been on my mind for a while.

During the first week of January 2015, I met up with a group of transdisciplinary scientists who are passionate about teaching Big Data skills during a “Train-the-Trainers” workshop hosted by Greg Wilson (Software Carpentry), Tracy Teal (Data Carpentry), and Titus Brown (UC Davis). The goals of this two-day workshop were to bring together individuals for whom training is a priority and to help us improve our own teaching skills. I learned a lot about philosophies of teaching and received helpful teaching advice.

Here I highlight seven tips that are aimed towards increasing student success or improving one’s own teaching skills.

Tip # 1: Introductions set the stage for learning

It’s important to first assess whether your students are novices, intermediates, masters, or a combination of the three, because this will influence how you structure your course and how you communicate with your students.

To begin your class, give a brief introduction that will convey your: 1) capacity to teach the material, 2) accessibility/approachability and 3) desire for student success, 4) enthusiasm. Tailor your introduction to the students’ skill level so that you convey competence (without seeming too advanced) and demonstrates that you can relate to the students. Continually demonstrate that you are interested in student progress and that you are enthusiastic about the topics.

Students should also introduce themselves. Try having the students break into small groups so they can actually meet their peers and listen to what they have to say. Encourage students to say something they’ve made or accomplished; this will reveal a unique side of their personality, evoke a sense of pride and capability, and help them get to know each other.

Tip #2: Define learning goals and develop assessment tools

Before you begin teaching, define learning goals for your students. Then, develop a series of diagnostic questions that give insight into the concepts your students do and do not yet understand and why. Even if no grades are given in your course, it’s important to incorporate both summative and formative assessment. Summative assessment is like a driver license exam, which if failed prevents you from driving a vehicle. Formative assessment is more like the feedback a track coach might give to an athlete during the season to continually improve her form and speed.

Formative assessment activity during the Train-the-Trainers Workshop. Photo Credit: Olga Botvinnik

Also, why wait till the end of the term to get student feedback? If you just designed a new lesson or covered a particularly challenging topic, ask the students to tell you one good and one bad thing about the lesson or one thing they understood and one thing they didn’t. The responses will help you improve your teaching throughout the semester.

Tip #3: Use peer teaching as a tool for increased comprehension and retention

The best way to learn is to teach

Putting students in pairs or small groups to teach each other works really well. The next time your students don’t comprehend a concept after a repeated explanations, utilize peer-teaching. The student-teacher may be able to communicate a concept in a way the student-learner understands more easily.

There are a few ways to break up the groups or pairs. Letting groups self-select is not ideal because groups should have a range of knowledge/skill. One effective way is to stratify them, making sure each group has knowledgeable students paired with novices who are struggling to grasp the concepts. If this exercise required a computer or some other equipment, have the novice type/drive while the expert looks along as the co-pilot.

Peer teaching in action. Here, workshop attendees explain complex concepts to each other in groups of 3. Photo Credit: Olga Botvinnik

Tip #4 Actively keep your students engaged

Students can easily lose interest in the material you are teaching, get distracted (especially with the internet at their fingertips), and fail to see the critical connections between topics.

To keep students engaged, break up your lecture as often as you can (every 15 min or so). Give students a chance to stop listening and do something. This will help them to see structure in the content and to see things as related pieces of information rather than just a bunch of individual, unrelated concepts.

Also, by helping students make connections or visualize patterns between concepts you will facilitate the transfer of this information to long-term memory. The next time you cover a really complex or lengthy subject, draw a concept that illustrates the relationships among key points. Use this to guide your teaching timeline for the lesson (or series of lessons).

By combining lecture time with intermittent activities, you show respect for the attention-span limits of your students AND for your own time and effort, ultimately keeping the students engaged in and excited about your lesson.

Tip #5: Watch videos of yourself teaching

“Oh no, I said “um” 100 times!”

Video screenshot of me teaching the relationship between RT-qPCR experimental protocol and the central dogma of molecular biology in 4 min. Video Credit: Fatma Imamoglu

That’s what I said the first time I watched a video of myself teaching. Have you ever watched a video of yourself giving a talk or lecture and cringed at your own quirks and distracting habits?

Seeing yourself on video can really give you a new perspective, so I urge you to try it! Pay attention to where you can improve your poise and delivery. Once you are conscious of distracting mannerisms, you can begin to alter your style to something you can be proud of.

Tip #6: Seek critical feedback from colleagues

We are intimately familiar with peer review for publications and grant proposals, but can you remember the last time your peers gave critical feedback on your teaching style?

Invite a colleague to sit in on one of your classes and give feedback on delivery and student engagement. Or, write a blog about your teaching experiences and ask for comments and feedback (or post it on twitter and just wait for them). While your colleagues may not have an hour to sit in your class, many will read a short blog.

Tip #7: Stay in touch with your community

I recently wrote a blog called “Tips for Thriving in Research”, and the first two tips were about mentor-mentee relationships. I think that in order to get better at teaching, it’s important to surround yourself with mentors and mentees who are also passionate about teaching.

Read, write, blog, and talk about your teaching experiences with like-minded scientists. Here are two really good two really good blogs on student evaluations written by my colleagues Olga Botvinnik and April Wright.

Before creating a lesson or exam from scratch (possibly reinventing the wheel) first see if you can find tried-and-tested syllabi from your community. Online resources like Code Academy’s Python Coding for Beginner’s, the Rosalind platform for learning bioinformatics, and Software Carpentry’s open access teaching materials are excellent tools for teaching Big Data concepts and skills to trainees.

Hopefully, with a continued community focus on training, the next generation of neuroscientists will be better adapt to deal with the challenges that still remain for Big Data research.

Thanks to:

I definitely want to thank the organizers and instructors (Greg Wilson, Tracy Teal, and Titus Brown, Bill Mills and Aleksandra Pawlik) for providing excellent examples of teaching by doing. I thank April Wright for encouraging me to attend and for securing funding from BEACON Center. Becca Tarvin and I reflected on what we learned and discussed ways to apply this to our burgeoning community of bioinformatic aficionados via the Center for Computational Biology and Bioinformatics (CCBB) at UT Austin (see her companion blog).

Re-posting: This blog was originally published via PLOS Neuroscience Community here. Disclaimer. The views expressed are my own, not necessarily those of PLOS.

swc  dc  teaching 
</body> </html> " class="button special small">swc<!DOCTYPE HTML> Effective Teaching Tips from a Train-the-Trainers Workshop
13 Feb 2015

Effective Teaching Tips from a Train-the-Trainers Workshop

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective?

At the 2014 Society for Neuroscience Annual Meeting, I picked up the November “Focus on Big Data” issue of Nature Neuroscience, a collection of research articles, reviews, and commentaries on Big Data in neuroscience, from epigenomics and connectomics to large behavioral data sets. A common theme is that while large-scale studies are increasingly common, many challenges remain for data collection, analysis, and interpretation. To my surprise, there was no explicit mention of training the next generation of neuroscientists, which is a central focus of NIH’s “Big Data to Knowledge (BD2K) “ initiative.

Biomedical research is rapidly becoming data-intensive…however, the ability to … utilize the data is often limited by the lack of tools, accessibility, and training. From NIH BD2K RFA-14–008.

Cover image of Nature Neuroscience “Focus on Big Data” Issue, November 2014 Volume 17 No 11. Image by: Erin Dewalt

Big Data & Teaching

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective? This question has been on my mind for a while.

During the first week of January 2015, I met up with a group of transdisciplinary scientists who are passionate about teaching Big Data skills during a “Train-the-Trainers” workshop hosted by Greg Wilson (Software Carpentry), Tracy Teal (Data Carpentry), and Titus Brown (UC Davis). The goals of this two-day workshop were to bring together individuals for whom training is a priority and to help us improve our own teaching skills. I learned a lot about philosophies of teaching and received helpful teaching advice.

Here I highlight seven tips that are aimed towards increasing student success or improving one’s own teaching skills.

Tip # 1: Introductions set the stage for learning

It’s important to first assess whether your students are novices, intermediates, masters, or a combination of the three, because this will influence how you structure your course and how you communicate with your students.

To begin your class, give a brief introduction that will convey your: 1) capacity to teach the material, 2) accessibility/approachability and 3) desire for student success, 4) enthusiasm. Tailor your introduction to the students’ skill level so that you convey competence (without seeming too advanced) and demonstrates that you can relate to the students. Continually demonstrate that you are interested in student progress and that you are enthusiastic about the topics.

Students should also introduce themselves. Try having the students break into small groups so they can actually meet their peers and listen to what they have to say. Encourage students to say something they’ve made or accomplished; this will reveal a unique side of their personality, evoke a sense of pride and capability, and help them get to know each other.

Tip #2: Define learning goals and develop assessment tools

Before you begin teaching, define learning goals for your students. Then, develop a series of diagnostic questions that give insight into the concepts your students do and do not yet understand and why. Even if no grades are given in your course, it’s important to incorporate both summative and formative assessment. Summative assessment is like a driver license exam, which if failed prevents you from driving a vehicle. Formative assessment is more like the feedback a track coach might give to an athlete during the season to continually improve her form and speed.

Formative assessment activity during the Train-the-Trainers Workshop. Photo Credit: Olga Botvinnik

Also, why wait till the end of the term to get student feedback? If you just designed a new lesson or covered a particularly challenging topic, ask the students to tell you one good and one bad thing about the lesson or one thing they understood and one thing they didn’t. The responses will help you improve your teaching throughout the semester.

Tip #3: Use peer teaching as a tool for increased comprehension and retention

The best way to learn is to teach

Putting students in pairs or small groups to teach each other works really well. The next time your students don’t comprehend a concept after a repeated explanations, utilize peer-teaching. The student-teacher may be able to communicate a concept in a way the student-learner understands more easily.

There are a few ways to break up the groups or pairs. Letting groups self-select is not ideal because groups should have a range of knowledge/skill. One effective way is to stratify them, making sure each group has knowledgeable students paired with novices who are struggling to grasp the concepts. If this exercise required a computer or some other equipment, have the novice type/drive while the expert looks along as the co-pilot.

Peer teaching in action. Here, workshop attendees explain complex concepts to each other in groups of 3. Photo Credit: Olga Botvinnik

Tip #4 Actively keep your students engaged

Students can easily lose interest in the material you are teaching, get distracted (especially with the internet at their fingertips), and fail to see the critical connections between topics.

To keep students engaged, break up your lecture as often as you can (every 15 min or so). Give students a chance to stop listening and do something. This will help them to see structure in the content and to see things as related pieces of information rather than just a bunch of individual, unrelated concepts.

Also, by helping students make connections or visualize patterns between concepts you will facilitate the transfer of this information to long-term memory. The next time you cover a really complex or lengthy subject, draw a concept that illustrates the relationships among key points. Use this to guide your teaching timeline for the lesson (or series of lessons).

By combining lecture time with intermittent activities, you show respect for the attention-span limits of your students AND for your own time and effort, ultimately keeping the students engaged in and excited about your lesson.

Tip #5: Watch videos of yourself teaching

“Oh no, I said “um” 100 times!”

Video screenshot of me teaching the relationship between RT-qPCR experimental protocol and the central dogma of molecular biology in 4 min. Video Credit: Fatma Imamoglu

That’s what I said the first time I watched a video of myself teaching. Have you ever watched a video of yourself giving a talk or lecture and cringed at your own quirks and distracting habits?

Seeing yourself on video can really give you a new perspective, so I urge you to try it! Pay attention to where you can improve your poise and delivery. Once you are conscious of distracting mannerisms, you can begin to alter your style to something you can be proud of.

Tip #6: Seek critical feedback from colleagues

We are intimately familiar with peer review for publications and grant proposals, but can you remember the last time your peers gave critical feedback on your teaching style?

Invite a colleague to sit in on one of your classes and give feedback on delivery and student engagement. Or, write a blog about your teaching experiences and ask for comments and feedback (or post it on twitter and just wait for them). While your colleagues may not have an hour to sit in your class, many will read a short blog.

Tip #7: Stay in touch with your community

I recently wrote a blog called “Tips for Thriving in Research”, and the first two tips were about mentor-mentee relationships. I think that in order to get better at teaching, it’s important to surround yourself with mentors and mentees who are also passionate about teaching.

Read, write, blog, and talk about your teaching experiences with like-minded scientists. Here are two really good two really good blogs on student evaluations written by my colleagues Olga Botvinnik and April Wright.

Before creating a lesson or exam from scratch (possibly reinventing the wheel) first see if you can find tried-and-tested syllabi from your community. Online resources like Code Academy’s Python Coding for Beginner’s, the Rosalind platform for learning bioinformatics, and Software Carpentry’s open access teaching materials are excellent tools for teaching Big Data concepts and skills to trainees.

Hopefully, with a continued community focus on training, the next generation of neuroscientists will be better adapt to deal with the challenges that still remain for Big Data research.

Thanks to:

I definitely want to thank the organizers and instructors (Greg Wilson, Tracy Teal, and Titus Brown, Bill Mills and Aleksandra Pawlik) for providing excellent examples of teaching by doing. I thank April Wright for encouraging me to attend and for securing funding from BEACON Center. Becca Tarvin and I reflected on what we learned and discussed ways to apply this to our burgeoning community of bioinformatic aficionados via the Center for Computational Biology and Bioinformatics (CCBB) at UT Austin (see her companion blog).

Re-posting: This blog was originally published via PLOS Neuroscience Community here. Disclaimer. The views expressed are my own, not necessarily those of PLOS.

swc  dc  teaching 
</body> </html> </a> <a href="/tags/dc<!DOCTYPE HTML> Effective Teaching Tips from a Train-the-Trainers Workshop
13 Feb 2015

Effective Teaching Tips from a Train-the-Trainers Workshop

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective?

At the 2014 Society for Neuroscience Annual Meeting, I picked up the November “Focus on Big Data” issue of Nature Neuroscience, a collection of research articles, reviews, and commentaries on Big Data in neuroscience, from epigenomics and connectomics to large behavioral data sets. A common theme is that while large-scale studies are increasingly common, many challenges remain for data collection, analysis, and interpretation. To my surprise, there was no explicit mention of training the next generation of neuroscientists, which is a central focus of NIH’s “Big Data to Knowledge (BD2K) “ initiative.

Biomedical research is rapidly becoming data-intensive…however, the ability to … utilize the data is often limited by the lack of tools, accessibility, and training. From NIH BD2K RFA-14–008.

Cover image of Nature Neuroscience “Focus on Big Data” Issue, November 2014 Volume 17 No 11. Image by: Erin Dewalt

Big Data & Teaching

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective? This question has been on my mind for a while.

During the first week of January 2015, I met up with a group of transdisciplinary scientists who are passionate about teaching Big Data skills during a “Train-the-Trainers” workshop hosted by Greg Wilson (Software Carpentry), Tracy Teal (Data Carpentry), and Titus Brown (UC Davis). The goals of this two-day workshop were to bring together individuals for whom training is a priority and to help us improve our own teaching skills. I learned a lot about philosophies of teaching and received helpful teaching advice.

Here I highlight seven tips that are aimed towards increasing student success or improving one’s own teaching skills.

Tip # 1: Introductions set the stage for learning

It’s important to first assess whether your students are novices, intermediates, masters, or a combination of the three, because this will influence how you structure your course and how you communicate with your students.

To begin your class, give a brief introduction that will convey your: 1) capacity to teach the material, 2) accessibility/approachability and 3) desire for student success, 4) enthusiasm. Tailor your introduction to the students’ skill level so that you convey competence (without seeming too advanced) and demonstrates that you can relate to the students. Continually demonstrate that you are interested in student progress and that you are enthusiastic about the topics.

Students should also introduce themselves. Try having the students break into small groups so they can actually meet their peers and listen to what they have to say. Encourage students to say something they’ve made or accomplished; this will reveal a unique side of their personality, evoke a sense of pride and capability, and help them get to know each other.

Tip #2: Define learning goals and develop assessment tools

Before you begin teaching, define learning goals for your students. Then, develop a series of diagnostic questions that give insight into the concepts your students do and do not yet understand and why. Even if no grades are given in your course, it’s important to incorporate both summative and formative assessment. Summative assessment is like a driver license exam, which if failed prevents you from driving a vehicle. Formative assessment is more like the feedback a track coach might give to an athlete during the season to continually improve her form and speed.

Formative assessment activity during the Train-the-Trainers Workshop. Photo Credit: Olga Botvinnik

Also, why wait till the end of the term to get student feedback? If you just designed a new lesson or covered a particularly challenging topic, ask the students to tell you one good and one bad thing about the lesson or one thing they understood and one thing they didn’t. The responses will help you improve your teaching throughout the semester.

Tip #3: Use peer teaching as a tool for increased comprehension and retention

The best way to learn is to teach

Putting students in pairs or small groups to teach each other works really well. The next time your students don’t comprehend a concept after a repeated explanations, utilize peer-teaching. The student-teacher may be able to communicate a concept in a way the student-learner understands more easily.

There are a few ways to break up the groups or pairs. Letting groups self-select is not ideal because groups should have a range of knowledge/skill. One effective way is to stratify them, making sure each group has knowledgeable students paired with novices who are struggling to grasp the concepts. If this exercise required a computer or some other equipment, have the novice type/drive while the expert looks along as the co-pilot.

Peer teaching in action. Here, workshop attendees explain complex concepts to each other in groups of 3. Photo Credit: Olga Botvinnik

Tip #4 Actively keep your students engaged

Students can easily lose interest in the material you are teaching, get distracted (especially with the internet at their fingertips), and fail to see the critical connections between topics.

To keep students engaged, break up your lecture as often as you can (every 15 min or so). Give students a chance to stop listening and do something. This will help them to see structure in the content and to see things as related pieces of information rather than just a bunch of individual, unrelated concepts.

Also, by helping students make connections or visualize patterns between concepts you will facilitate the transfer of this information to long-term memory. The next time you cover a really complex or lengthy subject, draw a concept that illustrates the relationships among key points. Use this to guide your teaching timeline for the lesson (or series of lessons).

By combining lecture time with intermittent activities, you show respect for the attention-span limits of your students AND for your own time and effort, ultimately keeping the students engaged in and excited about your lesson.

Tip #5: Watch videos of yourself teaching

“Oh no, I said “um” 100 times!”

Video screenshot of me teaching the relationship between RT-qPCR experimental protocol and the central dogma of molecular biology in 4 min. Video Credit: Fatma Imamoglu

That’s what I said the first time I watched a video of myself teaching. Have you ever watched a video of yourself giving a talk or lecture and cringed at your own quirks and distracting habits?

Seeing yourself on video can really give you a new perspective, so I urge you to try it! Pay attention to where you can improve your poise and delivery. Once you are conscious of distracting mannerisms, you can begin to alter your style to something you can be proud of.

Tip #6: Seek critical feedback from colleagues

We are intimately familiar with peer review for publications and grant proposals, but can you remember the last time your peers gave critical feedback on your teaching style?

Invite a colleague to sit in on one of your classes and give feedback on delivery and student engagement. Or, write a blog about your teaching experiences and ask for comments and feedback (or post it on twitter and just wait for them). While your colleagues may not have an hour to sit in your class, many will read a short blog.

Tip #7: Stay in touch with your community

I recently wrote a blog called “Tips for Thriving in Research”, and the first two tips were about mentor-mentee relationships. I think that in order to get better at teaching, it’s important to surround yourself with mentors and mentees who are also passionate about teaching.

Read, write, blog, and talk about your teaching experiences with like-minded scientists. Here are two really good two really good blogs on student evaluations written by my colleagues Olga Botvinnik and April Wright.

Before creating a lesson or exam from scratch (possibly reinventing the wheel) first see if you can find tried-and-tested syllabi from your community. Online resources like Code Academy’s Python Coding for Beginner’s, the Rosalind platform for learning bioinformatics, and Software Carpentry’s open access teaching materials are excellent tools for teaching Big Data concepts and skills to trainees.

Hopefully, with a continued community focus on training, the next generation of neuroscientists will be better adapt to deal with the challenges that still remain for Big Data research.

Thanks to:

I definitely want to thank the organizers and instructors (Greg Wilson, Tracy Teal, and Titus Brown, Bill Mills and Aleksandra Pawlik) for providing excellent examples of teaching by doing. I thank April Wright for encouraging me to attend and for securing funding from BEACON Center. Becca Tarvin and I reflected on what we learned and discussed ways to apply this to our burgeoning community of bioinformatic aficionados via the Center for Computational Biology and Bioinformatics (CCBB) at UT Austin (see her companion blog).

Re-posting: This blog was originally published via PLOS Neuroscience Community here. Disclaimer. The views expressed are my own, not necessarily those of PLOS.

swc  dc  teaching 
</body> </html> " class="button special small">dc<!DOCTYPE HTML> Effective Teaching Tips from a Train-the-Trainers Workshop
13 Feb 2015

Effective Teaching Tips from a Train-the-Trainers Workshop

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective?

At the 2014 Society for Neuroscience Annual Meeting, I picked up the November “Focus on Big Data” issue of Nature Neuroscience, a collection of research articles, reviews, and commentaries on Big Data in neuroscience, from epigenomics and connectomics to large behavioral data sets. A common theme is that while large-scale studies are increasingly common, many challenges remain for data collection, analysis, and interpretation. To my surprise, there was no explicit mention of training the next generation of neuroscientists, which is a central focus of NIH’s “Big Data to Knowledge (BD2K) “ initiative.

Biomedical research is rapidly becoming data-intensive…however, the ability to … utilize the data is often limited by the lack of tools, accessibility, and training. From NIH BD2K RFA-14–008.

Cover image of Nature Neuroscience “Focus on Big Data” Issue, November 2014 Volume 17 No 11. Image by: Erin Dewalt

Big Data & Teaching

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective? This question has been on my mind for a while.

During the first week of January 2015, I met up with a group of transdisciplinary scientists who are passionate about teaching Big Data skills during a “Train-the-Trainers” workshop hosted by Greg Wilson (Software Carpentry), Tracy Teal (Data Carpentry), and Titus Brown (UC Davis). The goals of this two-day workshop were to bring together individuals for whom training is a priority and to help us improve our own teaching skills. I learned a lot about philosophies of teaching and received helpful teaching advice.

Here I highlight seven tips that are aimed towards increasing student success or improving one’s own teaching skills.

Tip # 1: Introductions set the stage for learning

It’s important to first assess whether your students are novices, intermediates, masters, or a combination of the three, because this will influence how you structure your course and how you communicate with your students.

To begin your class, give a brief introduction that will convey your: 1) capacity to teach the material, 2) accessibility/approachability and 3) desire for student success, 4) enthusiasm. Tailor your introduction to the students’ skill level so that you convey competence (without seeming too advanced) and demonstrates that you can relate to the students. Continually demonstrate that you are interested in student progress and that you are enthusiastic about the topics.

Students should also introduce themselves. Try having the students break into small groups so they can actually meet their peers and listen to what they have to say. Encourage students to say something they’ve made or accomplished; this will reveal a unique side of their personality, evoke a sense of pride and capability, and help them get to know each other.

Tip #2: Define learning goals and develop assessment tools

Before you begin teaching, define learning goals for your students. Then, develop a series of diagnostic questions that give insight into the concepts your students do and do not yet understand and why. Even if no grades are given in your course, it’s important to incorporate both summative and formative assessment. Summative assessment is like a driver license exam, which if failed prevents you from driving a vehicle. Formative assessment is more like the feedback a track coach might give to an athlete during the season to continually improve her form and speed.

Formative assessment activity during the Train-the-Trainers Workshop. Photo Credit: Olga Botvinnik

Also, why wait till the end of the term to get student feedback? If you just designed a new lesson or covered a particularly challenging topic, ask the students to tell you one good and one bad thing about the lesson or one thing they understood and one thing they didn’t. The responses will help you improve your teaching throughout the semester.

Tip #3: Use peer teaching as a tool for increased comprehension and retention

The best way to learn is to teach

Putting students in pairs or small groups to teach each other works really well. The next time your students don’t comprehend a concept after a repeated explanations, utilize peer-teaching. The student-teacher may be able to communicate a concept in a way the student-learner understands more easily.

There are a few ways to break up the groups or pairs. Letting groups self-select is not ideal because groups should have a range of knowledge/skill. One effective way is to stratify them, making sure each group has knowledgeable students paired with novices who are struggling to grasp the concepts. If this exercise required a computer or some other equipment, have the novice type/drive while the expert looks along as the co-pilot.

Peer teaching in action. Here, workshop attendees explain complex concepts to each other in groups of 3. Photo Credit: Olga Botvinnik

Tip #4 Actively keep your students engaged

Students can easily lose interest in the material you are teaching, get distracted (especially with the internet at their fingertips), and fail to see the critical connections between topics.

To keep students engaged, break up your lecture as often as you can (every 15 min or so). Give students a chance to stop listening and do something. This will help them to see structure in the content and to see things as related pieces of information rather than just a bunch of individual, unrelated concepts.

Also, by helping students make connections or visualize patterns between concepts you will facilitate the transfer of this information to long-term memory. The next time you cover a really complex or lengthy subject, draw a concept that illustrates the relationships among key points. Use this to guide your teaching timeline for the lesson (or series of lessons).

By combining lecture time with intermittent activities, you show respect for the attention-span limits of your students AND for your own time and effort, ultimately keeping the students engaged in and excited about your lesson.

Tip #5: Watch videos of yourself teaching

“Oh no, I said “um” 100 times!”

Video screenshot of me teaching the relationship between RT-qPCR experimental protocol and the central dogma of molecular biology in 4 min. Video Credit: Fatma Imamoglu

That’s what I said the first time I watched a video of myself teaching. Have you ever watched a video of yourself giving a talk or lecture and cringed at your own quirks and distracting habits?

Seeing yourself on video can really give you a new perspective, so I urge you to try it! Pay attention to where you can improve your poise and delivery. Once you are conscious of distracting mannerisms, you can begin to alter your style to something you can be proud of.

Tip #6: Seek critical feedback from colleagues

We are intimately familiar with peer review for publications and grant proposals, but can you remember the last time your peers gave critical feedback on your teaching style?

Invite a colleague to sit in on one of your classes and give feedback on delivery and student engagement. Or, write a blog about your teaching experiences and ask for comments and feedback (or post it on twitter and just wait for them). While your colleagues may not have an hour to sit in your class, many will read a short blog.

Tip #7: Stay in touch with your community

I recently wrote a blog called “Tips for Thriving in Research”, and the first two tips were about mentor-mentee relationships. I think that in order to get better at teaching, it’s important to surround yourself with mentors and mentees who are also passionate about teaching.

Read, write, blog, and talk about your teaching experiences with like-minded scientists. Here are two really good two really good blogs on student evaluations written by my colleagues Olga Botvinnik and April Wright.

Before creating a lesson or exam from scratch (possibly reinventing the wheel) first see if you can find tried-and-tested syllabi from your community. Online resources like Code Academy’s Python Coding for Beginner’s, the Rosalind platform for learning bioinformatics, and Software Carpentry’s open access teaching materials are excellent tools for teaching Big Data concepts and skills to trainees.

Hopefully, with a continued community focus on training, the next generation of neuroscientists will be better adapt to deal with the challenges that still remain for Big Data research.

Thanks to:

I definitely want to thank the organizers and instructors (Greg Wilson, Tracy Teal, and Titus Brown, Bill Mills and Aleksandra Pawlik) for providing excellent examples of teaching by doing. I thank April Wright for encouraging me to attend and for securing funding from BEACON Center. Becca Tarvin and I reflected on what we learned and discussed ways to apply this to our burgeoning community of bioinformatic aficionados via the Center for Computational Biology and Bioinformatics (CCBB) at UT Austin (see her companion blog).

Re-posting: This blog was originally published via PLOS Neuroscience Community here. Disclaimer. The views expressed are my own, not necessarily those of PLOS.

swc  dc  teaching 
</body> </html> </a> <a href="/tags/teaching<!DOCTYPE HTML> Effective Teaching Tips from a Train-the-Trainers Workshop
13 Feb 2015

Effective Teaching Tips from a Train-the-Trainers Workshop

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective?

At the 2014 Society for Neuroscience Annual Meeting, I picked up the November “Focus on Big Data” issue of Nature Neuroscience, a collection of research articles, reviews, and commentaries on Big Data in neuroscience, from epigenomics and connectomics to large behavioral data sets. A common theme is that while large-scale studies are increasingly common, many challenges remain for data collection, analysis, and interpretation. To my surprise, there was no explicit mention of training the next generation of neuroscientists, which is a central focus of NIH’s “Big Data to Knowledge (BD2K) “ initiative.

Biomedical research is rapidly becoming data-intensive…however, the ability to … utilize the data is often limited by the lack of tools, accessibility, and training. From NIH BD2K RFA-14–008.

Cover image of Nature Neuroscience “Focus on Big Data” Issue, November 2014 Volume 17 No 11. Image by: Erin Dewalt

Big Data & Teaching

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective? This question has been on my mind for a while.

During the first week of January 2015, I met up with a group of transdisciplinary scientists who are passionate about teaching Big Data skills during a “Train-the-Trainers” workshop hosted by Greg Wilson (Software Carpentry), Tracy Teal (Data Carpentry), and Titus Brown (UC Davis). The goals of this two-day workshop were to bring together individuals for whom training is a priority and to help us improve our own teaching skills. I learned a lot about philosophies of teaching and received helpful teaching advice.

Here I highlight seven tips that are aimed towards increasing student success or improving one’s own teaching skills.

Tip # 1: Introductions set the stage for learning

It’s important to first assess whether your students are novices, intermediates, masters, or a combination of the three, because this will influence how you structure your course and how you communicate with your students.

To begin your class, give a brief introduction that will convey your: 1) capacity to teach the material, 2) accessibility/approachability and 3) desire for student success, 4) enthusiasm. Tailor your introduction to the students’ skill level so that you convey competence (without seeming too advanced) and demonstrates that you can relate to the students. Continually demonstrate that you are interested in student progress and that you are enthusiastic about the topics.

Students should also introduce themselves. Try having the students break into small groups so they can actually meet their peers and listen to what they have to say. Encourage students to say something they’ve made or accomplished; this will reveal a unique side of their personality, evoke a sense of pride and capability, and help them get to know each other.

Tip #2: Define learning goals and develop assessment tools

Before you begin teaching, define learning goals for your students. Then, develop a series of diagnostic questions that give insight into the concepts your students do and do not yet understand and why. Even if no grades are given in your course, it’s important to incorporate both summative and formative assessment. Summative assessment is like a driver license exam, which if failed prevents you from driving a vehicle. Formative assessment is more like the feedback a track coach might give to an athlete during the season to continually improve her form and speed.

Formative assessment activity during the Train-the-Trainers Workshop. Photo Credit: Olga Botvinnik

Also, why wait till the end of the term to get student feedback? If you just designed a new lesson or covered a particularly challenging topic, ask the students to tell you one good and one bad thing about the lesson or one thing they understood and one thing they didn’t. The responses will help you improve your teaching throughout the semester.

Tip #3: Use peer teaching as a tool for increased comprehension and retention

The best way to learn is to teach

Putting students in pairs or small groups to teach each other works really well. The next time your students don’t comprehend a concept after a repeated explanations, utilize peer-teaching. The student-teacher may be able to communicate a concept in a way the student-learner understands more easily.

There are a few ways to break up the groups or pairs. Letting groups self-select is not ideal because groups should have a range of knowledge/skill. One effective way is to stratify them, making sure each group has knowledgeable students paired with novices who are struggling to grasp the concepts. If this exercise required a computer or some other equipment, have the novice type/drive while the expert looks along as the co-pilot.

Peer teaching in action. Here, workshop attendees explain complex concepts to each other in groups of 3. Photo Credit: Olga Botvinnik

Tip #4 Actively keep your students engaged

Students can easily lose interest in the material you are teaching, get distracted (especially with the internet at their fingertips), and fail to see the critical connections between topics.

To keep students engaged, break up your lecture as often as you can (every 15 min or so). Give students a chance to stop listening and do something. This will help them to see structure in the content and to see things as related pieces of information rather than just a bunch of individual, unrelated concepts.

Also, by helping students make connections or visualize patterns between concepts you will facilitate the transfer of this information to long-term memory. The next time you cover a really complex or lengthy subject, draw a concept that illustrates the relationships among key points. Use this to guide your teaching timeline for the lesson (or series of lessons).

By combining lecture time with intermittent activities, you show respect for the attention-span limits of your students AND for your own time and effort, ultimately keeping the students engaged in and excited about your lesson.

Tip #5: Watch videos of yourself teaching

“Oh no, I said “um” 100 times!”

Video screenshot of me teaching the relationship between RT-qPCR experimental protocol and the central dogma of molecular biology in 4 min. Video Credit: Fatma Imamoglu

That’s what I said the first time I watched a video of myself teaching. Have you ever watched a video of yourself giving a talk or lecture and cringed at your own quirks and distracting habits?

Seeing yourself on video can really give you a new perspective, so I urge you to try it! Pay attention to where you can improve your poise and delivery. Once you are conscious of distracting mannerisms, you can begin to alter your style to something you can be proud of.

Tip #6: Seek critical feedback from colleagues

We are intimately familiar with peer review for publications and grant proposals, but can you remember the last time your peers gave critical feedback on your teaching style?

Invite a colleague to sit in on one of your classes and give feedback on delivery and student engagement. Or, write a blog about your teaching experiences and ask for comments and feedback (or post it on twitter and just wait for them). While your colleagues may not have an hour to sit in your class, many will read a short blog.

Tip #7: Stay in touch with your community

I recently wrote a blog called “Tips for Thriving in Research”, and the first two tips were about mentor-mentee relationships. I think that in order to get better at teaching, it’s important to surround yourself with mentors and mentees who are also passionate about teaching.

Read, write, blog, and talk about your teaching experiences with like-minded scientists. Here are two really good two really good blogs on student evaluations written by my colleagues Olga Botvinnik and April Wright.

Before creating a lesson or exam from scratch (possibly reinventing the wheel) first see if you can find tried-and-tested syllabi from your community. Online resources like Code Academy’s Python Coding for Beginner’s, the Rosalind platform for learning bioinformatics, and Software Carpentry’s open access teaching materials are excellent tools for teaching Big Data concepts and skills to trainees.

Hopefully, with a continued community focus on training, the next generation of neuroscientists will be better adapt to deal with the challenges that still remain for Big Data research.

Thanks to:

I definitely want to thank the organizers and instructors (Greg Wilson, Tracy Teal, and Titus Brown, Bill Mills and Aleksandra Pawlik) for providing excellent examples of teaching by doing. I thank April Wright for encouraging me to attend and for securing funding from BEACON Center. Becca Tarvin and I reflected on what we learned and discussed ways to apply this to our burgeoning community of bioinformatic aficionados via the Center for Computational Biology and Bioinformatics (CCBB) at UT Austin (see her companion blog).

Re-posting: This blog was originally published via PLOS Neuroscience Community here. Disclaimer. The views expressed are my own, not necessarily those of PLOS.

swc  dc  teaching 
</body> </html> " class="button special small">teaching<!DOCTYPE HTML> Effective Teaching Tips from a Train-the-Trainers Workshop
13 Feb 2015

Effective Teaching Tips from a Train-the-Trainers Workshop

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective?

At the 2014 Society for Neuroscience Annual Meeting, I picked up the November “Focus on Big Data” issue of Nature Neuroscience, a collection of research articles, reviews, and commentaries on Big Data in neuroscience, from epigenomics and connectomics to large behavioral data sets. A common theme is that while large-scale studies are increasingly common, many challenges remain for data collection, analysis, and interpretation. To my surprise, there was no explicit mention of training the next generation of neuroscientists, which is a central focus of NIH’s “Big Data to Knowledge (BD2K) “ initiative.

Biomedical research is rapidly becoming data-intensive…however, the ability to … utilize the data is often limited by the lack of tools, accessibility, and training. From NIH BD2K RFA-14–008.

Cover image of Nature Neuroscience “Focus on Big Data” Issue, November 2014 Volume 17 No 11. Image by: Erin Dewalt

Big Data & Teaching

How do we train the next generation of scientists to manage, analyze, and share data in a reproducible way so that they can be more productive and effective? This question has been on my mind for a while.

During the first week of January 2015, I met up with a group of transdisciplinary scientists who are passionate about teaching Big Data skills during a “Train-the-Trainers” workshop hosted by Greg Wilson (Software Carpentry), Tracy Teal (Data Carpentry), and Titus Brown (UC Davis). The goals of this two-day workshop were to bring together individuals for whom training is a priority and to help us improve our own teaching skills. I learned a lot about philosophies of teaching and received helpful teaching advice.

Here I highlight seven tips that are aimed towards increasing student success or improving one’s own teaching skills.

Tip # 1: Introductions set the stage for learning

It’s important to first assess whether your students are novices, intermediates, masters, or a combination of the three, because this will influence how you structure your course and how you communicate with your students.

To begin your class, give a brief introduction that will convey your: 1) capacity to teach the material, 2) accessibility/approachability and 3) desire for student success, 4) enthusiasm. Tailor your introduction to the students’ skill level so that you convey competence (without seeming too advanced) and demonstrates that you can relate to the students. Continually demonstrate that you are interested in student progress and that you are enthusiastic about the topics.

Students should also introduce themselves. Try having the students break into small groups so they can actually meet their peers and listen to what they have to say. Encourage students to say something they’ve made or accomplished; this will reveal a unique side of their personality, evoke a sense of pride and capability, and help them get to know each other.

Tip #2: Define learning goals and develop assessment tools

Before you begin teaching, define learning goals for your students. Then, develop a series of diagnostic questions that give insight into the concepts your students do and do not yet understand and why. Even if no grades are given in your course, it’s important to incorporate both summative and formative assessment. Summative assessment is like a driver license exam, which if failed prevents you from driving a vehicle. Formative assessment is more like the feedback a track coach might give to an athlete during the season to continually improve her form and speed.

Formative assessment activity during the Train-the-Trainers Workshop. Photo Credit: Olga Botvinnik

Also, why wait till the end of the term to get student feedback? If you just designed a new lesson or covered a particularly challenging topic, ask the students to tell you one good and one bad thing about the lesson or one thing they understood and one thing they didn’t. The responses will help you improve your teaching throughout the semester.

Tip #3: Use peer teaching as a tool for increased comprehension and retention

The best way to learn is to teach

Putting students in pairs or small groups to teach each other works really well. The next time your students don’t comprehend a concept after a repeated explanations, utilize peer-teaching. The student-teacher may be able to communicate a concept in a way the student-learner understands more easily.

There are a few ways to break up the groups or pairs. Letting groups self-select is not ideal because groups should have a range of knowledge/skill. One effective way is to stratify them, making sure each group has knowledgeable students paired with novices who are struggling to grasp the concepts. If this exercise required a computer or some other equipment, have the novice type/drive while the expert looks along as the co-pilot.

Peer teaching in action. Here, workshop attendees explain complex concepts to each other in groups of 3. Photo Credit: Olga Botvinnik

Tip #4 Actively keep your students engaged

Students can easily lose interest in the material you are teaching, get distracted (especially with the internet at their fingertips), and fail to see the critical connections between topics.

To keep students engaged, break up your lecture as often as you can (every 15 min or so). Give students a chance to stop listening and do something. This will help them to see structure in the content and to see things as related pieces of information rather than just a bunch of individual, unrelated concepts.

Also, by helping students make connections or visualize patterns between concepts you will facilitate the transfer of this information to long-term memory. The next time you cover a really complex or lengthy subject, draw a concept that illustrates the relationships among key points. Use this to guide your teaching timeline for the lesson (or series of lessons).

By combining lecture time with intermittent activities, you show respect for the attention-span limits of your students AND for your own time and effort, ultimately keeping the students engaged in and excited about your lesson.

Tip #5: Watch videos of yourself teaching

“Oh no, I said “um” 100 times!”

Video screenshot of me teaching the relationship between RT-qPCR experimental protocol and the central dogma of molecular biology in 4 min. Video Credit: Fatma Imamoglu

That’s what I said the first time I watched a video of myself teaching. Have you ever watched a video of yourself giving a talk or lecture and cringed at your own quirks and distracting habits?

Seeing yourself on video can really give you a new perspective, so I urge you to try it! Pay attention to where you can improve your poise and delivery. Once you are conscious of distracting mannerisms, you can begin to alter your style to something you can be proud of.

Tip #6: Seek critical feedback from colleagues

We are intimately familiar with peer review for publications and grant proposals, but can you remember the last time your peers gave critical feedback on your teaching style?

Invite a colleague to sit in on one of your classes and give feedback on delivery and student engagement. Or, write a blog about your teaching experiences and ask for comments and feedback (or post it on twitter and just wait for them). While your colleagues may not have an hour to sit in your class, many will read a short blog.

Tip #7: Stay in touch with your community

I recently wrote a blog called “Tips for Thriving in Research”, and the first two tips were about mentor-mentee relationships. I think that in order to get better at teaching, it’s important to surround yourself with mentors and mentees who are also passionate about teaching.

Read, write, blog, and talk about your teaching experiences with like-minded scientists. Here are two really good two really good blogs on student evaluations written by my colleagues Olga Botvinnik and April Wright.

Before creating a lesson or exam from scratch (possibly reinventing the wheel) first see if you can find tried-and-tested syllabi from your community. Online resources like Code Academy’s Python Coding for Beginner’s, the Rosalind platform for learning bioinformatics, and Software Carpentry’s open access teaching materials are excellent tools for teaching Big Data concepts and skills to trainees.

Hopefully, with a continued community focus on training, the next generation of neuroscientists will be better adapt to deal with the challenges that still remain for Big Data research.

Thanks to:

I definitely want to thank the organizers and instructors (Greg Wilson, Tracy Teal, and Titus Brown, Bill Mills and Aleksandra Pawlik) for providing excellent examples of teaching by doing. I thank April Wright for encouraging me to attend and for securing funding from BEACON Center. Becca Tarvin and I reflected on what we learned and discussed ways to apply this to our burgeoning community of bioinformatic aficionados via the Center for Computational Biology and Bioinformatics (CCBB) at UT Austin (see her companion blog).

Re-posting: This blog was originally published via PLOS Neuroscience Community here. Disclaimer. The views expressed are my own, not necessarily those of PLOS.

swc  dc  teaching 
</body> </html> </a> <a href="/tags/science<!DOCTYPE HTML> How my father shaped my career before and after his death
12 Jun 2018

How my father shaped my career before and after his death

A Father's Day reflection

Father’s Day is this Sunday. For me, this holiday usually comes and goes without much thought. I don’t have kids. My mother isn’t married to some man I have to call a step-father. My father died at the age of 57 on October 6, 2007, two days before my 25 birthday. That means its been 9 years since I last called or visited my dad to wish Happy Father’s Day. I don’t usually get too sentimental around this holiday, but this week I stumbled upon some Mike Eisen tweets about his father’s death, and I’ve been working to organize meetings that are very friendly to scientists with children, and now I can’t stop thinking about how my father’s life and death have impacted my career.

This is not a biography of my father, nor is it a complete summary of how his life has impacted me, but it does touch upon how his profession and personal life affected some decisions I made regarding my education and research topics.

Rudy Martin Harris (RMH, same initials as me) started working at LeTourneau, Inc as a mechanical engineer immediately after graduating from college, and he worked right up until a few weeks before he died from a 5 month battle with skin cancer. LeTourneau manufactured “earthmoving equipment” like offshore drilling rigs and the biggest bulldozers you’ve ever seen, but my dad worked with computers to automate the manufacturing process. I think at one point there were 5 computers in our “patio room” (a patio that he converted into a 2nd living room pretty much all by himself). My father was a self-proclaimed workaholic; he’d spend all day at the office and then get back to work tinkering with computers til late at night. Eventually, he moved up the ladder to Vice President of Manufacturing, so he spent less time hacking away at computers and more time flying around to visit other manufacturing plants. I never wanted to explicitly follow in my father’s footsteps, but I do remember thinking that it would be really cool to work my way from an entry-level position all the way to the top to the President’s office.

The few times I visited my father at work, the only females I encountered were secretaries. I don’t know if anyone every explicitly said it, but I assumed engineering was a man’s job and that females weren’t allowed. I remember being shocked during my first semester of college to meet female students that that were enrolled in the aerospace and petroleum engineering programs. I was like, “how did you know that was a thing?” Sometimes I wonder where I would be now if my dad had gotten me a summer internship at his company or encouraged me to study engineering. Even though he didn’t groom to follow in his footsteps, I think I inherited his intellectual acumen, his desire for everything to be well organized and efficient, and his half introvert/half extrovert personality. I think I would have made a good engineer, but I’m finding awesome ways to apply those traits to scientific and social problems, so no hard feelings.

There was a time, however, that I did harbour very negative feelings toward my father. Over Christmas break when I was 14, my mom and dad got in the only fight I’m aware of them ever having, and he moved out. I was crushed. I didn’t understand how my father could leave me to go live with some other woman who was raising her grandchildren because her own kids were too incompetent to be good parents. At that age, I didn’t really understand what an affair was, but I hated the fact that he was spending his time and money on someone’s else kids rather than spending them on me. At first, I lashed out by not speaking to my father for a whole year. He would come to my volleyball games and take we water skiing on the weekend, but I literally would not utter a single word to him. I must have been insufferable. I eventually started talking to my dad again, but it wasn’t until my junior year in college that I would say we had a decent relationship. I graduate in 4.5 years and then spent a semester TAing. The day I was moving out of my apartment to go live abroad for a year, my dad called to say he had really aggressive skin cancer and that had spread throughout all nearly all his major organs. I went to see him once a month for the next 5 month, and he looked as if he aged 10 years between every visit.

A lot of doctors (PhDs and MDs) get involved with cancer research after a loved one dies of cancer. Not me. I had no desire to be an MD, and I was set on being a scientist. While living in Costa Rica, I learned how to collect marine samples by SCUBA diving and got pretty good a culturing marine microbes and extracting their DNA. I was looking for a research tech job when I found a position in a lab that was using DNA microarrays to study parental behavior and mating behavior. I was like, “This is a thing?!” I was definitely intrigued by the possibility of understanding what makes some individual good dads and faithful partners whereas others not so much, so I joined the lab. I learned a lot about how different levels of molecules like dopamine, oxytocin, prolactin, and testosterone in the brain can influence how decision making and social behaviors. It was all pretty fascinating and enlightening for a while, but I eventually got bored reading about the same genes, brain regions, evolutionary theories, nasals sprays that influence social behavior. More importantly, I felt like I learned enough about the biological forces that may have shaped my father’s personal life that I no longer need to devote my professional life to understanding the future, not the past.

If you are looking for other science-themed Father’s Day related reads, Titus Brown, Mike Eisen, and Jonathan Eisen have all blogged about the life and death of their father and how it impacted their careers. Titus’s father was a well-known physicist who died in 2013 after failing to recover from an illness. Gerry Brown mentored over 100 graduate students! Who knows if Titus will officially mentor that many (he’s only at 10), but he has unofficially mentored hundreds through his Data Intensive Biology Summer Institute. Mike and Jonathan’s father, a respected scientist at NIH, took his own life in 1987. Mike writes about how he will never stop trying to figure responded the stress of work with suicide, and I can’t help but wonder if this doesn’t explain why he is often very critical of the NIH. To honor their father, Jonathan went on a mission to make all their father’s paper publicly available. On a lighter note, Jeremy Fox compared his own work ethic to that of his father and paternal grandfather who owned a local grocery store in a small town.

family  academia  science 
</body> </html> <!DOCTYPE HTML> Using music, beer, and pop-culture to communicate science
02 Jan 2018

Using music, beer, and pop-culture to communicate science

A little bit about my Nerd Nite talk called Zombie Brains: Microbial Mind Control. TLDR: David Attenborough meets Tom Waits meets Ed Yong

I recently gave a talk at The North Door for Nerd Nite Austin. This is a monthly event with an audience of 250 partially inebriated nerds, including about a dozen colleagues and friends. I put a lot of effort into making it fun and relatable, so I thought I would share some of the details about how and why I gave what I think is my best talk ever. You can view the video here and view my slides here.

"Zombie Brains: Microbial Mind Control," by Rayna Harris from Nerd Nite - Austin on Vimeo.

Science and sign language

I knew I would have a sign language interpreter with me on stage, so I tried to minimize jargon and define the scientific words I used. I recorded myself practicing my talk and critiqued the video playback about six times. I focused on reducing my use of filler words “um” and “like”. I specifically asked the interpreter to create a sign for “microbiome” because I knew I would use it more than a dozen times.

image1

On stage with a sign language translator and a ‘Tom Waits does David Attenborough’ impersonator. Instagram photos available at /.

Incorporating live performance and YouTube videos

I wanted to show this BBC David Attenborough video, but I was worried that people would be bored or that the sound quality would be bad, so I decided to play the video on silent and add my own sound. I invited my friend Joseph Palmer to narrate it using his amazing impersonation Tom Waits. With the help of the sound engineer, I cued a clip of Tom Waits Oily Night song to provide an eerie backdrop. Joseph’s performance received much applause and laughter. It was awesome!

image2

Watch this 30-second video clip of the Tom Waits-narrated footage of an infected insect being evicted from the social colony at https://twitter.com/R0mination/status/951295758615171072.

The 3 main themes of my talk

I decided that I would cover three main topics during my talk: parasitic mind control in insects, the link between the gut microbiome and the brain in humans, and the potential for parasitic mind control in humans. I opened with a definition of the word “microbiome” because I thought that was the best hook and it allowed me to engage the hearing-impaired viewers with a brand new sign. But, then, I launched into the 3 parts in the ordered described. This collage of images provides a good overview of my talk.

image3

These are all the images I used in my talk to illustrate beautiful biological phenomena and link it to current social phenomena.

First, I describe deadly host-pathogen relations in the jungle using photos from photos from Alex Wild and the Tom-Waits narrated video from the BBC. I describe research from Carolyn Elya, Michael Eisen, and colleagues on a fungal pathogen that manipulates Drosophila melanogaster in the lab. I take a moment to highlight other awesome neuroscience and molecular -development research in flies.

Then, I transition to talking about the dynamics of human microbiomes, with much of my inspiration coming from a book by Ed Yong on the multitudes of microscopic organisms living in our body. I got a lot of questions during the Q&A about how diet and disease affect and are affected by our microbiomes.

Finally, I talked about the possibility of microscopic organisms influencing social behaviors such as kissing, hand holding, breastfeeding, and more. The examples I used are inspired by basic research and by personal experience. I kept my language very casual to keep the audience engaged, and I got a lot of laughs and applause during this part of the talk. I hope they go away knowing what “horizontal gene transfer” is.

Similarities between host-parasite relationships and sexual harassment

This 2 min YouTube video (available at ) shows me practicing my talk. I make an analogy between host-parasite relationship and sexual harassment and summarize the 3 main points. See the twitter link above for what was actually said while the ant video played.

I wanted to have something in the talk that made it timely, so I decided to make an analogy between host-parasite relationship and current social movements related to sexual harassment and discrimination. I was very worried that this tangent on sexual harassment might not go over well, but I felt compelled to utilize my moment in the spotlight with a microphone to discuss an important social issue that affects many women in science.

I practiced this segment of my talk a lot, and I posted a short video of my last practice session here. What I said on stage was a little different than during that last practice session, but I kept the analogy between infected ants being evicted from colonies to women fearing job loss if they showed evidence of being harassed.

To my surprise, this portion of my talk drew even more applause than my friend’s impersonation of Tom Waits! However, this time people weren’t clapping and cheering because it was funny or novel; I think they were signaling to me that the could relate to what I was saying and that they were glad I had the courage to talk about it on stage.

The Q&A session

The Q&A lasted for what felt like 15 minutes. Most of the questions were of a biomedical nature that I felt I didn’t have the expertise to answer, so I tried to say “I don’t know for sure, but here is what I think…” when responding.

I did get one fun question and I responded with some research from the Lenski Lab. The audience member asked something along the lines of whether or not we should fear gut colonization by ancient bacteria that have been trapped in glaciers but are now being brought back to life.** **I responded by saying Lenski had done a lot of experiments competing older generation and newer generations of bacteria against each other and the newer bacterial almost always performed than the ancient ones. I didn’t give him a citation, but this paper on sustained fitness is what I should have given him.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Timeline for the Data Carpentry & Software Carpentry Reorganization
17 Jun 2017

Timeline for the Data Carpentry & Software Carpentry Reorganization

The future of the Carpentries

On Jun 8 & 9, we met in-person to continue discussing how to proceed with the merger of the Software Carpentry and Data Carpentry organizations to best achieve our strategic goals and serve our communities. We are happy to report that is was a very productive meeting.

We spent most of the meeting discussing the structure of the future organizational leadership. We have drafted a number of motions that we will present to our respective steering committees for approval at our next meetings. Among the motions, we will propose that the combined Carpentries governing structure be made up of both appointed and elected members. Additionally, we propose that it is in the best interest of the organization to seed the future steering committee with bylaws, which will be enumerated, written, and approved in the coming months.

Below is a timeline for the merger process. Various steps in this timeline require approval by both steering committees, and are dependent on results of previous steps, so this may change as we proceed.

Month Merger Process Milestones
June Communicate the in-person meeting outcomes and proposed governance structure to staff and community members.
July Present motions to approve the proposed goverance structure, executive leadership, and transfer of assets (e.g. finances, cross-organization subcommittees). Enumerate required bylaws.
August Present and approve an official motion to combine Software Carpentry and Data Carpentry into a unified organization. Approve nominations for the appointed seats to the steering committee.
September Approve a unified budget. Approve the transfer of assets.
October Call for candidates for elected members of the steering committee. Approve motions to dissolve the current steering committee and transfer assets as of January 1.
November Community call to announce candidates for the elected seats on the steering committee.
December Elect new elected steering committee members.
January New organization with new steering committee commences.

We are grateful for all the input we have and will to continue to received from community members, from staff, and from colleagues outside the Carpentries during this decision-making process. Please stayed tuned for updates and feel free to contact us with questions or concerns.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> " class="button special small">science<!DOCTYPE HTML> How my father shaped my career before and after his death
12 Jun 2018

How my father shaped my career before and after his death

A Father's Day reflection

Father’s Day is this Sunday. For me, this holiday usually comes and goes without much thought. I don’t have kids. My mother isn’t married to some man I have to call a step-father. My father died at the age of 57 on October 6, 2007, two days before my 25 birthday. That means its been 9 years since I last called or visited my dad to wish Happy Father’s Day. I don’t usually get too sentimental around this holiday, but this week I stumbled upon some Mike Eisen tweets about his father’s death, and I’ve been working to organize meetings that are very friendly to scientists with children, and now I can’t stop thinking about how my father’s life and death have impacted my career.

This is not a biography of my father, nor is it a complete summary of how his life has impacted me, but it does touch upon how his profession and personal life affected some decisions I made regarding my education and research topics.

Rudy Martin Harris (RMH, same initials as me) started working at LeTourneau, Inc as a mechanical engineer immediately after graduating from college, and he worked right up until a few weeks before he died from a 5 month battle with skin cancer. LeTourneau manufactured “earthmoving equipment” like offshore drilling rigs and the biggest bulldozers you’ve ever seen, but my dad worked with computers to automate the manufacturing process. I think at one point there were 5 computers in our “patio room” (a patio that he converted into a 2nd living room pretty much all by himself). My father was a self-proclaimed workaholic; he’d spend all day at the office and then get back to work tinkering with computers til late at night. Eventually, he moved up the ladder to Vice President of Manufacturing, so he spent less time hacking away at computers and more time flying around to visit other manufacturing plants. I never wanted to explicitly follow in my father’s footsteps, but I do remember thinking that it would be really cool to work my way from an entry-level position all the way to the top to the President’s office.

The few times I visited my father at work, the only females I encountered were secretaries. I don’t know if anyone every explicitly said it, but I assumed engineering was a man’s job and that females weren’t allowed. I remember being shocked during my first semester of college to meet female students that that were enrolled in the aerospace and petroleum engineering programs. I was like, “how did you know that was a thing?” Sometimes I wonder where I would be now if my dad had gotten me a summer internship at his company or encouraged me to study engineering. Even though he didn’t groom to follow in his footsteps, I think I inherited his intellectual acumen, his desire for everything to be well organized and efficient, and his half introvert/half extrovert personality. I think I would have made a good engineer, but I’m finding awesome ways to apply those traits to scientific and social problems, so no hard feelings.

There was a time, however, that I did harbour very negative feelings toward my father. Over Christmas break when I was 14, my mom and dad got in the only fight I’m aware of them ever having, and he moved out. I was crushed. I didn’t understand how my father could leave me to go live with some other woman who was raising her grandchildren because her own kids were too incompetent to be good parents. At that age, I didn’t really understand what an affair was, but I hated the fact that he was spending his time and money on someone’s else kids rather than spending them on me. At first, I lashed out by not speaking to my father for a whole year. He would come to my volleyball games and take we water skiing on the weekend, but I literally would not utter a single word to him. I must have been insufferable. I eventually started talking to my dad again, but it wasn’t until my junior year in college that I would say we had a decent relationship. I graduate in 4.5 years and then spent a semester TAing. The day I was moving out of my apartment to go live abroad for a year, my dad called to say he had really aggressive skin cancer and that had spread throughout all nearly all his major organs. I went to see him once a month for the next 5 month, and he looked as if he aged 10 years between every visit.

A lot of doctors (PhDs and MDs) get involved with cancer research after a loved one dies of cancer. Not me. I had no desire to be an MD, and I was set on being a scientist. While living in Costa Rica, I learned how to collect marine samples by SCUBA diving and got pretty good a culturing marine microbes and extracting their DNA. I was looking for a research tech job when I found a position in a lab that was using DNA microarrays to study parental behavior and mating behavior. I was like, “This is a thing?!” I was definitely intrigued by the possibility of understanding what makes some individual good dads and faithful partners whereas others not so much, so I joined the lab. I learned a lot about how different levels of molecules like dopamine, oxytocin, prolactin, and testosterone in the brain can influence how decision making and social behaviors. It was all pretty fascinating and enlightening for a while, but I eventually got bored reading about the same genes, brain regions, evolutionary theories, nasals sprays that influence social behavior. More importantly, I felt like I learned enough about the biological forces that may have shaped my father’s personal life that I no longer need to devote my professional life to understanding the future, not the past.

If you are looking for other science-themed Father’s Day related reads, Titus Brown, Mike Eisen, and Jonathan Eisen have all blogged about the life and death of their father and how it impacted their careers. Titus’s father was a well-known physicist who died in 2013 after failing to recover from an illness. Gerry Brown mentored over 100 graduate students! Who knows if Titus will officially mentor that many (he’s only at 10), but he has unofficially mentored hundreds through his Data Intensive Biology Summer Institute. Mike and Jonathan’s father, a respected scientist at NIH, took his own life in 1987. Mike writes about how he will never stop trying to figure responded the stress of work with suicide, and I can’t help but wonder if this doesn’t explain why he is often very critical of the NIH. To honor their father, Jonathan went on a mission to make all their father’s paper publicly available. On a lighter note, Jeremy Fox compared his own work ethic to that of his father and paternal grandfather who owned a local grocery store in a small town.

family  academia  science 
</body> </html> <!DOCTYPE HTML> Using music, beer, and pop-culture to communicate science
02 Jan 2018

Using music, beer, and pop-culture to communicate science

A little bit about my Nerd Nite talk called Zombie Brains: Microbial Mind Control. TLDR: David Attenborough meets Tom Waits meets Ed Yong

I recently gave a talk at The North Door for Nerd Nite Austin. This is a monthly event with an audience of 250 partially inebriated nerds, including about a dozen colleagues and friends. I put a lot of effort into making it fun and relatable, so I thought I would share some of the details about how and why I gave what I think is my best talk ever. You can view the video here and view my slides here.

"Zombie Brains: Microbial Mind Control," by Rayna Harris from Nerd Nite - Austin on Vimeo.

Science and sign language

I knew I would have a sign language interpreter with me on stage, so I tried to minimize jargon and define the scientific words I used. I recorded myself practicing my talk and critiqued the video playback about six times. I focused on reducing my use of filler words “um” and “like”. I specifically asked the interpreter to create a sign for “microbiome” because I knew I would use it more than a dozen times.

image1

On stage with a sign language translator and a ‘Tom Waits does David Attenborough’ impersonator. Instagram photos available at /.

Incorporating live performance and YouTube videos

I wanted to show this BBC David Attenborough video, but I was worried that people would be bored or that the sound quality would be bad, so I decided to play the video on silent and add my own sound. I invited my friend Joseph Palmer to narrate it using his amazing impersonation Tom Waits. With the help of the sound engineer, I cued a clip of Tom Waits Oily Night song to provide an eerie backdrop. Joseph’s performance received much applause and laughter. It was awesome!

image2

Watch this 30-second video clip of the Tom Waits-narrated footage of an infected insect being evicted from the social colony at https://twitter.com/R0mination/status/951295758615171072.

The 3 main themes of my talk

I decided that I would cover three main topics during my talk: parasitic mind control in insects, the link between the gut microbiome and the brain in humans, and the potential for parasitic mind control in humans. I opened with a definition of the word “microbiome” because I thought that was the best hook and it allowed me to engage the hearing-impaired viewers with a brand new sign. But, then, I launched into the 3 parts in the ordered described. This collage of images provides a good overview of my talk.

image3

These are all the images I used in my talk to illustrate beautiful biological phenomena and link it to current social phenomena.

First, I describe deadly host-pathogen relations in the jungle using photos from photos from Alex Wild and the Tom-Waits narrated video from the BBC. I describe research from Carolyn Elya, Michael Eisen, and colleagues on a fungal pathogen that manipulates Drosophila melanogaster in the lab. I take a moment to highlight other awesome neuroscience and molecular -development research in flies.

Then, I transition to talking about the dynamics of human microbiomes, with much of my inspiration coming from a book by Ed Yong on the multitudes of microscopic organisms living in our body. I got a lot of questions during the Q&A about how diet and disease affect and are affected by our microbiomes.

Finally, I talked about the possibility of microscopic organisms influencing social behaviors such as kissing, hand holding, breastfeeding, and more. The examples I used are inspired by basic research and by personal experience. I kept my language very casual to keep the audience engaged, and I got a lot of laughs and applause during this part of the talk. I hope they go away knowing what “horizontal gene transfer” is.

Similarities between host-parasite relationships and sexual harassment

This 2 min YouTube video (available at ) shows me practicing my talk. I make an analogy between host-parasite relationship and sexual harassment and summarize the 3 main points. See the twitter link above for what was actually said while the ant video played.

I wanted to have something in the talk that made it timely, so I decided to make an analogy between host-parasite relationship and current social movements related to sexual harassment and discrimination. I was very worried that this tangent on sexual harassment might not go over well, but I felt compelled to utilize my moment in the spotlight with a microphone to discuss an important social issue that affects many women in science.

I practiced this segment of my talk a lot, and I posted a short video of my last practice session here. What I said on stage was a little different than during that last practice session, but I kept the analogy between infected ants being evicted from colonies to women fearing job loss if they showed evidence of being harassed.

To my surprise, this portion of my talk drew even more applause than my friend’s impersonation of Tom Waits! However, this time people weren’t clapping and cheering because it was funny or novel; I think they were signaling to me that the could relate to what I was saying and that they were glad I had the courage to talk about it on stage.

The Q&A session

The Q&A lasted for what felt like 15 minutes. Most of the questions were of a biomedical nature that I felt I didn’t have the expertise to answer, so I tried to say “I don’t know for sure, but here is what I think…” when responding.

I did get one fun question and I responded with some research from the Lenski Lab. The audience member asked something along the lines of whether or not we should fear gut colonization by ancient bacteria that have been trapped in glaciers but are now being brought back to life.** **I responded by saying Lenski had done a lot of experiments competing older generation and newer generations of bacteria against each other and the newer bacterial almost always performed than the ancient ones. I didn’t give him a citation, but this paper on sustained fitness is what I should have given him.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Timeline for the Data Carpentry & Software Carpentry Reorganization
17 Jun 2017

Timeline for the Data Carpentry & Software Carpentry Reorganization

The future of the Carpentries

On Jun 8 & 9, we met in-person to continue discussing how to proceed with the merger of the Software Carpentry and Data Carpentry organizations to best achieve our strategic goals and serve our communities. We are happy to report that is was a very productive meeting.

We spent most of the meeting discussing the structure of the future organizational leadership. We have drafted a number of motions that we will present to our respective steering committees for approval at our next meetings. Among the motions, we will propose that the combined Carpentries governing structure be made up of both appointed and elected members. Additionally, we propose that it is in the best interest of the organization to seed the future steering committee with bylaws, which will be enumerated, written, and approved in the coming months.

Below is a timeline for the merger process. Various steps in this timeline require approval by both steering committees, and are dependent on results of previous steps, so this may change as we proceed.

Month Merger Process Milestones
June Communicate the in-person meeting outcomes and proposed governance structure to staff and community members.
July Present motions to approve the proposed goverance structure, executive leadership, and transfer of assets (e.g. finances, cross-organization subcommittees). Enumerate required bylaws.
August Present and approve an official motion to combine Software Carpentry and Data Carpentry into a unified organization. Approve nominations for the appointed seats to the steering committee.
September Approve a unified budget. Approve the transfer of assets.
October Call for candidates for elected members of the steering committee. Approve motions to dissolve the current steering committee and transfer assets as of January 1.
November Community call to announce candidates for the elected seats on the steering committee.
December Elect new elected steering committee members.
January New organization with new steering committee commences.

We are grateful for all the input we have and will to continue to received from community members, from staff, and from colleagues outside the Carpentries during this decision-making process. Please stayed tuned for updates and feel free to contact us with questions or concerns.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> </a> <a href="/tags/reproducible<!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> " class="button special small">reproducible<!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> </a> <a href="/tags/datadriven<!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> " class="button special small">datadriven<!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> </a> <a href="/tags/scicomm<!DOCTYPE HTML> Using music, beer, and pop-culture to communicate science
02 Jan 2018

Using music, beer, and pop-culture to communicate science

A little bit about my Nerd Nite talk called Zombie Brains: Microbial Mind Control. TLDR: David Attenborough meets Tom Waits meets Ed Yong

I recently gave a talk at The North Door for Nerd Nite Austin. This is a monthly event with an audience of 250 partially inebriated nerds, including about a dozen colleagues and friends. I put a lot of effort into making it fun and relatable, so I thought I would share some of the details about how and why I gave what I think is my best talk ever. You can view the video here and view my slides here.

"Zombie Brains: Microbial Mind Control," by Rayna Harris from Nerd Nite - Austin on Vimeo.

Science and sign language

I knew I would have a sign language interpreter with me on stage, so I tried to minimize jargon and define the scientific words I used. I recorded myself practicing my talk and critiqued the video playback about six times. I focused on reducing my use of filler words “um” and “like”. I specifically asked the interpreter to create a sign for “microbiome” because I knew I would use it more than a dozen times.

image1

On stage with a sign language translator and a ‘Tom Waits does David Attenborough’ impersonator. Instagram photos available at /.

Incorporating live performance and YouTube videos

I wanted to show this BBC David Attenborough video, but I was worried that people would be bored or that the sound quality would be bad, so I decided to play the video on silent and add my own sound. I invited my friend Joseph Palmer to narrate it using his amazing impersonation Tom Waits. With the help of the sound engineer, I cued a clip of Tom Waits Oily Night song to provide an eerie backdrop. Joseph’s performance received much applause and laughter. It was awesome!

image2

Watch this 30-second video clip of the Tom Waits-narrated footage of an infected insect being evicted from the social colony at https://twitter.com/R0mination/status/951295758615171072.

The 3 main themes of my talk

I decided that I would cover three main topics during my talk: parasitic mind control in insects, the link between the gut microbiome and the brain in humans, and the potential for parasitic mind control in humans. I opened with a definition of the word “microbiome” because I thought that was the best hook and it allowed me to engage the hearing-impaired viewers with a brand new sign. But, then, I launched into the 3 parts in the ordered described. This collage of images provides a good overview of my talk.

image3

These are all the images I used in my talk to illustrate beautiful biological phenomena and link it to current social phenomena.

First, I describe deadly host-pathogen relations in the jungle using photos from photos from Alex Wild and the Tom-Waits narrated video from the BBC. I describe research from Carolyn Elya, Michael Eisen, and colleagues on a fungal pathogen that manipulates Drosophila melanogaster in the lab. I take a moment to highlight other awesome neuroscience and molecular -development research in flies.

Then, I transition to talking about the dynamics of human microbiomes, with much of my inspiration coming from a book by Ed Yong on the multitudes of microscopic organisms living in our body. I got a lot of questions during the Q&A about how diet and disease affect and are affected by our microbiomes.

Finally, I talked about the possibility of microscopic organisms influencing social behaviors such as kissing, hand holding, breastfeeding, and more. The examples I used are inspired by basic research and by personal experience. I kept my language very casual to keep the audience engaged, and I got a lot of laughs and applause during this part of the talk. I hope they go away knowing what “horizontal gene transfer” is.

Similarities between host-parasite relationships and sexual harassment

This 2 min YouTube video (available at ) shows me practicing my talk. I make an analogy between host-parasite relationship and sexual harassment and summarize the 3 main points. See the twitter link above for what was actually said while the ant video played.

I wanted to have something in the talk that made it timely, so I decided to make an analogy between host-parasite relationship and current social movements related to sexual harassment and discrimination. I was very worried that this tangent on sexual harassment might not go over well, but I felt compelled to utilize my moment in the spotlight with a microphone to discuss an important social issue that affects many women in science.

I practiced this segment of my talk a lot, and I posted a short video of my last practice session here. What I said on stage was a little different than during that last practice session, but I kept the analogy between infected ants being evicted from colonies to women fearing job loss if they showed evidence of being harassed.

To my surprise, this portion of my talk drew even more applause than my friend’s impersonation of Tom Waits! However, this time people weren’t clapping and cheering because it was funny or novel; I think they were signaling to me that the could relate to what I was saying and that they were glad I had the courage to talk about it on stage.

The Q&A session

The Q&A lasted for what felt like 15 minutes. Most of the questions were of a biomedical nature that I felt I didn’t have the expertise to answer, so I tried to say “I don’t know for sure, but here is what I think…” when responding.

I did get one fun question and I responded with some research from the Lenski Lab. The audience member asked something along the lines of whether or not we should fear gut colonization by ancient bacteria that have been trapped in glaciers but are now being brought back to life.** **I responded by saying Lenski had done a lot of experiments competing older generation and newer generations of bacteria against each other and the newer bacterial almost always performed than the ancient ones. I didn’t give him a citation, but this paper on sustained fitness is what I should have given him.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Timeline for the Data Carpentry & Software Carpentry Reorganization
17 Jun 2017

Timeline for the Data Carpentry & Software Carpentry Reorganization

The future of the Carpentries

On Jun 8 & 9, we met in-person to continue discussing how to proceed with the merger of the Software Carpentry and Data Carpentry organizations to best achieve our strategic goals and serve our communities. We are happy to report that is was a very productive meeting.

We spent most of the meeting discussing the structure of the future organizational leadership. We have drafted a number of motions that we will present to our respective steering committees for approval at our next meetings. Among the motions, we will propose that the combined Carpentries governing structure be made up of both appointed and elected members. Additionally, we propose that it is in the best interest of the organization to seed the future steering committee with bylaws, which will be enumerated, written, and approved in the coming months.

Below is a timeline for the merger process. Various steps in this timeline require approval by both steering committees, and are dependent on results of previous steps, so this may change as we proceed.

Month Merger Process Milestones
June Communicate the in-person meeting outcomes and proposed governance structure to staff and community members.
July Present motions to approve the proposed goverance structure, executive leadership, and transfer of assets (e.g. finances, cross-organization subcommittees). Enumerate required bylaws.
August Present and approve an official motion to combine Software Carpentry and Data Carpentry into a unified organization. Approve nominations for the appointed seats to the steering committee.
September Approve a unified budget. Approve the transfer of assets.
October Call for candidates for elected members of the steering committee. Approve motions to dissolve the current steering committee and transfer assets as of January 1.
November Community call to announce candidates for the elected seats on the steering committee.
December Elect new elected steering committee members.
January New organization with new steering committee commences.

We are grateful for all the input we have and will to continue to received from community members, from staff, and from colleagues outside the Carpentries during this decision-making process. Please stayed tuned for updates and feel free to contact us with questions or concerns.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> " class="button special small">scicomm<!DOCTYPE HTML> Using music, beer, and pop-culture to communicate science
02 Jan 2018

Using music, beer, and pop-culture to communicate science

A little bit about my Nerd Nite talk called Zombie Brains: Microbial Mind Control. TLDR: David Attenborough meets Tom Waits meets Ed Yong

I recently gave a talk at The North Door for Nerd Nite Austin. This is a monthly event with an audience of 250 partially inebriated nerds, including about a dozen colleagues and friends. I put a lot of effort into making it fun and relatable, so I thought I would share some of the details about how and why I gave what I think is my best talk ever. You can view the video here and view my slides here.

"Zombie Brains: Microbial Mind Control," by Rayna Harris from Nerd Nite - Austin on Vimeo.

Science and sign language

I knew I would have a sign language interpreter with me on stage, so I tried to minimize jargon and define the scientific words I used. I recorded myself practicing my talk and critiqued the video playback about six times. I focused on reducing my use of filler words “um” and “like”. I specifically asked the interpreter to create a sign for “microbiome” because I knew I would use it more than a dozen times.

image1

On stage with a sign language translator and a ‘Tom Waits does David Attenborough’ impersonator. Instagram photos available at /.

Incorporating live performance and YouTube videos

I wanted to show this BBC David Attenborough video, but I was worried that people would be bored or that the sound quality would be bad, so I decided to play the video on silent and add my own sound. I invited my friend Joseph Palmer to narrate it using his amazing impersonation Tom Waits. With the help of the sound engineer, I cued a clip of Tom Waits Oily Night song to provide an eerie backdrop. Joseph’s performance received much applause and laughter. It was awesome!

image2

Watch this 30-second video clip of the Tom Waits-narrated footage of an infected insect being evicted from the social colony at https://twitter.com/R0mination/status/951295758615171072.

The 3 main themes of my talk

I decided that I would cover three main topics during my talk: parasitic mind control in insects, the link between the gut microbiome and the brain in humans, and the potential for parasitic mind control in humans. I opened with a definition of the word “microbiome” because I thought that was the best hook and it allowed me to engage the hearing-impaired viewers with a brand new sign. But, then, I launched into the 3 parts in the ordered described. This collage of images provides a good overview of my talk.

image3

These are all the images I used in my talk to illustrate beautiful biological phenomena and link it to current social phenomena.

First, I describe deadly host-pathogen relations in the jungle using photos from photos from Alex Wild and the Tom-Waits narrated video from the BBC. I describe research from Carolyn Elya, Michael Eisen, and colleagues on a fungal pathogen that manipulates Drosophila melanogaster in the lab. I take a moment to highlight other awesome neuroscience and molecular -development research in flies.

Then, I transition to talking about the dynamics of human microbiomes, with much of my inspiration coming from a book by Ed Yong on the multitudes of microscopic organisms living in our body. I got a lot of questions during the Q&A about how diet and disease affect and are affected by our microbiomes.

Finally, I talked about the possibility of microscopic organisms influencing social behaviors such as kissing, hand holding, breastfeeding, and more. The examples I used are inspired by basic research and by personal experience. I kept my language very casual to keep the audience engaged, and I got a lot of laughs and applause during this part of the talk. I hope they go away knowing what “horizontal gene transfer” is.

Similarities between host-parasite relationships and sexual harassment

This 2 min YouTube video (available at ) shows me practicing my talk. I make an analogy between host-parasite relationship and sexual harassment and summarize the 3 main points. See the twitter link above for what was actually said while the ant video played.

I wanted to have something in the talk that made it timely, so I decided to make an analogy between host-parasite relationship and current social movements related to sexual harassment and discrimination. I was very worried that this tangent on sexual harassment might not go over well, but I felt compelled to utilize my moment in the spotlight with a microphone to discuss an important social issue that affects many women in science.

I practiced this segment of my talk a lot, and I posted a short video of my last practice session here. What I said on stage was a little different than during that last practice session, but I kept the analogy between infected ants being evicted from colonies to women fearing job loss if they showed evidence of being harassed.

To my surprise, this portion of my talk drew even more applause than my friend’s impersonation of Tom Waits! However, this time people weren’t clapping and cheering because it was funny or novel; I think they were signaling to me that the could relate to what I was saying and that they were glad I had the courage to talk about it on stage.

The Q&A session

The Q&A lasted for what felt like 15 minutes. Most of the questions were of a biomedical nature that I felt I didn’t have the expertise to answer, so I tried to say “I don’t know for sure, but here is what I think…” when responding.

I did get one fun question and I responded with some research from the Lenski Lab. The audience member asked something along the lines of whether or not we should fear gut colonization by ancient bacteria that have been trapped in glaciers but are now being brought back to life.** **I responded by saying Lenski had done a lot of experiments competing older generation and newer generations of bacteria against each other and the newer bacterial almost always performed than the ancient ones. I didn’t give him a citation, but this paper on sustained fitness is what I should have given him.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Timeline for the Data Carpentry & Software Carpentry Reorganization
17 Jun 2017

Timeline for the Data Carpentry & Software Carpentry Reorganization

The future of the Carpentries

On Jun 8 & 9, we met in-person to continue discussing how to proceed with the merger of the Software Carpentry and Data Carpentry organizations to best achieve our strategic goals and serve our communities. We are happy to report that is was a very productive meeting.

We spent most of the meeting discussing the structure of the future organizational leadership. We have drafted a number of motions that we will present to our respective steering committees for approval at our next meetings. Among the motions, we will propose that the combined Carpentries governing structure be made up of both appointed and elected members. Additionally, we propose that it is in the best interest of the organization to seed the future steering committee with bylaws, which will be enumerated, written, and approved in the coming months.

Below is a timeline for the merger process. Various steps in this timeline require approval by both steering committees, and are dependent on results of previous steps, so this may change as we proceed.

Month Merger Process Milestones
June Communicate the in-person meeting outcomes and proposed governance structure to staff and community members.
July Present motions to approve the proposed goverance structure, executive leadership, and transfer of assets (e.g. finances, cross-organization subcommittees). Enumerate required bylaws.
August Present and approve an official motion to combine Software Carpentry and Data Carpentry into a unified organization. Approve nominations for the appointed seats to the steering committee.
September Approve a unified budget. Approve the transfer of assets.
October Call for candidates for elected members of the steering committee. Approve motions to dissolve the current steering committee and transfer assets as of January 1.
November Community call to announce candidates for the elected seats on the steering committee.
December Elect new elected steering committee members.
January New organization with new steering committee commences.

We are grateful for all the input we have and will to continue to received from community members, from staff, and from colleagues outside the Carpentries during this decision-making process. Please stayed tuned for updates and feel free to contact us with questions or concerns.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> </a> <a href="/tags/education<!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> " class="button special small">education<!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> </a> <a href="/tags/datacarpentry<!DOCTYPE HTML> Three years in the making for Instructor training in Latin America
24 Aug 2018

Three years in the making for Instructor training in Latin America

Building global communities of Spanish-speaking Carpentry instructors and lesson developers

This month I (Rayna Harris) co-taught a remote The Carpentries Instructor Training Workshop for 25 Spanish-speaking trainees in six countries in Latin America. It was awesome! One thing that made this workshop so special for me is that it has been three-plus years in the making. So, I thought I would tell the story, from my perspective, about all the things that came into play to make this workshop a reality.

The early days of The Carpentries workshops in Spanish

In 2016, Greg Wilson introduced me to Selene Fernandez-Valverde to discuss a Software Carpentry meets Spanish-speaking bioinformatics endeavour. Back then my Spanish was eight years out of practice and I was still learning to program. I didn’t think I had the expertise to teach programming in Spanish. Sue McClatchy had more expertise and practice, but it is still difficult for a native English speaker to live-translate a lesson from English to Spanish while live coding in front of a classroom.

This observation led to two simultaneous efforts: support a community-wide effort for collaborative lesson translation and provide instructor training for Spanish speaking instructors. That is exactly what many staff and volunteers have done over the past three years.

Spanish translations hacakathon and lesson maintenance

In November 2017, I went to Germany to attend OpenCon and worked on translating Software Carpentry lessons into Spanish with Paula Andrea Martinez. Our hackathon session has been immortalized in the promotional materials for OpenCon2018.

In December 2017, I finished my PhD, and I decided to go visit all the awesome open-science advocates that I met at OpenCon in Buenos Aires. I met Juli Aranco from Buenos Aires and we organized a lesson translation hackathon where we made huge progress on the Git and R lessons. We also ran a one-day Software Carpentry Workshop using those translated lessons. It was a huge success. The translated UNIX lesson was flawless. The translated Git lesson ran long but was good. Everyone brought snacks to share. All attendees and four of the five instructors were female. It was a great day.

The release of three stable Spanish translations meant that we needed lesson maintainers. So, while living in Buenos Aires, I also co-taught Carpentry Maintainer training in Spanish! I couldn’t have done this without Erin Becker, Ivan Gonzalez, and François Michonneau. Living in Argentina gave them the confidence to speak in Spanish about programming. I also immersed myself in the maintainer role, and my Git and GitHub skill levels skyrocketed. I can pretty much do all things Git now.

Instructor Training workshops for Puerto Rico and Argentina

Back in March 2017, Sue and I travelled to Puerto Rico to run instructor training in English that coincided with a Data Carpentry Replicathon (hackathon for replicating scientific results) taught by Tracy Teal, Phillip Brooks and a few others. We conducted the course in English, but we chatted in Spanish over coffee breaks and at parties. It was very cool. We hosted a few virtual bilingual demos and discussions after the workshop and that was fun but we lost momentum.

The real momentum for me for instructor training came from being introduced to the R Ladies Buenos Aires community in February 2018. Paola Prieto (one my co-instructors for the pilot The Carpentries workshop in Spanish) invited me to give a talk at their group meeting, so I decided to talk The Carpentries and reproducible research with R in Spanish! Everyone was really enthusiastic, so I started working to incorporate them into the instructor training program.

In June 2018, Sue taught a workshop at Jackson lab with about 20 people, but I Zoomed in with two RLadies from Argentina, Laura Acion and Maria Florencia. They did their practice teaching using R Gapminder Spanish lesson. I’m proud to say that Laura and Maria have already completed their instructor training, and the three of us are continuing to work together via RLadies Buenos Aires and the LatinR conference!

The first bilingual Instructor Training workshop for Latin America

Finally, in August 2018 we make it to the thing that people have been waiting for, a fully distributed online instructor training with participants in Argentina, Colombia, Costa Rica, Educador, Mexico and Peru. This was really a global event with four co-trainers and helpers (me, Sue McClatchy, Greg Wilson, Alejandra Gonzalez-Beltran, Paula Andrea Martinez). We were located in Canada, the USA, the UK, and Belgium. Everyone but Greg spoke Spanish to some degree. The students were encouraged to ask questions or make comments in either English or Spanish, so the Etherpad supported a really bilingual mix of stories and notes.

On Day One, Sue and I taught the lessons completely in English. While all the attendees acknowledged that the workshop would be taught in English, I knew some didn’t understand as well as the others. So, while Sue talked, I live translated what she was saying into Spanish in the Etherpad. Paula and some of the attendees were kind enough to help out to improve the notes. For me, the best part of day one was the episode on mindset and grit. I asked the attendees to share a recent time when they persevered despite wanting to quit. Two people said that they almost didn’t show up to this workshop but that they were thankful they did. I responded by saying that I had also considered not teaching this workshop but I’m glad I did. I started crying because I was so grateful for the community support that helped everyone persevere.

On Day Two after lunch, Alejandra taught an episode on introductions speaking only in Spanish! (You can view the original episode in English or the translation.) Since I could read and listen to this episode in Spanish, note taking in Spanish was a lot easier. This really solidified in my mind how hard it is to translate and learn at the same time and why it is so important to have a library of lessons in Spanish. I decided to continue speaking in Spanish when I taught the last two episodes regarding The Carpentries teaching practices and operations. While I didn’t have a translated lesson to use, I have already one slideshow and given one talk about The Carpentries in Spanish, so I felt comfortable speaking about The Carpentries in Spanish.

During the final 20 minutes of the workshop, we had a roundtable discussion about what everyone was excited about moving forward. After two days of reading people’s thoughts in the Etherpad, it was great to have a face-to-face discussion and hear everyone’s voices. While everyone said something slightly different, the main theme is everyone wants to improve their local training programs by organizing and teaching Software Carpentry and Data Carpentry workshops.

Outlook

I think we’ve come a long way growing communities of people who are passionate about improving research and teaching all over the world. You can read more about the translation and lesson release in the Carpentries blog in English and Spanish. As with the lesson translations, everyone is enthusiastic about organizing more workshops and expanding the curricula. These will be a long-term community project. To get involved, check out our GitHub repository for Spanish translations or join the Carpentries Latin America mailing list.

I’ve also come along way since this started. In three years, my fluency in verbal and computing languages has grown. In 2015 I didn’t think I was talented enough to teach programming in Spanish, but by early 2018 I had gained the experience and expertise necessary. It required some perseverance, but I didn’t do it alone; many colleagues around the globe contributed support to help turn some of these ideas into a reality. I think it is a beautiful example of how having a growth mindset, grit, and community support is really important when we think about expanding the Carpentries into new communities.

Thanks

I want to thank Paula Andrea Martinez, Maria Florencia and Raniere Silva for comments on earlier versions of this post. Thanks to everyone who helped make all these events happen!

softwarecarpentry  datacarpentry  instructortraining 
</body> </html> <!DOCTYPE HTML> CarpentryCon West 2018
06 May 2018

CarpentryCon West 2018

A community gathering of Data, Software, and Library Carpenters in sunny Davis, CA. For details visit: http://ivory.idyll.org/dibsi/CarpentryConWest.html

Note: If you are looking for the international CarpentryCon event taking place in Dublin on 30 May - 1 June, 2018, please visit http://www.carpentrycon.org/.

We’re inviting Carpentries folks of all stripes — from new fans to veteran community-members, from all disciplines, near and far — to join us for CarpentryCon West! We’ve got housing and space for DIBSI 2018, our annual bioinformatics summer institute, so we’ve set aside Friday evening through Sunday morning, June 29-July 1, for a Carpentries gathering in sunny Davis, California. Things you can expect to find include:

What to expect

  • Lots of social time with a small, friendly Carpentries community!
  • Keynote address from Anelda van der Walt on Carpentries communities in Africa
  • Other keynotes (TBD!)
  • Discussions about our new Spanish curriculum
  • An introduction to Binder as an instructional tool and a hackyfest to binderize repositories
  • On-boarding and mentorship opportunities to help new and experienced instructors connect and become familiar with Carpentries curriculum
  • Check-out opportunities for new instructors! Attendance will be counted as your Discussion session requirement, and we will also offer Demo opportunities for anyone who needs it!
  • Un-conference style activities proposed by attendees

It’s also worth noting that we still have room at our Carpentries Instructor Training (with Anelda and Sher!) on June 25-26, and will be running a variety of Carpentries workshops on June 27-28. See DIBSI 2018 for more details!

Contibute your ideas!

Want to organize a meet-up or activity? We’re happy to facilitate! File an issue in our planning repo: https://github.com/dib-lab/CarpentryConWest18! Or, contact us at dibsi.training@gmail.com. We can help to arrange space and connect you with collaborators to start the planning process.

How to sign up!

Registration is $50. Housing is available from 6/29-7/2 for $225, which includes breakfast and dinner (but not lunch).

Please register by May 15th to guarantee your place at DIBSI West Coast Carpentry Con. If you’re coming from afar, you’ll need to register soon to obtain on-campus housing, which includes breakfast and dinner, as these spaces are limited.

Local registration (no housing needed) is here: https://registration.genomecenter.ucdavis.edu/events/WCCC_DIBSI_2018/

Out-of-town registration (includes housing)* is here; https://registration.genomecenter.ucdavis.edu/events/WCCC_with_Housing_DIBSI_2018/

* If you’ve already registered for another DIBSI housing block – Week 1 or the ANGUS 2-week workshop – please contact dibsi.training@gmail.com to request a registration link that accounts for overlap between the housing reservation blocks.

Additional needs

If you have any additional needs of any kind, please do not hesitate to ask! We will be adding information about local activities for children, nursing rooms, and ways we support people of all abilities. We welcome inquiries!

Code of Conduct

All contributions are expected to follow the Carpentries’ code of conduct.

softwarecarpentry  datacarpentry  postdoclife  DIBlab 
</body> </html> <!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> " class="button special small">datacarpentry<!DOCTYPE HTML> Three years in the making for Instructor training in Latin America
24 Aug 2018

Three years in the making for Instructor training in Latin America

Building global communities of Spanish-speaking Carpentry instructors and lesson developers

This month I (Rayna Harris) co-taught a remote The Carpentries Instructor Training Workshop for 25 Spanish-speaking trainees in six countries in Latin America. It was awesome! One thing that made this workshop so special for me is that it has been three-plus years in the making. So, I thought I would tell the story, from my perspective, about all the things that came into play to make this workshop a reality.

The early days of The Carpentries workshops in Spanish

In 2016, Greg Wilson introduced me to Selene Fernandez-Valverde to discuss a Software Carpentry meets Spanish-speaking bioinformatics endeavour. Back then my Spanish was eight years out of practice and I was still learning to program. I didn’t think I had the expertise to teach programming in Spanish. Sue McClatchy had more expertise and practice, but it is still difficult for a native English speaker to live-translate a lesson from English to Spanish while live coding in front of a classroom.

This observation led to two simultaneous efforts: support a community-wide effort for collaborative lesson translation and provide instructor training for Spanish speaking instructors. That is exactly what many staff and volunteers have done over the past three years.

Spanish translations hacakathon and lesson maintenance

In November 2017, I went to Germany to attend OpenCon and worked on translating Software Carpentry lessons into Spanish with Paula Andrea Martinez. Our hackathon session has been immortalized in the promotional materials for OpenCon2018.

In December 2017, I finished my PhD, and I decided to go visit all the awesome open-science advocates that I met at OpenCon in Buenos Aires. I met Juli Aranco from Buenos Aires and we organized a lesson translation hackathon where we made huge progress on the Git and R lessons. We also ran a one-day Software Carpentry Workshop using those translated lessons. It was a huge success. The translated UNIX lesson was flawless. The translated Git lesson ran long but was good. Everyone brought snacks to share. All attendees and four of the five instructors were female. It was a great day.

The release of three stable Spanish translations meant that we needed lesson maintainers. So, while living in Buenos Aires, I also co-taught Carpentry Maintainer training in Spanish! I couldn’t have done this without Erin Becker, Ivan Gonzalez, and François Michonneau. Living in Argentina gave them the confidence to speak in Spanish about programming. I also immersed myself in the maintainer role, and my Git and GitHub skill levels skyrocketed. I can pretty much do all things Git now.

Instructor Training workshops for Puerto Rico and Argentina

Back in March 2017, Sue and I travelled to Puerto Rico to run instructor training in English that coincided with a Data Carpentry Replicathon (hackathon for replicating scientific results) taught by Tracy Teal, Phillip Brooks and a few others. We conducted the course in English, but we chatted in Spanish over coffee breaks and at parties. It was very cool. We hosted a few virtual bilingual demos and discussions after the workshop and that was fun but we lost momentum.

The real momentum for me for instructor training came from being introduced to the R Ladies Buenos Aires community in February 2018. Paola Prieto (one my co-instructors for the pilot The Carpentries workshop in Spanish) invited me to give a talk at their group meeting, so I decided to talk The Carpentries and reproducible research with R in Spanish! Everyone was really enthusiastic, so I started working to incorporate them into the instructor training program.

In June 2018, Sue taught a workshop at Jackson lab with about 20 people, but I Zoomed in with two RLadies from Argentina, Laura Acion and Maria Florencia. They did their practice teaching using R Gapminder Spanish lesson. I’m proud to say that Laura and Maria have already completed their instructor training, and the three of us are continuing to work together via RLadies Buenos Aires and the LatinR conference!

The first bilingual Instructor Training workshop for Latin America

Finally, in August 2018 we make it to the thing that people have been waiting for, a fully distributed online instructor training with participants in Argentina, Colombia, Costa Rica, Educador, Mexico and Peru. This was really a global event with four co-trainers and helpers (me, Sue McClatchy, Greg Wilson, Alejandra Gonzalez-Beltran, Paula Andrea Martinez). We were located in Canada, the USA, the UK, and Belgium. Everyone but Greg spoke Spanish to some degree. The students were encouraged to ask questions or make comments in either English or Spanish, so the Etherpad supported a really bilingual mix of stories and notes.

On Day One, Sue and I taught the lessons completely in English. While all the attendees acknowledged that the workshop would be taught in English, I knew some didn’t understand as well as the others. So, while Sue talked, I live translated what she was saying into Spanish in the Etherpad. Paula and some of the attendees were kind enough to help out to improve the notes. For me, the best part of day one was the episode on mindset and grit. I asked the attendees to share a recent time when they persevered despite wanting to quit. Two people said that they almost didn’t show up to this workshop but that they were thankful they did. I responded by saying that I had also considered not teaching this workshop but I’m glad I did. I started crying because I was so grateful for the community support that helped everyone persevere.

On Day Two after lunch, Alejandra taught an episode on introductions speaking only in Spanish! (You can view the original episode in English or the translation.) Since I could read and listen to this episode in Spanish, note taking in Spanish was a lot easier. This really solidified in my mind how hard it is to translate and learn at the same time and why it is so important to have a library of lessons in Spanish. I decided to continue speaking in Spanish when I taught the last two episodes regarding The Carpentries teaching practices and operations. While I didn’t have a translated lesson to use, I have already one slideshow and given one talk about The Carpentries in Spanish, so I felt comfortable speaking about The Carpentries in Spanish.

During the final 20 minutes of the workshop, we had a roundtable discussion about what everyone was excited about moving forward. After two days of reading people’s thoughts in the Etherpad, it was great to have a face-to-face discussion and hear everyone’s voices. While everyone said something slightly different, the main theme is everyone wants to improve their local training programs by organizing and teaching Software Carpentry and Data Carpentry workshops.

Outlook

I think we’ve come a long way growing communities of people who are passionate about improving research and teaching all over the world. You can read more about the translation and lesson release in the Carpentries blog in English and Spanish. As with the lesson translations, everyone is enthusiastic about organizing more workshops and expanding the curricula. These will be a long-term community project. To get involved, check out our GitHub repository for Spanish translations or join the Carpentries Latin America mailing list.

I’ve also come along way since this started. In three years, my fluency in verbal and computing languages has grown. In 2015 I didn’t think I was talented enough to teach programming in Spanish, but by early 2018 I had gained the experience and expertise necessary. It required some perseverance, but I didn’t do it alone; many colleagues around the globe contributed support to help turn some of these ideas into a reality. I think it is a beautiful example of how having a growth mindset, grit, and community support is really important when we think about expanding the Carpentries into new communities.

Thanks

I want to thank Paula Andrea Martinez, Maria Florencia and Raniere Silva for comments on earlier versions of this post. Thanks to everyone who helped make all these events happen!

softwarecarpentry  datacarpentry  instructortraining 
</body> </html> <!DOCTYPE HTML> CarpentryCon West 2018
06 May 2018

CarpentryCon West 2018

A community gathering of Data, Software, and Library Carpenters in sunny Davis, CA. For details visit: http://ivory.idyll.org/dibsi/CarpentryConWest.html

Note: If you are looking for the international CarpentryCon event taking place in Dublin on 30 May - 1 June, 2018, please visit http://www.carpentrycon.org/.

We’re inviting Carpentries folks of all stripes — from new fans to veteran community-members, from all disciplines, near and far — to join us for CarpentryCon West! We’ve got housing and space for DIBSI 2018, our annual bioinformatics summer institute, so we’ve set aside Friday evening through Sunday morning, June 29-July 1, for a Carpentries gathering in sunny Davis, California. Things you can expect to find include:

What to expect

  • Lots of social time with a small, friendly Carpentries community!
  • Keynote address from Anelda van der Walt on Carpentries communities in Africa
  • Other keynotes (TBD!)
  • Discussions about our new Spanish curriculum
  • An introduction to Binder as an instructional tool and a hackyfest to binderize repositories
  • On-boarding and mentorship opportunities to help new and experienced instructors connect and become familiar with Carpentries curriculum
  • Check-out opportunities for new instructors! Attendance will be counted as your Discussion session requirement, and we will also offer Demo opportunities for anyone who needs it!
  • Un-conference style activities proposed by attendees

It’s also worth noting that we still have room at our Carpentries Instructor Training (with Anelda and Sher!) on June 25-26, and will be running a variety of Carpentries workshops on June 27-28. See DIBSI 2018 for more details!

Contibute your ideas!

Want to organize a meet-up or activity? We’re happy to facilitate! File an issue in our planning repo: https://github.com/dib-lab/CarpentryConWest18! Or, contact us at dibsi.training@gmail.com. We can help to arrange space and connect you with collaborators to start the planning process.

How to sign up!

Registration is $50. Housing is available from 6/29-7/2 for $225, which includes breakfast and dinner (but not lunch).

Please register by May 15th to guarantee your place at DIBSI West Coast Carpentry Con. If you’re coming from afar, you’ll need to register soon to obtain on-campus housing, which includes breakfast and dinner, as these spaces are limited.

Local registration (no housing needed) is here: https://registration.genomecenter.ucdavis.edu/events/WCCC_DIBSI_2018/

Out-of-town registration (includes housing)* is here; https://registration.genomecenter.ucdavis.edu/events/WCCC_with_Housing_DIBSI_2018/

* If you’ve already registered for another DIBSI housing block – Week 1 or the ANGUS 2-week workshop – please contact dibsi.training@gmail.com to request a registration link that accounts for overlap between the housing reservation blocks.

Additional needs

If you have any additional needs of any kind, please do not hesitate to ask! We will be adding information about local activities for children, nursing rooms, and ways we support people of all abilities. We welcome inquiries!

Code of Conduct

All contributions are expected to follow the Carpentries’ code of conduct.

softwarecarpentry  datacarpentry  postdoclife  DIBlab 
</body> </html> <!DOCTYPE HTML> Reproducible Data-Driven Discovery
24 Feb 2017

Reproducible Data-Driven Discovery

Report back from the Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks and the Moore Foundation Early Career Researcher Symposium Control

I spent the two weeks in January hanging out with some awesome scientists who are all passionate about the future of science. I was participating in two professional development events with support from Data Carpentry, and I’d like to share some of the highlights.

A Curriculum Development Hackathon for Reproducible Research using Jupyter Notebooks

On January 9–11, 2017, I attended my first hackathon at the Berkeley Institute for Data Science! The event was organized jointly by Data Carpentry and the Jupyter Notebook project. The goal of the hackathon was to develop a two-day workshop curriculum to teach reproducible research using the Jupyter Notebook. There attendees were a group of 25 scientists from the US, Canada, and the UK with diverse backgrounds with a unique set of skills and expertise. I was one of a handful of attendees that uses R Markdown more than iPython or Jupyter Notebooks; however, after seeing the notebook’s power and utility, I’m really excited about adding this to my reproducible workflow.

On the first day of the hackathon, we all sketched out the general workshop overview and learning objectives. Then, we broke out into small groups to design the specific lessons. I worked closely with Erin Becker, Elizabeth Wickes, Daniel Soto, and Mike Pacer to develop the lesson on publication and sharing. This particular lesson focuses on exporting reports for sharing, best practices for documenting your workflow, best practices for using metadata, and using DOIs and ORCiD to get credit for your scholarly work. Even thought the workshop curricula is not completely polished and ready to teach, we are all very proud of the made significant progress we collectively made. You can view workshop website here.

This curriculum is still being developed and revised on an ongoing basis. Want to contribute? If you are interested in helping with the development, have a look a this list of GitHub issues to see what is happening and what needs to be done. We’d appreciate your contributions.

Data-Driven Discovery Postdoc and Early Career Researcher Symposium

On January 17-21, 2017, the Gordon and Betty Moore Foundation hosted the Data-Driven Discovery Postdoc and Early Career Researcher Symposium. Over 50 young investigators supported from 14 different time zones gathered at Waikoloa Beach, Hawaii to network and discuss challenges and opportunities for research and careers in data science. The symposium was of the “un-conference” style that promoted group discussions among like-minded attendees and deemphasized traditional panels and speakers.

Each day the participants engaged in ice-breaker activities that gave us a chance to meet and get to know nearly everyone of the attendees. You might think that it’s a little cheesy to introduce yourself and also say your favorite comfort who or which famous person you share a birthday with, but I was pleasantly surprised at how often those bits of helped the participants get to know each other better. Another favorite icebreaker was the living poster session, where we spent about an hour illustrating our research or teaching and then another two hours learning more about everyone’s interests.

All participants played a major role in crafting the agenda by pitching and then attending “birds of a feather” breakout sessions. You can see the diversity of suggested topics by viewing the open and closed GitHub issues or the session notes. One day I participated in a breakout session about science communication. It was awesome to hear how everyone struggled with and/or managed the tricky balance of doing science and communicating science. To report back to the group, we listed some challenges and resources for science communication on big pieces of white board paper, which you can view here. The next breakout session I attended was about science activism. It was a little unfortunate the symposium conflicted with the presidential inauguration and women’s marches, but some of us stayed very engaged in what was happening five time zones away. The 15 or so of us in the activism group (for lack of a better word) are committed to staying in touch to share news and opportunities for promoting science awareness and literacy in our local and global communities.

Overall, the symposium was #MooreUseful and #MooreInspiring than I anticipated. On of the more useful things (in my opinion) was an around-the-room discussion of each person’s favorite new tool; take a look at this list to see the kind of tools and methods we shared. It was so inspiring to learn what the other grad students, postdocs, and research scientists were working on and to hear their career struggles and successes. I was able to synthesize tons of ideas for my future research and career, and my eyes have been opened to more of the challenges and opportunities that data-driven researchers are facing.

Reproducible Data-Driven Discovery

I’m not sure if anyone has already coined the phrase “Reproducible Data-Driven Discovery”, but I think its an awesome way to summarize these two events and the communities that made them happen. The Moore Foundation funds researchers who do science with lots and lots of data, and Data Carpentry and Project Jupyter are two of the Moore-funded organizations that are helping make sure the data-driven research is freely available, open access, and reproducible. I can’t wait to see all the new awesome things that these communities create and build!

Thanks!

I especially want to thank Tracy for the opportunity to attend both of these events. I thank Hilmar Lapp, François Michonneau, Jasmine Nirody, Kellie Ottoboni, Tracy Teal, and Jamie Whitacre for organizing the Hackathon and Chris Mentzel, Carly Strasser, and Natalie Caulk for organizing the symposium. I thank everyone who participated and helped make these events awesome! I thank Laura Noren for feedback on an earlier version of this post.

science  reproducible  datadriven  scicomm  education  datacarpentry 
</body> </html> </a> <a href="/tags/neuroscience<!DOCTYPE HTML> Using music, beer, and pop-culture to communicate science
02 Jan 2018

Using music, beer, and pop-culture to communicate science

A little bit about my Nerd Nite talk called Zombie Brains: Microbial Mind Control. TLDR: David Attenborough meets Tom Waits meets Ed Yong

I recently gave a talk at The North Door for Nerd Nite Austin. This is a monthly event with an audience of 250 partially inebriated nerds, including about a dozen colleagues and friends. I put a lot of effort into making it fun and relatable, so I thought I would share some of the details about how and why I gave what I think is my best talk ever. You can view the video here and view my slides here.

"Zombie Brains: Microbial Mind Control," by Rayna Harris from Nerd Nite - Austin on Vimeo.

Science and sign language

I knew I would have a sign language interpreter with me on stage, so I tried to minimize jargon and define the scientific words I used. I recorded myself practicing my talk and critiqued the video playback about six times. I focused on reducing my use of filler words “um” and “like”. I specifically asked the interpreter to create a sign for “microbiome” because I knew I would use it more than a dozen times.

image1

On stage with a sign language translator and a ‘Tom Waits does David Attenborough’ impersonator. Instagram photos available at /.

Incorporating live performance and YouTube videos

I wanted to show this BBC David Attenborough video, but I was worried that people would be bored or that the sound quality would be bad, so I decided to play the video on silent and add my own sound. I invited my friend Joseph Palmer to narrate it using his amazing impersonation Tom Waits. With the help of the sound engineer, I cued a clip of Tom Waits Oily Night song to provide an eerie backdrop. Joseph’s performance received much applause and laughter. It was awesome!

image2

Watch this 30-second video clip of the Tom Waits-narrated footage of an infected insect being evicted from the social colony at https://twitter.com/R0mination/status/951295758615171072.

The 3 main themes of my talk

I decided that I would cover three main topics during my talk: parasitic mind control in insects, the link between the gut microbiome and the brain in humans, and the potential for parasitic mind control in humans. I opened with a definition of the word “microbiome” because I thought that was the best hook and it allowed me to engage the hearing-impaired viewers with a brand new sign. But, then, I launched into the 3 parts in the ordered described. This collage of images provides a good overview of my talk.

image3

These are all the images I used in my talk to illustrate beautiful biological phenomena and link it to current social phenomena.

First, I describe deadly host-pathogen relations in the jungle using photos from photos from Alex Wild and the Tom-Waits narrated video from the BBC. I describe research from Carolyn Elya, Michael Eisen, and colleagues on a fungal pathogen that manipulates Drosophila melanogaster in the lab. I take a moment to highlight other awesome neuroscience and molecular -development research in flies.

Then, I transition to talking about the dynamics of human microbiomes, with much of my inspiration coming from a book by Ed Yong on the multitudes of microscopic organisms living in our body. I got a lot of questions during the Q&A about how diet and disease affect and are affected by our microbiomes.

Finally, I talked about the possibility of microscopic organisms influencing social behaviors such as kissing, hand holding, breastfeeding, and more. The examples I used are inspired by basic research and by personal experience. I kept my language very casual to keep the audience engaged, and I got a lot of laughs and applause during this part of the talk. I hope they go away knowing what “horizontal gene transfer” is.

Similarities between host-parasite relationships and sexual harassment

This 2 min YouTube video (available at ) shows me practicing my talk. I make an analogy between host-parasite relationship and sexual harassment and summarize the 3 main points. See the twitter link above for what was actually said while the ant video played.

I wanted to have something in the talk that made it timely, so I decided to make an analogy between host-parasite relationship and current social movements related to sexual harassment and discrimination. I was very worried that this tangent on sexual harassment might not go over well, but I felt compelled to utilize my moment in the spotlight with a microphone to discuss an important social issue that affects many women in science.

I practiced this segment of my talk a lot, and I posted a short video of my last practice session here. What I said on stage was a little different than during that last practice session, but I kept the analogy between infected ants being evicted from colonies to women fearing job loss if they showed evidence of being harassed.

To my surprise, this portion of my talk drew even more applause than my friend’s impersonation of Tom Waits! However, this time people weren’t clapping and cheering because it was funny or novel; I think they were signaling to me that the could relate to what I was saying and that they were glad I had the courage to talk about it on stage.

The Q&A session

The Q&A lasted for what felt like 15 minutes. Most of the questions were of a biomedical nature that I felt I didn’t have the expertise to answer, so I tried to say “I don’t know for sure, but here is what I think…” when responding.

I did get one fun question and I responded with some research from the Lenski Lab. The audience member asked something along the lines of whether or not we should fear gut colonization by ancient bacteria that have been trapped in glaciers but are now being brought back to life.** **I responded by saying Lenski had done a lot of experiments competing older generation and newer generations of bacteria against each other and the newer bacterial almost always performed than the ancient ones. I didn’t give him a citation, but this paper on sustained fitness is what I should have given him.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Timeline for the Data Carpentry & Software Carpentry Reorganization
17 Jun 2017

Timeline for the Data Carpentry & Software Carpentry Reorganization

The future of the Carpentries

On Jun 8 & 9, we met in-person to continue discussing how to proceed with the merger of the Software Carpentry and Data Carpentry organizations to best achieve our strategic goals and serve our communities. We are happy to report that is was a very productive meeting.

We spent most of the meeting discussing the structure of the future organizational leadership. We have drafted a number of motions that we will present to our respective steering committees for approval at our next meetings. Among the motions, we will propose that the combined Carpentries governing structure be made up of both appointed and elected members. Additionally, we propose that it is in the best interest of the organization to seed the future steering committee with bylaws, which will be enumerated, written, and approved in the coming months.

Below is a timeline for the merger process. Various steps in this timeline require approval by both steering committees, and are dependent on results of previous steps, so this may change as we proceed.

Month Merger Process Milestones
June Communicate the in-person meeting outcomes and proposed governance structure to staff and community members.
July Present motions to approve the proposed goverance structure, executive leadership, and transfer of assets (e.g. finances, cross-organization subcommittees). Enumerate required bylaws.
August Present and approve an official motion to combine Software Carpentry and Data Carpentry into a unified organization. Approve nominations for the appointed seats to the steering committee.
September Approve a unified budget. Approve the transfer of assets.
October Call for candidates for elected members of the steering committee. Approve motions to dissolve the current steering committee and transfer assets as of January 1.
November Community call to announce candidates for the elected seats on the steering committee.
December Elect new elected steering committee members.
January New organization with new steering committee commences.

We are grateful for all the input we have and will to continue to received from community members, from staff, and from colleagues outside the Carpentries during this decision-making process. Please stayed tuned for updates and feel free to contact us with questions or concerns.

science  neuroscience  microbiome  scicomm 
</body> </html> " class="button special small">neuroscience<!DOCTYPE HTML> Using music, beer, and pop-culture to communicate science
02 Jan 2018

Using music, beer, and pop-culture to communicate science

A little bit about my Nerd Nite talk called Zombie Brains: Microbial Mind Control. TLDR: David Attenborough meets Tom Waits meets Ed Yong

I recently gave a talk at The North Door for Nerd Nite Austin. This is a monthly event with an audience of 250 partially inebriated nerds, including about a dozen colleagues and friends. I put a lot of effort into making it fun and relatable, so I thought I would share some of the details about how and why I gave what I think is my best talk ever. You can view the video here and view my slides here.

"Zombie Brains: Microbial Mind Control," by Rayna Harris from Nerd Nite - Austin on Vimeo.

Science and sign language

I knew I would have a sign language interpreter with me on stage, so I tried to minimize jargon and define the scientific words I used. I recorded myself practicing my talk and critiqued the video playback about six times. I focused on reducing my use of filler words “um” and “like”. I specifically asked the interpreter to create a sign for “microbiome” because I knew I would use it more than a dozen times.

image1

On stage with a sign language translator and a ‘Tom Waits does David Attenborough’ impersonator. Instagram photos available at /.

Incorporating live performance and YouTube videos

I wanted to show this BBC David Attenborough video, but I was worried that people would be bored or that the sound quality would be bad, so I decided to play the video on silent and add my own sound. I invited my friend Joseph Palmer to narrate it using his amazing impersonation Tom Waits. With the help of the sound engineer, I cued a clip of Tom Waits Oily Night song to provide an eerie backdrop. Joseph’s performance received much applause and laughter. It was awesome!

image2

Watch this 30-second video clip of the Tom Waits-narrated footage of an infected insect being evicted from the social colony at https://twitter.com/R0mination/status/951295758615171072.

The 3 main themes of my talk

I decided that I would cover three main topics during my talk: parasitic mind control in insects, the link between the gut microbiome and the brain in humans, and the potential for parasitic mind control in humans. I opened with a definition of the word “microbiome” because I thought that was the best hook and it allowed me to engage the hearing-impaired viewers with a brand new sign. But, then, I launched into the 3 parts in the ordered described. This collage of images provides a good overview of my talk.

image3

These are all the images I used in my talk to illustrate beautiful biological phenomena and link it to current social phenomena.

First, I describe deadly host-pathogen relations in the jungle using photos from photos from Alex Wild and the Tom-Waits narrated video from the BBC. I describe research from Carolyn Elya, Michael Eisen, and colleagues on a fungal pathogen that manipulates Drosophila melanogaster in the lab. I take a moment to highlight other awesome neuroscience and molecular -development research in flies.

Then, I transition to talking about the dynamics of human microbiomes, with much of my inspiration coming from a book by Ed Yong on the multitudes of microscopic organisms living in our body. I got a lot of questions during the Q&A about how diet and disease affect and are affected by our microbiomes.

Finally, I talked about the possibility of microscopic organisms influencing social behaviors such as kissing, hand holding, breastfeeding, and more. The examples I used are inspired by basic research and by personal experience. I kept my language very casual to keep the audience engaged, and I got a lot of laughs and applause during this part of the talk. I hope they go away knowing what “horizontal gene transfer” is.

Similarities between host-parasite relationships and sexual harassment

This 2 min YouTube video (available at ) shows me practicing my talk. I make an analogy between host-parasite relationship and sexual harassment and summarize the 3 main points. See the twitter link above for what was actually said while the ant video played.

I wanted to have something in the talk that made it timely, so I decided to make an analogy between host-parasite relationship and current social movements related to sexual harassment and discrimination. I was very worried that this tangent on sexual harassment might not go over well, but I felt compelled to utilize my moment in the spotlight with a microphone to discuss an important social issue that affects many women in science.

I practiced this segment of my talk a lot, and I posted a short video of my last practice session here. What I said on stage was a little different than during that last practice session, but I kept the analogy between infected ants being evicted from colonies to women fearing job loss if they showed evidence of being harassed.

To my surprise, this portion of my talk drew even more applause than my friend’s impersonation of Tom Waits! However, this time people weren’t clapping and cheering because it was funny or novel; I think they were signaling to me that the could relate to what I was saying and that they were glad I had the courage to talk about it on stage.

The Q&A session

The Q&A lasted for what felt like 15 minutes. Most of the questions were of a biomedical nature that I felt I didn’t have the expertise to answer, so I tried to say “I don’t know for sure, but here is what I think…” when responding.

I did get one fun question and I responded with some research from the Lenski Lab. The audience member asked something along the lines of whether or not we should fear gut colonization by ancient bacteria that have been trapped in glaciers but are now being brought back to life.** **I responded by saying Lenski had done a lot of experiments competing older generation and newer generations of bacteria against each other and the newer bacterial almost always performed than the ancient ones. I didn’t give him a citation, but this paper on sustained fitness is what I should have given him.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Timeline for the Data Carpentry & Software Carpentry Reorganization
17 Jun 2017

Timeline for the Data Carpentry & Software Carpentry Reorganization

The future of the Carpentries

On Jun 8 & 9, we met in-person to continue discussing how to proceed with the merger of the Software Carpentry and Data Carpentry organizations to best achieve our strategic goals and serve our communities. We are happy to report that is was a very productive meeting.

We spent most of the meeting discussing the structure of the future organizational leadership. We have drafted a number of motions that we will present to our respective steering committees for approval at our next meetings. Among the motions, we will propose that the combined Carpentries governing structure be made up of both appointed and elected members. Additionally, we propose that it is in the best interest of the organization to seed the future steering committee with bylaws, which will be enumerated, written, and approved in the coming months.

Below is a timeline for the merger process. Various steps in this timeline require approval by both steering committees, and are dependent on results of previous steps, so this may change as we proceed.

Month Merger Process Milestones
June Communicate the in-person meeting outcomes and proposed governance structure to staff and community members.
July Present motions to approve the proposed goverance structure, executive leadership, and transfer of assets (e.g. finances, cross-organization subcommittees). Enumerate required bylaws.
August Present and approve an official motion to combine Software Carpentry and Data Carpentry into a unified organization. Approve nominations for the appointed seats to the steering committee.
September Approve a unified budget. Approve the transfer of assets.
October Call for candidates for elected members of the steering committee. Approve motions to dissolve the current steering committee and transfer assets as of January 1.
November Community call to announce candidates for the elected seats on the steering committee.
December Elect new elected steering committee members.
January New organization with new steering committee commences.

We are grateful for all the input we have and will to continue to received from community members, from staff, and from colleagues outside the Carpentries during this decision-making process. Please stayed tuned for updates and feel free to contact us with questions or concerns.

science  neuroscience  microbiome  scicomm 
</body> </html> </a> <a href="/tags/microbiome<!DOCTYPE HTML> Using music, beer, and pop-culture to communicate science
02 Jan 2018

Using music, beer, and pop-culture to communicate science

A little bit about my Nerd Nite talk called Zombie Brains: Microbial Mind Control. TLDR: David Attenborough meets Tom Waits meets Ed Yong

I recently gave a talk at The North Door for Nerd Nite Austin. This is a monthly event with an audience of 250 partially inebriated nerds, including about a dozen colleagues and friends. I put a lot of effort into making it fun and relatable, so I thought I would share some of the details about how and why I gave what I think is my best talk ever. You can view the video here and view my slides here.

"Zombie Brains: Microbial Mind Control," by Rayna Harris from Nerd Nite - Austin on Vimeo.

Science and sign language

I knew I would have a sign language interpreter with me on stage, so I tried to minimize jargon and define the scientific words I used. I recorded myself practicing my talk and critiqued the video playback about six times. I focused on reducing my use of filler words “um” and “like”. I specifically asked the interpreter to create a sign for “microbiome” because I knew I would use it more than a dozen times.

image1

On stage with a sign language translator and a ‘Tom Waits does David Attenborough’ impersonator. Instagram photos available at /.

Incorporating live performance and YouTube videos

I wanted to show this BBC David Attenborough video, but I was worried that people would be bored or that the sound quality would be bad, so I decided to play the video on silent and add my own sound. I invited my friend Joseph Palmer to narrate it using his amazing impersonation Tom Waits. With the help of the sound engineer, I cued a clip of Tom Waits Oily Night song to provide an eerie backdrop. Joseph’s performance received much applause and laughter. It was awesome!

image2

Watch this 30-second video clip of the Tom Waits-narrated footage of an infected insect being evicted from the social colony at https://twitter.com/R0mination/status/951295758615171072.

The 3 main themes of my talk

I decided that I would cover three main topics during my talk: parasitic mind control in insects, the link between the gut microbiome and the brain in humans, and the potential for parasitic mind control in humans. I opened with a definition of the word “microbiome” because I thought that was the best hook and it allowed me to engage the hearing-impaired viewers with a brand new sign. But, then, I launched into the 3 parts in the ordered described. This collage of images provides a good overview of my talk.

image3

These are all the images I used in my talk to illustrate beautiful biological phenomena and link it to current social phenomena.

First, I describe deadly host-pathogen relations in the jungle using photos from photos from Alex Wild and the Tom-Waits narrated video from the BBC. I describe research from Carolyn Elya, Michael Eisen, and colleagues on a fungal pathogen that manipulates Drosophila melanogaster in the lab. I take a moment to highlight other awesome neuroscience and molecular -development research in flies.

Then, I transition to talking about the dynamics of human microbiomes, with much of my inspiration coming from a book by Ed Yong on the multitudes of microscopic organisms living in our body. I got a lot of questions during the Q&A about how diet and disease affect and are affected by our microbiomes.

Finally, I talked about the possibility of microscopic organisms influencing social behaviors such as kissing, hand holding, breastfeeding, and more. The examples I used are inspired by basic research and by personal experience. I kept my language very casual to keep the audience engaged, and I got a lot of laughs and applause during this part of the talk. I hope they go away knowing what “horizontal gene transfer” is.

Similarities between host-parasite relationships and sexual harassment

This 2 min YouTube video (available at ) shows me practicing my talk. I make an analogy between host-parasite relationship and sexual harassment and summarize the 3 main points. See the twitter link above for what was actually said while the ant video played.

I wanted to have something in the talk that made it timely, so I decided to make an analogy between host-parasite relationship and current social movements related to sexual harassment and discrimination. I was very worried that this tangent on sexual harassment might not go over well, but I felt compelled to utilize my moment in the spotlight with a microphone to discuss an important social issue that affects many women in science.

I practiced this segment of my talk a lot, and I posted a short video of my last practice session here. What I said on stage was a little different than during that last practice session, but I kept the analogy between infected ants being evicted from colonies to women fearing job loss if they showed evidence of being harassed.

To my surprise, this portion of my talk drew even more applause than my friend’s impersonation of Tom Waits! However, this time people weren’t clapping and cheering because it was funny or novel; I think they were signaling to me that the could relate to what I was saying and that they were glad I had the courage to talk about it on stage.

The Q&A session

The Q&A lasted for what felt like 15 minutes. Most of the questions were of a biomedical nature that I felt I didn’t have the expertise to answer, so I tried to say “I don’t know for sure, but here is what I think…” when responding.

I did get one fun question and I responded with some research from the Lenski Lab. The audience member asked something along the lines of whether or not we should fear gut colonization by ancient bacteria that have been trapped in glaciers but are now being brought back to life.** **I responded by saying Lenski had done a lot of experiments competing older generation and newer generations of bacteria against each other and the newer bacterial almost always performed than the ancient ones. I didn’t give him a citation, but this paper on sustained fitness is what I should have given him.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Timeline for the Data Carpentry & Software Carpentry Reorganization
17 Jun 2017

Timeline for the Data Carpentry & Software Carpentry Reorganization

The future of the Carpentries

On Jun 8 & 9, we met in-person to continue discussing how to proceed with the merger of the Software Carpentry and Data Carpentry organizations to best achieve our strategic goals and serve our communities. We are happy to report that is was a very productive meeting.

We spent most of the meeting discussing the structure of the future organizational leadership. We have drafted a number of motions that we will present to our respective steering committees for approval at our next meetings. Among the motions, we will propose that the combined Carpentries governing structure be made up of both appointed and elected members. Additionally, we propose that it is in the best interest of the organization to seed the future steering committee with bylaws, which will be enumerated, written, and approved in the coming months.

Below is a timeline for the merger process. Various steps in this timeline require approval by both steering committees, and are dependent on results of previous steps, so this may change as we proceed.

Month Merger Process Milestones
June Communicate the in-person meeting outcomes and proposed governance structure to staff and community members.
July Present motions to approve the proposed goverance structure, executive leadership, and transfer of assets (e.g. finances, cross-organization subcommittees). Enumerate required bylaws.
August Present and approve an official motion to combine Software Carpentry and Data Carpentry into a unified organization. Approve nominations for the appointed seats to the steering committee.
September Approve a unified budget. Approve the transfer of assets.
October Call for candidates for elected members of the steering committee. Approve motions to dissolve the current steering committee and transfer assets as of January 1.
November Community call to announce candidates for the elected seats on the steering committee.
December Elect new elected steering committee members.
January New organization with new steering committee commences.

We are grateful for all the input we have and will to continue to received from community members, from staff, and from colleagues outside the Carpentries during this decision-making process. Please stayed tuned for updates and feel free to contact us with questions or concerns.

science  neuroscience  microbiome  scicomm 
</body> </html> " class="button special small">microbiome<!DOCTYPE HTML> Using music, beer, and pop-culture to communicate science
02 Jan 2018

Using music, beer, and pop-culture to communicate science

A little bit about my Nerd Nite talk called Zombie Brains: Microbial Mind Control. TLDR: David Attenborough meets Tom Waits meets Ed Yong

I recently gave a talk at The North Door for Nerd Nite Austin. This is a monthly event with an audience of 250 partially inebriated nerds, including about a dozen colleagues and friends. I put a lot of effort into making it fun and relatable, so I thought I would share some of the details about how and why I gave what I think is my best talk ever. You can view the video here and view my slides here.

"Zombie Brains: Microbial Mind Control," by Rayna Harris from Nerd Nite - Austin on Vimeo.

Science and sign language

I knew I would have a sign language interpreter with me on stage, so I tried to minimize jargon and define the scientific words I used. I recorded myself practicing my talk and critiqued the video playback about six times. I focused on reducing my use of filler words “um” and “like”. I specifically asked the interpreter to create a sign for “microbiome” because I knew I would use it more than a dozen times.

image1

On stage with a sign language translator and a ‘Tom Waits does David Attenborough’ impersonator. Instagram photos available at /.

Incorporating live performance and YouTube videos

I wanted to show this BBC David Attenborough video, but I was worried that people would be bored or that the sound quality would be bad, so I decided to play the video on silent and add my own sound. I invited my friend Joseph Palmer to narrate it using his amazing impersonation Tom Waits. With the help of the sound engineer, I cued a clip of Tom Waits Oily Night song to provide an eerie backdrop. Joseph’s performance received much applause and laughter. It was awesome!

image2

Watch this 30-second video clip of the Tom Waits-narrated footage of an infected insect being evicted from the social colony at https://twitter.com/R0mination/status/951295758615171072.

The 3 main themes of my talk

I decided that I would cover three main topics during my talk: parasitic mind control in insects, the link between the gut microbiome and the brain in humans, and the potential for parasitic mind control in humans. I opened with a definition of the word “microbiome” because I thought that was the best hook and it allowed me to engage the hearing-impaired viewers with a brand new sign. But, then, I launched into the 3 parts in the ordered described. This collage of images provides a good overview of my talk.

image3

These are all the images I used in my talk to illustrate beautiful biological phenomena and link it to current social phenomena.

First, I describe deadly host-pathogen relations in the jungle using photos from photos from Alex Wild and the Tom-Waits narrated video from the BBC. I describe research from Carolyn Elya, Michael Eisen, and colleagues on a fungal pathogen that manipulates Drosophila melanogaster in the lab. I take a moment to highlight other awesome neuroscience and molecular -development research in flies.

Then, I transition to talking about the dynamics of human microbiomes, with much of my inspiration coming from a book by Ed Yong on the multitudes of microscopic organisms living in our body. I got a lot of questions during the Q&A about how diet and disease affect and are affected by our microbiomes.

Finally, I talked about the possibility of microscopic organisms influencing social behaviors such as kissing, hand holding, breastfeeding, and more. The examples I used are inspired by basic research and by personal experience. I kept my language very casual to keep the audience engaged, and I got a lot of laughs and applause during this part of the talk. I hope they go away knowing what “horizontal gene transfer” is.

Similarities between host-parasite relationships and sexual harassment

This 2 min YouTube video (available at ) shows me practicing my talk. I make an analogy between host-parasite relationship and sexual harassment and summarize the 3 main points. See the twitter link above for what was actually said while the ant video played.

I wanted to have something in the talk that made it timely, so I decided to make an analogy between host-parasite relationship and current social movements related to sexual harassment and discrimination. I was very worried that this tangent on sexual harassment might not go over well, but I felt compelled to utilize my moment in the spotlight with a microphone to discuss an important social issue that affects many women in science.

I practiced this segment of my talk a lot, and I posted a short video of my last practice session here. What I said on stage was a little different than during that last practice session, but I kept the analogy between infected ants being evicted from colonies to women fearing job loss if they showed evidence of being harassed.

To my surprise, this portion of my talk drew even more applause than my friend’s impersonation of Tom Waits! However, this time people weren’t clapping and cheering because it was funny or novel; I think they were signaling to me that the could relate to what I was saying and that they were glad I had the courage to talk about it on stage.

The Q&A session

The Q&A lasted for what felt like 15 minutes. Most of the questions were of a biomedical nature that I felt I didn’t have the expertise to answer, so I tried to say “I don’t know for sure, but here is what I think…” when responding.

I did get one fun question and I responded with some research from the Lenski Lab. The audience member asked something along the lines of whether or not we should fear gut colonization by ancient bacteria that have been trapped in glaciers but are now being brought back to life.** **I responded by saying Lenski had done a lot of experiments competing older generation and newer generations of bacteria against each other and the newer bacterial almost always performed than the ancient ones. I didn’t give him a citation, but this paper on sustained fitness is what I should have given him.

science  neuroscience  microbiome  scicomm 
</body> </html> <!DOCTYPE HTML> Timeline for the Data Carpentry & Software Carpentry Reorganization
17 Jun 2017

Timeline for the Data Carpentry & Software Carpentry Reorganization

The future of the Carpentries

On Jun 8 & 9, we met in-person to continue discussing how to proceed with the merger of the Software Carpentry and Data Carpentry organizations to best achieve our strategic goals and serve our communities. We are happy to report that is was a very productive meeting.

We spent most of the meeting discussing the structure of the future organizational leadership. We have drafted a number of motions that we will present to our respective steering committees for approval at our next meetings. Among the motions, we will propose that the combined Carpentries governing structure be made up of both appointed and elected members. Additionally, we propose that it is in the best interest of the organization to seed the future steering committee with bylaws, which will be enumerated, written, and approved in the coming months.

Below is a timeline for the merger process. Various steps in this timeline require approval by both steering committees, and are dependent on results of previous steps, so this may change as we proceed.

Month Merger Process Milestones
June Communicate the in-person meeting outcomes and proposed governance structure to staff and community members.
July Present motions to approve the proposed goverance structure, executive leadership, and transfer of assets (e.g. finances, cross-organization subcommittees). Enumerate required bylaws.
August Present and approve an official motion to combine Software Carpentry and Data Carpentry into a unified organization. Approve nominations for the appointed seats to the steering committee.
September Approve a unified budget. Approve the transfer of assets.
October Call for candidates for elected members of the steering committee. Approve motions to dissolve the current steering committee and transfer assets as of January 1.
November Community call to announce candidates for the elected seats on the steering committee.
December Elect new elected steering committee members.
January New organization with new steering committee commences.

We are grateful for all the input we have and will to continue to received from community members, from staff, and from colleagues outside the Carpentries during this decision-making process. Please stayed tuned for updates and feel free to contact us with questions or concerns.

science  neuroscience  microbiome  scicomm 
</body> </html> </a> <a href="/tags/datacommons<!DOCTYPE HTML> Open-source style community engagement for the Data Commons Pilot Phase Consortium
29 May 2018

Open-source style community engagement for the Data Commons Pilot Phase Consortium

This blog post discusses how we are building an open community around a larger goal of making big data more findable and usable to accelerate biomedical discovery

In November 2017, the National Institutes of Health (NIH) announced the formation of a Data Commons Pilot Phase Consortium (DCPPC) to accelerate biomedical discovery by making big biomedical data more findable and usable.

It’s called a consortium because the awardees are all working together in concert and collaboration to achieve the larger goal. Those awardees (big cats who run academic research labs or companies) have each brought on numerous students, postdocs, and staff, so the size of the consortium has already grown to over 300 people! That’s a lot of cats to herd.

So, how are we keeping everyone in the community coordinated and engaged? Here’s a little insight into our approach, which was first outlined by Titus in this blog post.

DCPPC Key Capabilities and teams

The overall structure of the DCPPC is a little complex, especially to the uninitiated. Members of the consortium organized themselves into “Key Capabilities” or focus groups that correspond to elements of the funding call and the major objectives of the Data Commons. Key Capabilities (KC) 1-9 are described in more detail here.

On top of the KC lingo, each of the awardees all adopted team names from the elements of the periodic table, so you’ll hear thing things like “KC1 has a meeting on Wednesday” or “Team Copper is meeting on Tuesday”. I made infographic below to help myself see the connections between the DCPPC objections, key capacities and teams.

fig1

I am a member of Team Copper, which consistes of members or affiliates of the Data Intensive Biology Lab at UC Davis (C. Titus Brown, Phillip Brooks, Rebecca Calisi Rodriguez, Amanda Charbonneau, Rayna Harris, Luiz Irber, Tamer Mansour, Charles Reid, Daniel Standage and Karen Word), the Biomedical data analysis company Curoverse (Alexander (Sasha) Wait Zaranek, VM (Vicky) Brasseur, Sarah Edrie, Meredith Gamble and Sarah Wait Zaranek), and the Harvard Chan Bioinformatics Core (Brad Chapman, Radhika Khetani and Mary Piper).

GitHub for project management of 522 milestones and 50 deliverables

Very early on, it was decided that GitHub would be our authoritative and canonical source for all DCPPC milestones and deliverables. What are milestones and deliverables? Milestones are team-defined tasks that must be completed in order to achieve the long-term objective of the DCPPC. Deliverables are the currency by which we evaluate whether or not a milestone has been reached. Deliverables can be in either the form of a demo (activities or documentation that demonstrate completion of goals of the Commons) or products (resources such as standards and conventions, APIs, data resources, websites, repositories, documentation, and training or outreach materials). The DCPPC has defined 522 milestones and 50 deliverables that are due in the first 180 days (between April 1 and September 28, 2018).

_Why GitHub?__ We chose GitHub because it makes cross-project linking and commenting easy and many people are familiar with it.

How did we get all the information about 500 milestones ingot GitHub issues? We automated it! One of the first accomplishments of Team Copper was developed a collection of scripts (collectively referred to as the “DCPPC bot”) that takes a CSV file of all the milestones and deliverables and opens GitHub issues with a brief description, a due date, and a label corresponding the relevant Team.

Right now, the DCPPC bot only deals with DCPPC milestones and deliverables, but you could imagine how this tools could be modified and adapted to many other large-scale community projects.

fig2

On-boarding existing and new members

To get everyone on the same page, we put in place some loose guidelines for communication (we’ll be using this platform for e-mail, that project for documents, etc.). We defined a community code of conduct and have adopted open and transparent workflows to the best of our ability.

We wrote some simple onboarding documents and checklists to connect people to those guidelines, communication channels, and useful resources. New members fill out a Google form providing basic contact information and their affiliation to the DCPPC. Then Team Copper gives them access to all the various communication channels. Finally, we send a follow-up email pointing new members to all the relevant resources and documentation. We haven’t perfected on onboarding process, but this thank you note is evidence that we are on the right track!

“Thank you so much for this information! I just started with [the DCPPC] 3 weeks ago and the learning curve has been steep. These docs have been the best crash course. Thank you!” - Anonymous DCPPC member

It is important to note that we are paying attention to what communication avenues are actually being used or working well and are fine-tuning accordingly. For instance, we started using Google Calendars, but it wasn’t working, so we switched to the Groups.io calendar. Our goal is to layer on more structure only when the need becomes apparent (but without doing so too early or often) to preserve flexibility and adaptation to suit the needs of the community.

The best thing (in my opinion) about using Groups.io, GitHub, and Slack for communication is that new members have access to all the conversation that has taken place since the beginning. This provides a wealth of information that would be lost if all communication took place via personal email or face to face communication.

Another excellent feature of the tools we are using is the availability of APIs for automating processes and reconciling access lists. We configured our groups.io calendars to automatically post upcoming meeting notifications to the appropriate Slack channel, so that’s cool! We also built a tool that calls the Slack, GitHub, and Groups.io APIs and returns a list of everyone with access. This is really useful for checking to be sure that everyone who needs access has it (or that no one who shouldn’t doesn’t).

Monthly, unconference style meetings and hackathons

Virtual tools like Slack, GitHub, Twitter, and Zoom make synchronous and asynchronous communication possible from nearly anywhere in the world, but the power of face to face (f2f) communication is undeniable a powerful way to boost collaboration and creativity. As a testament to the Consortium’s commitment to community engagement, a significant part of our budget is being used to cover all the associated travel, lodging, and food costs.

Team Copper (see the list of members below) has taken on the role of organizing or facilitating these f2f meeting. We are adopting an “unconference style” format where the attendees determine the topics of discussion or direction of a hackathon.

The goal of the first f2f meetings in December 2017 was to determine what the DCPPC actually needed to do during the first 180 days of this effort (aka Pilot Phase I). This meeting was attended by NIH staff, awardees, cloud service providers, and data stewards. You can read more about the outcomes of this meeting in a blog post written by C. Titus Brown. The second f2f meeting took place on April 2018. The goal of the April meeting the goal was to showcase our progress to the NIH.

Moving forward, we are planning a f2f meeting every month at various sites around the US. The goals of the DCPPC May workshop are to build community, to facilitate planned and serendipitous collaboration across teams, and to surface hidden issues around technical and conceptual interoperability. A major focus of the June meeting will be a multi-team, multi-KC hackathon. The goals and topics for our meetings in July - October meetings have yet to be determined but will likely correspond to relevant milestones and deliverable that are due those months or the near future.

Want more updates?

There’s a lot that I didn’t cover, so stay tuned for more in-depth blog posts about building an open-source style community around the Data Commons. In the mean time, get regular updates by following the #CommonsPilot hashtag or the @nih_dcppc ‏and @NIH_CommonFund accounts on Twitter.

datacommons 
<!DOCTYPE HTML> Video tutorial: how to GitHub notifications
17 May 2018

Video tutorial: how to GitHub notifications

Have you ever wondered: I'm missing information, how do I get notified of things? These notifications aren't useful, how do I turn them off? Is so, this video is for you!

This is a 4 minute video tutorial for adjusting notification settings.

Link to YouTube: https://youtu.be/4vhWJ_lgG0c

I recommend watching it a 2x speed.

It has three parts.

  1. Exploring an organizational dashboard.
  2. Exploring repository insights
  3. Changing individual and global repository settings

I hope you find it useful!

datacommons 
</body> </html> <!DOCTYPE HTML> Increasing transparency in postdoc hiring and on-boarding
02 May 2018

Increasing transparency in postdoc hiring and on-boarding

A brief summary of the interview process for my postdoc with Titus Brown. Highlights include: collaborative documents for interview questions, salary negotiations, and science communication

This week I started a post-doc working in Titus Brown’s Data Intensive Biology lab. If there is such a thing as a dream job, this is it. I’ve interacted with Titus and his lab members many times through BEACON, the Marine Biological Laboratory, Software Carpentry, and Data Carpentry.

One of the things I appreciate so much about Titus’s style is his transparency. Here are a few of my thoughts about why interview process and the on-boarding have gone so well.

The quick turn around

Titus posted the job announcement on the Software Carpentry discuss list and on hackmd on March 15. During April, I had an interview, received an offer, accepted the offer, and set a May 1 start date. I wish all things in academia could move so fast.

The interview questions

The really cool part about the interview process what Titus posted the interview questions ahead of time here, and I submitted my responses here. This meant I could be more relaxed during the interview because the questions weren’t out of the blue. Titus and his lab mates were able to ask me to delve into the details a little more or say, “cool, let’s move on to the next topic”.

Even before Titus informed me that I would be given the interview questions ahead of time, I knew this was coming because, well, he wrote a blog post with the interview questions used for a postdoc position building pipelines. I hope to see more of this transparency and sharing of interview questions in the future.

The salary

The salary was posted with the job announcement, so I was never in doubt about what my salary would be. Additionally, in May 2016, Titus posted a blog about increasing postdoc pay. In this post, he makes it clear that he pays all his postdocs the same and that he doesn’t negotiate salary. So, when he made me an offer, I didn’t have to waste my energy negotiating salary, which freed up time to talk about other things that were valuable to me.

Code of Conduct

I’ve always liked that Titus has a Code of Conduct on his lab’s website. Back in January of 2017, I was recruiting some undergrads, and I wondered if I should put a Code of Conduct on my personal website (many PIs that are affiliated with The Carpentries have one on their website, but my grad advisor did not). So, I reached out to Titus and asked him what he thought. He gave me some really good advice about how the purpose of the CoC was to convey that “these are my expectations for our behavior, and these are the paths to resolution”.

What I’ve come to realize over the past year is that even though I and many of my colleagues point to CoCs at conferences and workshops, very few of us feel equipped to responding to Code of Conduct incidents. So, I’m excited that this Friday I’ll be participating in a workshop on Training for Code of Conduct Incident Response with some Carpentry Colleagues. I think this is an important step toward increasing diversity in our community.

Communication

Right now, were use Slack and GitHub for most of our communication. This means that progress on all projects is visible to the rest of the lab, and most of it is under version control. I really like both of these technologies because they work synchronously or asynchronously and collaboratively on projects and easily keep track of what’s working well or not.

Summary

In the last two years, I applied for 13 different postdocs positions or jobs and had 10 interviews, but this is one is my dream job. I super excited about being in an environment with our goal is increase transparency in both our scientific methodology but also with respect to the social aspects of science. Stay tuned for more updates about our progress!

datacommons  postdoclife  DIBlab 
</body> </html> " class="button special small">datacommons<!DOCTYPE HTML> Open-source style community engagement for the Data Commons Pilot Phase Consortium
29 May 2018

Open-source style community engagement for the Data Commons Pilot Phase Consortium

This blog post discusses how we are building an open community around a larger goal of making big data more findable and usable to accelerate biomedical discovery

In November 2017, the National Institutes of Health (NIH) announced the formation of a Data Commons Pilot Phase Consortium (DCPPC) to accelerate biomedical discovery by making big biomedical data more findable and usable.

It’s called a consortium because the awardees are all working together in concert and collaboration to achieve the larger goal. Those awardees (big cats who run academic research labs or companies) have each brought on numerous students, postdocs, and staff, so the size of the consortium has already grown to over 300 people! That’s a lot of cats to herd.

So, how are we keeping everyone in the community coordinated and engaged? Here’s a little insight into our approach, which was first outlined by Titus in this blog post.

DCPPC Key Capabilities and teams

The overall structure of the DCPPC is a little complex, especially to the uninitiated. Members of the consortium organized themselves into “Key Capabilities” or focus groups that correspond to elements of the funding call and the major objectives of the Data Commons. Key Capabilities (KC) 1-9 are described in more detail here.

On top of the KC lingo, each of the awardees all adopted team names from the elements of the periodic table, so you’ll hear thing things like “KC1 has a meeting on Wednesday” or “Team Copper is meeting on Tuesday”. I made infographic below to help myself see the connections between the DCPPC objections, key capacities and teams.

fig1

I am a member of Team Copper, which consistes of members or affiliates of the Data Intensive Biology Lab at UC Davis (C. Titus Brown, Phillip Brooks, Rebecca Calisi Rodriguez, Amanda Charbonneau, Rayna Harris, Luiz Irber, Tamer Mansour, Charles Reid, Daniel Standage and Karen Word), the Biomedical data analysis company Curoverse (Alexander (Sasha) Wait Zaranek, VM (Vicky) Brasseur, Sarah Edrie, Meredith Gamble and Sarah Wait Zaranek), and the Harvard Chan Bioinformatics Core (Brad Chapman, Radhika Khetani and Mary Piper).

GitHub for project management of 522 milestones and 50 deliverables

Very early on, it was decided that GitHub would be our authoritative and canonical source for all DCPPC milestones and deliverables. What are milestones and deliverables? Milestones are team-defined tasks that must be completed in order to achieve the long-term objective of the DCPPC. Deliverables are the currency by which we evaluate whether or not a milestone has been reached. Deliverables can be in either the form of a demo (activities or documentation that demonstrate completion of goals of the Commons) or products (resources such as standards and conventions, APIs, data resources, websites, repositories, documentation, and training or outreach materials). The DCPPC has defined 522 milestones and 50 deliverables that are due in the first 180 days (between April 1 and September 28, 2018).

_Why GitHub?__ We chose GitHub because it makes cross-project linking and commenting easy and many people are familiar with it.

How did we get all the information about 500 milestones ingot GitHub issues? We automated it! One of the first accomplishments of Team Copper was developed a collection of scripts (collectively referred to as the “DCPPC bot”) that takes a CSV file of all the milestones and deliverables and opens GitHub issues with a brief description, a due date, and a label corresponding the relevant Team.

Right now, the DCPPC bot only deals with DCPPC milestones and deliverables, but you could imagine how this tools could be modified and adapted to many other large-scale community projects.

fig2

On-boarding existing and new members

To get everyone on the same page, we put in place some loose guidelines for communication (we’ll be using this platform for e-mail, that project for documents, etc.). We defined a community code of conduct and have adopted open and transparent workflows to the best of our ability.

We wrote some simple onboarding documents and checklists to connect people to those guidelines, communication channels, and useful resources. New members fill out a Google form providing basic contact information and their affiliation to the DCPPC. Then Team Copper gives them access to all the various communication channels. Finally, we send a follow-up email pointing new members to all the relevant resources and documentation. We haven’t perfected on onboarding process, but this thank you note is evidence that we are on the right track!

“Thank you so much for this information! I just started with [the DCPPC] 3 weeks ago and the learning curve has been steep. These docs have been the best crash course. Thank you!” - Anonymous DCPPC member

It is important to note that we are paying attention to what communication avenues are actually being used or working well and are fine-tuning accordingly. For instance, we started using Google Calendars, but it wasn’t working, so we switched to the Groups.io calendar. Our goal is to layer on more structure only when the need becomes apparent (but without doing so too early or often) to preserve flexibility and adaptation to suit the needs of the community.

The best thing (in my opinion) about using Groups.io, GitHub, and Slack for communication is that new members have access to all the conversation that has taken place since the beginning. This provides a wealth of information that would be lost if all communication took place via personal email or face to face communication.

Another excellent feature of the tools we are using is the availability of APIs for automating processes and reconciling access lists. We configured our groups.io calendars to automatically post upcoming meeting notifications to the appropriate Slack channel, so that’s cool! We also built a tool that calls the Slack, GitHub, and Groups.io APIs and returns a list of everyone with access. This is really useful for checking to be sure that everyone who needs access has it (or that no one who shouldn’t doesn’t).

Monthly, unconference style meetings and hackathons

Virtual tools like Slack, GitHub, Twitter, and Zoom make synchronous and asynchronous communication possible from nearly anywhere in the world, but the power of face to face (f2f) communication is undeniable a powerful way to boost collaboration and creativity. As a testament to the Consortium’s commitment to community engagement, a significant part of our budget is being used to cover all the associated travel, lodging, and food costs.

Team Copper (see the list of members below) has taken on the role of organizing or facilitating these f2f meeting. We are adopting an “unconference style” format where the attendees determine the topics of discussion or direction of a hackathon.

The goal of the first f2f meetings in December 2017 was to determine what the DCPPC actually needed to do during the first 180 days of this effort (aka Pilot Phase I). This meeting was attended by NIH staff, awardees, cloud service providers, and data stewards. You can read more about the outcomes of this meeting in a blog post written by C. Titus Brown. The second f2f meeting took place on April 2018. The goal of the April meeting the goal was to showcase our progress to the NIH.

Moving forward, we are planning a f2f meeting every month at various sites around the US. The goals of the DCPPC May workshop are to build community, to facilitate planned and serendipitous collaboration across teams, and to surface hidden issues around technical and conceptual interoperability. A major focus of the June meeting will be a multi-team, multi-KC hackathon. The goals and topics for our meetings in July - October meetings have yet to be determined but will likely correspond to relevant milestones and deliverable that are due those months or the near future.

Want more updates?

There’s a lot that I didn’t cover, so stay tuned for more in-depth blog posts about building an open-source style community around the Data Commons. In the mean time, get regular updates by following the #CommonsPilot hashtag or the @nih_dcppc ‏and @NIH_CommonFund accounts on Twitter.

datacommons 
<!DOCTYPE HTML> Video tutorial: how to GitHub notifications
17 May 2018

Video tutorial: how to GitHub notifications

Have you ever wondered: I'm missing information, how do I get notified of things? These notifications aren't useful, how do I turn them off? Is so, this video is for you!

This is a 4 minute video tutorial for adjusting notification settings.

Link to YouTube: https://youtu.be/4vhWJ_lgG0c

I recommend watching it a 2x speed.

It has three parts.

  1. Exploring an organizational dashboard.
  2. Exploring repository insights
  3. Changing individual and global repository settings

I hope you find it useful!

datacommons 
</body> </html> <!DOCTYPE HTML> Increasing transparency in postdoc hiring and on-boarding
02 May 2018

Increasing transparency in postdoc hiring and on-boarding

A brief summary of the interview process for my postdoc with Titus Brown. Highlights include: collaborative documents for interview questions, salary negotiations, and science communication

This week I started a post-doc working in Titus Brown’s Data Intensive Biology lab. If there is such a thing as a dream job, this is it. I’ve interacted with Titus and his lab members many times through BEACON, the Marine Biological Laboratory, Software Carpentry, and Data Carpentry.

One of the things I appreciate so much about Titus’s style is his transparency. Here are a few of my thoughts about why interview process and the on-boarding have gone so well.

The quick turn around

Titus posted the job announcement on the Software Carpentry discuss list and on hackmd on March 15. During April, I had an interview, received an offer, accepted the offer, and set a May 1 start date. I wish all things in academia could move so fast.

The interview questions

The really cool part about the interview process what Titus posted the interview questions ahead of time here, and I submitted my responses here. This meant I could be more relaxed during the interview because the questions weren’t out of the blue. Titus and his lab mates were able to ask me to delve into the details a little more or say, “cool, let’s move on to the next topic”.

Even before Titus informed me that I would be given the interview questions ahead of time, I knew this was coming because, well, he wrote a blog post with the interview questions used for a postdoc position building pipelines. I hope to see more of this transparency and sharing of interview questions in the future.

The salary

The salary was posted with the job announcement, so I was never in doubt about what my salary would be. Additionally, in May 2016, Titus posted a blog about increasing postdoc pay. In this post, he makes it clear that he pays all his postdocs the same and that he doesn’t negotiate salary. So, when he made me an offer, I didn’t have to waste my energy negotiating salary, which freed up time to talk about other things that were valuable to me.

Code of Conduct

I’ve always liked that Titus has a Code of Conduct on his lab’s website. Back in January of 2017, I was recruiting some undergrads, and I wondered if I should put a Code of Conduct on my personal website (many PIs that are affiliated with The Carpentries have one on their website, but my grad advisor did not). So, I reached out to Titus and asked him what he thought. He gave me some really good advice about how the purpose of the CoC was to convey that “these are my expectations for our behavior, and these are the paths to resolution”.

What I’ve come to realize over the past year is that even though I and many of my colleagues point to CoCs at conferences and workshops, very few of us feel equipped to responding to Code of Conduct incidents. So, I’m excited that this Friday I’ll be participating in a workshop on Training for Code of Conduct Incident Response with some Carpentry Colleagues. I think this is an important step toward increasing diversity in our community.

Communication

Right now, were use Slack and GitHub for most of our communication. This means that progress on all projects is visible to the rest of the lab, and most of it is under version control. I really like both of these technologies because they work synchronously or asynchronously and collaboratively on projects and easily keep track of what’s working well or not.

Summary

In the last two years, I applied for 13 different postdocs positions or jobs and had 10 interviews, but this is one is my dream job. I super excited about being in an environment with our goal is increase transparency in both our scientific methodology but also with respect to the social aspects of science. Stay tuned for more updates about our progress!

datacommons  postdoclife  DIBlab 
</body> </html> </a> <a href="/tags/postdoclife<!DOCTYPE HTML> CarpentryCon West 2018
06 May 2018

CarpentryCon West 2018

A community gathering of Data, Software, and Library Carpenters in sunny Davis, CA. For details visit: http://ivory.idyll.org/dibsi/CarpentryConWest.html

Note: If you are looking for the international CarpentryCon event taking place in Dublin on 30 May - 1 June, 2018, please visit http://www.carpentrycon.org/.

We’re inviting Carpentries folks of all stripes — from new fans to veteran community-members, from all disciplines, near and far — to join us for CarpentryCon West! We’ve got housing and space for DIBSI 2018, our annual bioinformatics summer institute, so we’ve set aside Friday evening through Sunday morning, June 29-July 1, for a Carpentries gathering in sunny Davis, California. Things you can expect to find include:

What to expect

  • Lots of social time with a small, friendly Carpentries community!
  • Keynote address from Anelda van der Walt on Carpentries communities in Africa
  • Other keynotes (TBD!)
  • Discussions about our new Spanish curriculum
  • An introduction to Binder as an instructional tool and a hackyfest to binderize repositories
  • On-boarding and mentorship opportunities to help new and experienced instructors connect and become familiar with Carpentries curriculum
  • Check-out opportunities for new instructors! Attendance will be counted as your Discussion session requirement, and we will also offer Demo opportunities for anyone who needs it!
  • Un-conference style activities proposed by attendees

It’s also worth noting that we still have room at our Carpentries Instructor Training (with Anelda and Sher!) on June 25-26, and will be running a variety of Carpentries workshops on June 27-28. See DIBSI 2018 for more details!

Contibute your ideas!

Want to organize a meet-up or activity? We’re happy to facilitate! File an issue in our planning repo: https://github.com/dib-lab/CarpentryConWest18! Or, contact us at dibsi.training@gmail.com. We can help to arrange space and connect you with collaborators to start the planning process.

How to sign up!

Registration is $50. Housing is available from 6/29-7/2 for $225, which includes breakfast and dinner (but not lunch).

Please register by May 15th to guarantee your place at DIBSI West Coast Carpentry Con. If you’re coming from afar, you’ll need to register soon to obtain on-campus housing, which includes breakfast and dinner, as these spaces are limited.

Local registration (no housing needed) is here: https://registration.genomecenter.ucdavis.edu/events/WCCC_DIBSI_2018/

Out-of-town registration (includes housing)* is here; https://registration.genomecenter.ucdavis.edu/events/WCCC_with_Housing_DIBSI_2018/

* If you’ve already registered for another DIBSI housing block – Week 1 or the ANGUS 2-week workshop – please contact dibsi.training@gmail.com to request a registration link that accounts for overlap between the housing reservation blocks.

Additional needs

If you have any additional needs of any kind, please do not hesitate to ask! We will be adding information about local activities for children, nursing rooms, and ways we support people of all abilities. We welcome inquiries!

Code of Conduct

All contributions are expected to follow the Carpentries’ code of conduct.

softwarecarpentry  datacarpentry  postdoclife  DIBlab 
</body> </html> <!DOCTYPE HTML> Increasing transparency in postdoc hiring and on-boarding
02 May 2018

Increasing transparency in postdoc hiring and on-boarding

A brief summary of the interview process for my postdoc with Titus Brown. Highlights include: collaborative documents for interview questions, salary negotiations, and science communication

This week I started a post-doc working in Titus Brown’s Data Intensive Biology lab. If there is such a thing as a dream job, this is it. I’ve interacted with Titus and his lab members many times through BEACON, the Marine Biological Laboratory, Software Carpentry, and Data Carpentry.

One of the things I appreciate so much about Titus’s style is his transparency. Here are a few of my thoughts about why interview process and the on-boarding have gone so well.

The quick turn around

Titus posted the job announcement on the Software Carpentry discuss list and on hackmd on March 15. During April, I had an interview, received an offer, accepted the offer, and set a May 1 start date. I wish all things in academia could move so fast.

The interview questions

The really cool part about the interview process what Titus posted the interview questions ahead of time here, and I submitted my responses here. This meant I could be more relaxed during the interview because the questions weren’t out of the blue. Titus and his lab mates were able to ask me to delve into the details a little more or say, “cool, let’s move on to the next topic”.

Even before Titus informed me that I would be given the interview questions ahead of time, I knew this was coming because, well, he wrote a blog post with the interview questions used for a postdoc position building pipelines. I hope to see more of this transparency and sharing of interview questions in the future.

The salary

The salary was posted with the job announcement, so I was never in doubt about what my salary would be. Additionally, in May 2016, Titus posted a blog about increasing postdoc pay. In this post, he makes it clear that he pays all his postdocs the same and that he doesn’t negotiate salary. So, when he made me an offer, I didn’t have to waste my energy negotiating salary, which freed up time to talk about other things that were valuable to me.

Code of Conduct

I’ve always liked that Titus has a Code of Conduct on his lab’s website. Back in January of 2017, I was recruiting some undergrads, and I wondered if I should put a Code of Conduct on my personal website (many PIs that are affiliated with The Carpentries have one on their website, but my grad advisor did not). So, I reached out to Titus and asked him what he thought. He gave me some really good advice about how the purpose of the CoC was to convey that “these are my expectations for our behavior, and these are the paths to resolution”.

What I’ve come to realize over the past year is that even though I and many of my colleagues point to CoCs at conferences and workshops, very few of us feel equipped to responding to Code of Conduct incidents. So, I’m excited that this Friday I’ll be participating in a workshop on Training for Code of Conduct Incident Response with some Carpentry Colleagues. I think this is an important step toward increasing diversity in our community.

Communication

Right now, were use Slack and GitHub for most of our communication. This means that progress on all projects is visible to the rest of the lab, and most of it is under version control. I really like both of these technologies because they work synchronously or asynchronously and collaboratively on projects and easily keep track of what’s working well or not.

Summary

In the last two years, I applied for 13 different postdocs positions or jobs and had 10 interviews, but this is one is my dream job. I super excited about being in an environment with our goal is increase transparency in both our scientific methodology but also with respect to the social aspects of science. Stay tuned for more updates about our progress!

datacommons  postdoclife  DIBlab 
</body> </html> " class="button special small">postdoclife<!DOCTYPE HTML> CarpentryCon West 2018
06 May 2018

CarpentryCon West 2018

A community gathering of Data, Software, and Library Carpenters in sunny Davis, CA. For details visit: http://ivory.idyll.org/dibsi/CarpentryConWest.html

Note: If you are looking for the international CarpentryCon event taking place in Dublin on 30 May - 1 June, 2018, please visit http://www.carpentrycon.org/.

We’re inviting Carpentries folks of all stripes — from new fans to veteran community-members, from all disciplines, near and far — to join us for CarpentryCon West! We’ve got housing and space for DIBSI 2018, our annual bioinformatics summer institute, so we’ve set aside Friday evening through Sunday morning, June 29-July 1, for a Carpentries gathering in sunny Davis, California. Things you can expect to find include:

What to expect

  • Lots of social time with a small, friendly Carpentries community!
  • Keynote address from Anelda van der Walt on Carpentries communities in Africa
  • Other keynotes (TBD!)
  • Discussions about our new Spanish curriculum
  • An introduction to Binder as an instructional tool and a hackyfest to binderize repositories
  • On-boarding and mentorship opportunities to help new and experienced instructors connect and become familiar with Carpentries curriculum
  • Check-out opportunities for new instructors! Attendance will be counted as your Discussion session requirement, and we will also offer Demo opportunities for anyone who needs it!
  • Un-conference style activities proposed by attendees

It’s also worth noting that we still have room at our Carpentries Instructor Training (with Anelda and Sher!) on June 25-26, and will be running a variety of Carpentries workshops on June 27-28. See DIBSI 2018 for more details!

Contibute your ideas!

Want to organize a meet-up or activity? We’re happy to facilitate! File an issue in our planning repo: https://github.com/dib-lab/CarpentryConWest18! Or, contact us at dibsi.training@gmail.com. We can help to arrange space and connect you with collaborators to start the planning process.

How to sign up!

Registration is $50. Housing is available from 6/29-7/2 for $225, which includes breakfast and dinner (but not lunch).

Please register by May 15th to guarantee your place at DIBSI West Coast Carpentry Con. If you’re coming from afar, you’ll need to register soon to obtain on-campus housing, which includes breakfast and dinner, as these spaces are limited.

Local registration (no housing needed) is here: https://registration.genomecenter.ucdavis.edu/events/WCCC_DIBSI_2018/

Out-of-town registration (includes housing)* is here; https://registration.genomecenter.ucdavis.edu/events/WCCC_with_Housing_DIBSI_2018/

* If you’ve already registered for another DIBSI housing block – Week 1 or the ANGUS 2-week workshop – please contact dibsi.training@gmail.com to request a registration link that accounts for overlap between the housing reservation blocks.

Additional needs

If you have any additional needs of any kind, please do not hesitate to ask! We will be adding information about local activities for children, nursing rooms, and ways we support people of all abilities. We welcome inquiries!

Code of Conduct

All contributions are expected to follow the Carpentries’ code of conduct.

softwarecarpentry  datacarpentry  postdoclife  DIBlab 
</body> </html> <!DOCTYPE HTML> Increasing transparency in postdoc hiring and on-boarding
02 May 2018

Increasing transparency in postdoc hiring and on-boarding

A brief summary of the interview process for my postdoc with Titus Brown. Highlights include: collaborative documents for interview questions, salary negotiations, and science communication

This week I started a post-doc working in Titus Brown’s Data Intensive Biology lab. If there is such a thing as a dream job, this is it. I’ve interacted with Titus and his lab members many times through BEACON, the Marine Biological Laboratory, Software Carpentry, and Data Carpentry.

One of the things I appreciate so much about Titus’s style is his transparency. Here are a few of my thoughts about why interview process and the on-boarding have gone so well.

The quick turn around

Titus posted the job announcement on the Software Carpentry discuss list and on hackmd on March 15. During April, I had an interview, received an offer, accepted the offer, and set a May 1 start date. I wish all things in academia could move so fast.

The interview questions

The really cool part about the interview process what Titus posted the interview questions ahead of time here, and I submitted my responses here. This meant I could be more relaxed during the interview because the questions weren’t out of the blue. Titus and his lab mates were able to ask me to delve into the details a little more or say, “cool, let’s move on to the next topic”.

Even before Titus informed me that I would be given the interview questions ahead of time, I knew this was coming because, well, he wrote a blog post with the interview questions used for a postdoc position building pipelines. I hope to see more of this transparency and sharing of interview questions in the future.

The salary

The salary was posted with the job announcement, so I was never in doubt about what my salary would be. Additionally, in May 2016, Titus posted a blog about increasing postdoc pay. In this post, he makes it clear that he pays all his postdocs the same and that he doesn’t negotiate salary. So, when he made me an offer, I didn’t have to waste my energy negotiating salary, which freed up time to talk about other things that were valuable to me.

Code of Conduct

I’ve always liked that Titus has a Code of Conduct on his lab’s website. Back in January of 2017, I was recruiting some undergrads, and I wondered if I should put a Code of Conduct on my personal website (many PIs that are affiliated with The Carpentries have one on their website, but my grad advisor did not). So, I reached out to Titus and asked him what he thought. He gave me some really good advice about how the purpose of the CoC was to convey that “these are my expectations for our behavior, and these are the paths to resolution”.

What I’ve come to realize over the past year is that even though I and many of my colleagues point to CoCs at conferences and workshops, very few of us feel equipped to responding to Code of Conduct incidents. So, I’m excited that this Friday I’ll be participating in a workshop on Training for Code of Conduct Incident Response with some Carpentry Colleagues. I think this is an important step toward increasing diversity in our community.

Communication

Right now, were use Slack and GitHub for most of our communication. This means that progress on all projects is visible to the rest of the lab, and most of it is under version control. I really like both of these technologies because they work synchronously or asynchronously and collaboratively on projects and easily keep track of what’s working well or not.

Summary

In the last two years, I applied for 13 different postdocs positions or jobs and had 10 interviews, but this is one is my dream job. I super excited about being in an environment with our goal is increase transparency in both our scientific methodology but also with respect to the social aspects of science. Stay tuned for more updates about our progress!

datacommons  postdoclife  DIBlab 
</body> </html> </a> <a href="/tags/DIBlab<!DOCTYPE HTML> CarpentryCon West 2018
06 May 2018

CarpentryCon West 2018

A community gathering of Data, Software, and Library Carpenters in sunny Davis, CA. For details visit: http://ivory.idyll.org/dibsi/CarpentryConWest.html

Note: If you are looking for the international CarpentryCon event taking place in Dublin on 30 May - 1 June, 2018, please visit http://www.carpentrycon.org/.

We’re inviting Carpentries folks of all stripes — from new fans to veteran community-members, from all disciplines, near and far — to join us for CarpentryCon West! We’ve got housing and space for DIBSI 2018, our annual bioinformatics summer institute, so we’ve set aside Friday evening through Sunday morning, June 29-July 1, for a Carpentries gathering in sunny Davis, California. Things you can expect to find include:

What to expect

  • Lots of social time with a small, friendly Carpentries community!
  • Keynote address from Anelda van der Walt on Carpentries communities in Africa
  • Other keynotes (TBD!)
  • Discussions about our new Spanish curriculum
  • An introduction to Binder as an instructional tool and a hackyfest to binderize repositories
  • On-boarding and mentorship opportunities to help new and experienced instructors connect and become familiar with Carpentries curriculum
  • Check-out opportunities for new instructors! Attendance will be counted as your Discussion session requirement, and we will also offer Demo opportunities for anyone who needs it!
  • Un-conference style activities proposed by attendees

It’s also worth noting that we still have room at our Carpentries Instructor Training (with Anelda and Sher!) on June 25-26, and will be running a variety of Carpentries workshops on June 27-28. See DIBSI 2018 for more details!

Contibute your ideas!

Want to organize a meet-up or activity? We’re happy to facilitate! File an issue in our planning repo: https://github.com/dib-lab/CarpentryConWest18! Or, contact us at dibsi.training@gmail.com. We can help to arrange space and connect you with collaborators to start the planning process.

How to sign up!

Registration is $50. Housing is available from 6/29-7/2 for $225, which includes breakfast and dinner (but not lunch).

Please register by May 15th to guarantee your place at DIBSI West Coast Carpentry Con. If you’re coming from afar, you’ll need to register soon to obtain on-campus housing, which includes breakfast and dinner, as these spaces are limited.

Local registration (no housing needed) is here: https://registration.genomecenter.ucdavis.edu/events/WCCC_DIBSI_2018/

Out-of-town registration (includes housing)* is here; https://registration.genomecenter.ucdavis.edu/events/WCCC_with_Housing_DIBSI_2018/

* If you’ve already registered for another DIBSI housing block – Week 1 or the ANGUS 2-week workshop – please contact dibsi.training@gmail.com to request a registration link that accounts for overlap between the housing reservation blocks.

Additional needs

If you have any additional needs of any kind, please do not hesitate to ask! We will be adding information about local activities for children, nursing rooms, and ways we support people of all abilities. We welcome inquiries!

Code of Conduct

All contributions are expected to follow the Carpentries’ code of conduct.

softwarecarpentry  datacarpentry  postdoclife  DIBlab 
</body> </html> <!DOCTYPE HTML> Increasing transparency in postdoc hiring and on-boarding
02 May 2018

Increasing transparency in postdoc hiring and on-boarding

A brief summary of the interview process for my postdoc with Titus Brown. Highlights include: collaborative documents for interview questions, salary negotiations, and science communication

This week I started a post-doc working in Titus Brown’s Data Intensive Biology lab. If there is such a thing as a dream job, this is it. I’ve interacted with Titus and his lab members many times through BEACON, the Marine Biological Laboratory, Software Carpentry, and Data Carpentry.

One of the things I appreciate so much about Titus’s style is his transparency. Here are a few of my thoughts about why interview process and the on-boarding have gone so well.

The quick turn around

Titus posted the job announcement on the Software Carpentry discuss list and on hackmd on March 15. During April, I had an interview, received an offer, accepted the offer, and set a May 1 start date. I wish all things in academia could move so fast.

The interview questions

The really cool part about the interview process what Titus posted the interview questions ahead of time here, and I submitted my responses here. This meant I could be more relaxed during the interview because the questions weren’t out of the blue. Titus and his lab mates were able to ask me to delve into the details a little more or say, “cool, let’s move on to the next topic”.

Even before Titus informed me that I would be given the interview questions ahead of time, I knew this was coming because, well, he wrote a blog post with the interview questions used for a postdoc position building pipelines. I hope to see more of this transparency and sharing of interview questions in the future.

The salary

The salary was posted with the job announcement, so I was never in doubt about what my salary would be. Additionally, in May 2016, Titus posted a blog about increasing postdoc pay. In this post, he makes it clear that he pays all his postdocs the same and that he doesn’t negotiate salary. So, when he made me an offer, I didn’t have to waste my energy negotiating salary, which freed up time to talk about other things that were valuable to me.

Code of Conduct

I’ve always liked that Titus has a Code of Conduct on his lab’s website. Back in January of 2017, I was recruiting some undergrads, and I wondered if I should put a Code of Conduct on my personal website (many PIs that are affiliated with The Carpentries have one on their website, but my grad advisor did not). So, I reached out to Titus and asked him what he thought. He gave me some really good advice about how the purpose of the CoC was to convey that “these are my expectations for our behavior, and these are the paths to resolution”.

What I’ve come to realize over the past year is that even though I and many of my colleagues point to CoCs at conferences and workshops, very few of us feel equipped to responding to Code of Conduct incidents. So, I’m excited that this Friday I’ll be participating in a workshop on Training for Code of Conduct Incident Response with some Carpentry Colleagues. I think this is an important step toward increasing diversity in our community.

Communication

Right now, were use Slack and GitHub for most of our communication. This means that progress on all projects is visible to the rest of the lab, and most of it is under version control. I really like both of these technologies because they work synchronously or asynchronously and collaboratively on projects and easily keep track of what’s working well or not.

Summary

In the last two years, I applied for 13 different postdocs positions or jobs and had 10 interviews, but this is one is my dream job. I super excited about being in an environment with our goal is increase transparency in both our scientific methodology but also with respect to the social aspects of science. Stay tuned for more updates about our progress!

datacommons  postdoclife  DIBlab 
</body> </html> " class="button special small">DIBlab<!DOCTYPE HTML> CarpentryCon West 2018
06 May 2018

CarpentryCon West 2018

A community gathering of Data, Software, and Library Carpenters in sunny Davis, CA. For details visit: http://ivory.idyll.org/dibsi/CarpentryConWest.html

Note: If you are looking for the international CarpentryCon event taking place in Dublin on 30 May - 1 June, 2018, please visit http://www.carpentrycon.org/.

We’re inviting Carpentries folks of all stripes — from new fans to veteran community-members, from all disciplines, near and far — to join us for CarpentryCon West! We’ve got housing and space for DIBSI 2018, our annual bioinformatics summer institute, so we’ve set aside Friday evening through Sunday morning, June 29-July 1, for a Carpentries gathering in sunny Davis, California. Things you can expect to find include:

What to expect

  • Lots of social time with a small, friendly Carpentries community!
  • Keynote address from Anelda van der Walt on Carpentries communities in Africa
  • Other keynotes (TBD!)
  • Discussions about our new Spanish curriculum
  • An introduction to Binder as an instructional tool and a hackyfest to binderize repositories
  • On-boarding and mentorship opportunities to help new and experienced instructors connect and become familiar with Carpentries curriculum
  • Check-out opportunities for new instructors! Attendance will be counted as your Discussion session requirement, and we will also offer Demo opportunities for anyone who needs it!
  • Un-conference style activities proposed by attendees

It’s also worth noting that we still have room at our Carpentries Instructor Training (with Anelda and Sher!) on June 25-26, and will be running a variety of Carpentries workshops on June 27-28. See DIBSI 2018 for more details!

Contibute your ideas!

Want to organize a meet-up or activity? We’re happy to facilitate! File an issue in our planning repo: https://github.com/dib-lab/CarpentryConWest18! Or, contact us at dibsi.training@gmail.com. We can help to arrange space and connect you with collaborators to start the planning process.

How to sign up!

Registration is $50. Housing is available from 6/29-7/2 for $225, which includes breakfast and dinner (but not lunch).

Please register by May 15th to guarantee your place at DIBSI West Coast Carpentry Con. If you’re coming from afar, you’ll need to register soon to obtain on-campus housing, which includes breakfast and dinner, as these spaces are limited.

Local registration (no housing needed) is here: https://registration.genomecenter.ucdavis.edu/events/WCCC_DIBSI_2018/

Out-of-town registration (includes housing)* is here; https://registration.genomecenter.ucdavis.edu/events/WCCC_with_Housing_DIBSI_2018/

* If you’ve already registered for another DIBSI housing block – Week 1 or the ANGUS 2-week workshop – please contact dibsi.training@gmail.com to request a registration link that accounts for overlap between the housing reservation blocks.

Additional needs

If you have any additional needs of any kind, please do not hesitate to ask! We will be adding information about local activities for children, nursing rooms, and ways we support people of all abilities. We welcome inquiries!

Code of Conduct

All contributions are expected to follow the Carpentries’ code of conduct.

softwarecarpentry  datacarpentry  postdoclife  DIBlab 
</body> </html> <!DOCTYPE HTML> Increasing transparency in postdoc hiring and on-boarding
02 May 2018

Increasing transparency in postdoc hiring and on-boarding

A brief summary of the interview process for my postdoc with Titus Brown. Highlights include: collaborative documents for interview questions, salary negotiations, and science communication

This week I started a post-doc working in Titus Brown’s Data Intensive Biology lab. If there is such a thing as a dream job, this is it. I’ve interacted with Titus and his lab members many times through BEACON, the Marine Biological Laboratory, Software Carpentry, and Data Carpentry.

One of the things I appreciate so much about Titus’s style is his transparency. Here are a few of my thoughts about why interview process and the on-boarding have gone so well.

The quick turn around

Titus posted the job announcement on the Software Carpentry discuss list and on hackmd on March 15. During April, I had an interview, received an offer, accepted the offer, and set a May 1 start date. I wish all things in academia could move so fast.

The interview questions

The really cool part about the interview process what Titus posted the interview questions ahead of time here, and I submitted my responses here. This meant I could be more relaxed during the interview because the questions weren’t out of the blue. Titus and his lab mates were able to ask me to delve into the details a little more or say, “cool, let’s move on to the next topic”.

Even before Titus informed me that I would be given the interview questions ahead of time, I knew this was coming because, well, he wrote a blog post with the interview questions used for a postdoc position building pipelines. I hope to see more of this transparency and sharing of interview questions in the future.

The salary

The salary was posted with the job announcement, so I was never in doubt about what my salary would be. Additionally, in May 2016, Titus posted a blog about increasing postdoc pay. In this post, he makes it clear that he pays all his postdocs the same and that he doesn’t negotiate salary. So, when he made me an offer, I didn’t have to waste my energy negotiating salary, which freed up time to talk about other things that were valuable to me.

Code of Conduct

I’ve always liked that Titus has a Code of Conduct on his lab’s website. Back in January of 2017, I was recruiting some undergrads, and I wondered if I should put a Code of Conduct on my personal website (many PIs that are affiliated with The Carpentries have one on their website, but my grad advisor did not). So, I reached out to Titus and asked him what he thought. He gave me some really good advice about how the purpose of the CoC was to convey that “these are my expectations for our behavior, and these are the paths to resolution”.

What I’ve come to realize over the past year is that even though I and many of my colleagues point to CoCs at conferences and workshops, very few of us feel equipped to responding to Code of Conduct incidents. So, I’m excited that this Friday I’ll be participating in a workshop on Training for Code of Conduct Incident Response with some Carpentry Colleagues. I think this is an important step toward increasing diversity in our community.

Communication

Right now, were use Slack and GitHub for most of our communication. This means that progress on all projects is visible to the rest of the lab, and most of it is under version control. I really like both of these technologies because they work synchronously or asynchronously and collaboratively on projects and easily keep track of what’s working well or not.

Summary

In the last two years, I applied for 13 different postdocs positions or jobs and had 10 interviews, but this is one is my dream job. I super excited about being in an environment with our goal is increase transparency in both our scientific methodology but also with respect to the social aspects of science. Stay tuned for more updates about our progress!

datacommons  postdoclife  DIBlab 
</body> </html> </a> <a href="/tags/softwarecarpentry<!DOCTYPE HTML> Three years in the making for Instructor training in Latin America
24 Aug 2018

Three years in the making for Instructor training in Latin America

Building global communities of Spanish-speaking Carpentry instructors and lesson developers

This month I (Rayna Harris) co-taught a remote The Carpentries Instructor Training Workshop for 25 Spanish-speaking trainees in six countries in Latin America. It was awesome! One thing that made this workshop so special for me is that it has been three-plus years in the making. So, I thought I would tell the story, from my perspective, about all the things that came into play to make this workshop a reality.

The early days of The Carpentries workshops in Spanish

In 2016, Greg Wilson introduced me to Selene Fernandez-Valverde to discuss a Software Carpentry meets Spanish-speaking bioinformatics endeavour. Back then my Spanish was eight years out of practice and I was still learning to program. I didn’t think I had the expertise to teach programming in Spanish. Sue McClatchy had more expertise and practice, but it is still difficult for a native English speaker to live-translate a lesson from English to Spanish while live coding in front of a classroom.

This observation led to two simultaneous efforts: support a community-wide effort for collaborative lesson translation and provide instructor training for Spanish speaking instructors. That is exactly what many staff and volunteers have done over the past three years.

Spanish translations hacakathon and lesson maintenance

In November 2017, I went to Germany to attend OpenCon and worked on translating Software Carpentry lessons into Spanish with Paula Andrea Martinez. Our hackathon session has been immortalized in the promotional materials for OpenCon2018.

In December 2017, I finished my PhD, and I decided to go visit all the awesome open-science advocates that I met at OpenCon in Buenos Aires. I met Juli Aranco from Buenos Aires and we organized a lesson translation hackathon where we made huge progress on the Git and R lessons. We also ran a one-day Software Carpentry Workshop using those translated lessons. It was a huge success. The translated UNIX lesson was flawless. The translated Git lesson ran long but was good. Everyone brought snacks to share. All attendees and four of the five instructors were female. It was a great day.

The release of three stable Spanish translations meant that we needed lesson maintainers. So, while living in Buenos Aires, I also co-taught Carpentry Maintainer training in Spanish! I couldn’t have done this without Erin Becker, Ivan Gonzalez, and François Michonneau. Living in Argentina gave them the confidence to speak in Spanish about programming. I also immersed myself in the maintainer role, and my Git and GitHub skill levels skyrocketed. I can pretty much do all things Git now.

Instructor Training workshops for Puerto Rico and Argentina

Back in March 2017, Sue and I travelled to Puerto Rico to run instructor training in English that coincided with a Data Carpentry Replicathon (hackathon for replicating scientific results) taught by Tracy Teal, Phillip Brooks and a few others. We conducted the course in English, but we chatted in Spanish over coffee breaks and at parties. It was very cool. We hosted a few virtual bilingual demos and discussions after the workshop and that was fun but we lost momentum.

The real momentum for me for instructor training came from being introduced to the R Ladies Buenos Aires community in February 2018. Paola Prieto (one my co-instructors for the pilot The Carpentries workshop in Spanish) invited me to give a talk at their group meeting, so I decided to talk The Carpentries and reproducible research with R in Spanish! Everyone was really enthusiastic, so I started working to incorporate them into the instructor training program.

In June 2018, Sue taught a workshop at Jackson lab with about 20 people, but I Zoomed in with two RLadies from Argentina, Laura Acion and Maria Florencia. They did their practice teaching using R Gapminder Spanish lesson. I’m proud to say that Laura and Maria have already completed their instructor training, and the three of us are continuing to work together via RLadies Buenos Aires and the LatinR conference!

The first bilingual Instructor Training workshop for Latin America

Finally, in August 2018 we make it to the thing that people have been waiting for, a fully distributed online instructor training with participants in Argentina, Colombia, Costa Rica, Educador, Mexico and Peru. This was really a global event with four co-trainers and helpers (me, Sue McClatchy, Greg Wilson, Alejandra Gonzalez-Beltran, Paula Andrea Martinez). We were located in Canada, the USA, the UK, and Belgium. Everyone but Greg spoke Spanish to some degree. The students were encouraged to ask questions or make comments in either English or Spanish, so the Etherpad supported a really bilingual mix of stories and notes.

On Day One, Sue and I taught the lessons completely in English. While all the attendees acknowledged that the workshop would be taught in English, I knew some didn’t understand as well as the others. So, while Sue talked, I live translated what she was saying into Spanish in the Etherpad. Paula and some of the attendees were kind enough to help out to improve the notes. For me, the best part of day one was the episode on mindset and grit. I asked the attendees to share a recent time when they persevered despite wanting to quit. Two people said that they almost didn’t show up to this workshop but that they were thankful they did. I responded by saying that I had also considered not teaching this workshop but I’m glad I did. I started crying because I was so grateful for the community support that helped everyone persevere.

On Day Two after lunch, Alejandra taught an episode on introductions speaking only in Spanish! (You can view the original episode in English or the translation.) Since I could read and listen to this episode in Spanish, note taking in Spanish was a lot easier. This really solidified in my mind how hard it is to translate and learn at the same time and why it is so important to have a library of lessons in Spanish. I decided to continue speaking in Spanish when I taught the last two episodes regarding The Carpentries teaching practices and operations. While I didn’t have a translated lesson to use, I have already one slideshow and given one talk about The Carpentries in Spanish, so I felt comfortable speaking about The Carpentries in Spanish.

During the final 20 minutes of the workshop, we had a roundtable discussion about what everyone was excited about moving forward. After two days of reading people’s thoughts in the Etherpad, it was great to have a face-to-face discussion and hear everyone’s voices. While everyone said something slightly different, the main theme is everyone wants to improve their local training programs by organizing and teaching Software Carpentry and Data Carpentry workshops.

Outlook

I think we’ve come a long way growing communities of people who are passionate about improving research and teaching all over the world. You can read more about the translation and lesson release in the Carpentries blog in English and Spanish. As with the lesson translations, everyone is enthusiastic about organizing more workshops and expanding the curricula. These will be a long-term community project. To get involved, check out our GitHub repository for Spanish translations or join the Carpentries Latin America mailing list.

I’ve also come along way since this started. In three years, my fluency in verbal and computing languages has grown. In 2015 I didn’t think I was talented enough to teach programming in Spanish, but by early 2018 I had gained the experience and expertise necessary. It required some perseverance, but I didn’t do it alone; many colleagues around the globe contributed support to help turn some of these ideas into a reality. I think it is a beautiful example of how having a growth mindset, grit, and community support is really important when we think about expanding the Carpentries into new communities.

Thanks

I want to thank Paula Andrea Martinez, Maria Florencia and Raniere Silva for comments on earlier versions of this post. Thanks to everyone who helped make all these events happen!

softwarecarpentry  datacarpentry  instructortraining 
</body> </html> <!DOCTYPE HTML> CarpentryCon West 2018
06 May 2018

CarpentryCon West 2018

A community gathering of Data, Software, and Library Carpenters in sunny Davis, CA. For details visit: http://ivory.idyll.org/dibsi/CarpentryConWest.html

Note: If you are looking for the international CarpentryCon event taking place in Dublin on 30 May - 1 June, 2018, please visit http://www.carpentrycon.org/.

We’re inviting Carpentries folks of all stripes — from new fans to veteran community-members, from all disciplines, near and far — to join us for CarpentryCon West! We’ve got housing and space for DIBSI 2018, our annual bioinformatics summer institute, so we’ve set aside Friday evening through Sunday morning, June 29-July 1, for a Carpentries gathering in sunny Davis, California. Things you can expect to find include:

What to expect

  • Lots of social time with a small, friendly Carpentries community!
  • Keynote address from Anelda van der Walt on Carpentries communities in Africa
  • Other keynotes (TBD!)
  • Discussions about our new Spanish curriculum
  • An introduction to Binder as an instructional tool and a hackyfest to binderize repositories
  • On-boarding and mentorship opportunities to help new and experienced instructors connect and become familiar with Carpentries curriculum
  • Check-out opportunities for new instructors! Attendance will be counted as your Discussion session requirement, and we will also offer Demo opportunities for anyone who needs it!
  • Un-conference style activities proposed by attendees

It’s also worth noting that we still have room at our Carpentries Instructor Training (with Anelda and Sher!) on June 25-26, and will be running a variety of Carpentries workshops on June 27-28. See DIBSI 2018 for more details!

Contibute your ideas!

Want to organize a meet-up or activity? We’re happy to facilitate! File an issue in our planning repo: https://github.com/dib-lab/CarpentryConWest18! Or, contact us at dibsi.training@gmail.com. We can help to arrange space and connect you with collaborators to start the planning process.

How to sign up!

Registration is $50. Housing is available from 6/29-7/2 for $225, which includes breakfast and dinner (but not lunch).

Please register by May 15th to guarantee your place at DIBSI West Coast Carpentry Con. If you’re coming from afar, you’ll need to register soon to obtain on-campus housing, which includes breakfast and dinner, as these spaces are limited.

Local registration (no housing needed) is here: https://registration.genomecenter.ucdavis.edu/events/WCCC_DIBSI_2018/

Out-of-town registration (includes housing)* is here; https://registration.genomecenter.ucdavis.edu/events/WCCC_with_Housing_DIBSI_2018/

* If you’ve already registered for another DIBSI housing block – Week 1 or the ANGUS 2-week workshop – please contact dibsi.training@gmail.com to request a registration link that accounts for overlap between the housing reservation blocks.

Additional needs

If you have any additional needs of any kind, please do not hesitate to ask! We will be adding information about local activities for children, nursing rooms, and ways we support people of all abilities. We welcome inquiries!

Code of Conduct

All contributions are expected to follow the Carpentries’ code of conduct.

softwarecarpentry  datacarpentry  postdoclife  DIBlab 
</body> </html> " class="button special small">softwarecarpentry<!DOCTYPE HTML> Three years in the making for Instructor training in Latin America
24 Aug 2018

Three years in the making for Instructor training in Latin America

Building global communities of Spanish-speaking Carpentry instructors and lesson developers

This month I (Rayna Harris) co-taught a remote The Carpentries Instructor Training Workshop for 25 Spanish-speaking trainees in six countries in Latin America. It was awesome! One thing that made this workshop so special for me is that it has been three-plus years in the making. So, I thought I would tell the story, from my perspective, about all the things that came into play to make this workshop a reality.

The early days of The Carpentries workshops in Spanish

In 2016, Greg Wilson introduced me to Selene Fernandez-Valverde to discuss a Software Carpentry meets Spanish-speaking bioinformatics endeavour. Back then my Spanish was eight years out of practice and I was still learning to program. I didn’t think I had the expertise to teach programming in Spanish. Sue McClatchy had more expertise and practice, but it is still difficult for a native English speaker to live-translate a lesson from English to Spanish while live coding in front of a classroom.

This observation led to two simultaneous efforts: support a community-wide effort for collaborative lesson translation and provide instructor training for Spanish speaking instructors. That is exactly what many staff and volunteers have done over the past three years.

Spanish translations hacakathon and lesson maintenance

In November 2017, I went to Germany to attend OpenCon and worked on translating Software Carpentry lessons into Spanish with Paula Andrea Martinez. Our hackathon session has been immortalized in the promotional materials for OpenCon2018.

In December 2017, I finished my PhD, and I decided to go visit all the awesome open-science advocates that I met at OpenCon in Buenos Aires. I met Juli Aranco from Buenos Aires and we organized a lesson translation hackathon where we made huge progress on the Git and R lessons. We also ran a one-day Software Carpentry Workshop using those translated lessons. It was a huge success. The translated UNIX lesson was flawless. The translated Git lesson ran long but was good. Everyone brought snacks to share. All attendees and four of the five instructors were female. It was a great day.

The release of three stable Spanish translations meant that we needed lesson maintainers. So, while living in Buenos Aires, I also co-taught Carpentry Maintainer training in Spanish! I couldn’t have done this without Erin Becker, Ivan Gonzalez, and François Michonneau. Living in Argentina gave them the confidence to speak in Spanish about programming. I also immersed myself in the maintainer role, and my Git and GitHub skill levels skyrocketed. I can pretty much do all things Git now.

Instructor Training workshops for Puerto Rico and Argentina

Back in March 2017, Sue and I travelled to Puerto Rico to run instructor training in English that coincided with a Data Carpentry Replicathon (hackathon for replicating scientific results) taught by Tracy Teal, Phillip Brooks and a few others. We conducted the course in English, but we chatted in Spanish over coffee breaks and at parties. It was very cool. We hosted a few virtual bilingual demos and discussions after the workshop and that was fun but we lost momentum.

The real momentum for me for instructor training came from being introduced to the R Ladies Buenos Aires community in February 2018. Paola Prieto (one my co-instructors for the pilot The Carpentries workshop in Spanish) invited me to give a talk at their group meeting, so I decided to talk The Carpentries and reproducible research with R in Spanish! Everyone was really enthusiastic, so I started working to incorporate them into the instructor training program.

In June 2018, Sue taught a workshop at Jackson lab with about 20 people, but I Zoomed in with two RLadies from Argentina, Laura Acion and Maria Florencia. They did their practice teaching using R Gapminder Spanish lesson. I’m proud to say that Laura and Maria have already completed their instructor training, and the three of us are continuing to work together via RLadies Buenos Aires and the LatinR conference!

The first bilingual Instructor Training workshop for Latin America

Finally, in August 2018 we make it to the thing that people have been waiting for, a fully distributed online instructor training with participants in Argentina, Colombia, Costa Rica, Educador, Mexico and Peru. This was really a global event with four co-trainers and helpers (me, Sue McClatchy, Greg Wilson, Alejandra Gonzalez-Beltran, Paula Andrea Martinez). We were located in Canada, the USA, the UK, and Belgium. Everyone but Greg spoke Spanish to some degree. The students were encouraged to ask questions or make comments in either English or Spanish, so the Etherpad supported a really bilingual mix of stories and notes.

On Day One, Sue and I taught the lessons completely in English. While all the attendees acknowledged that the workshop would be taught in English, I knew some didn’t understand as well as the others. So, while Sue talked, I live translated what she was saying into Spanish in the Etherpad. Paula and some of the attendees were kind enough to help out to improve the notes. For me, the best part of day one was the episode on mindset and grit. I asked the attendees to share a recent time when they persevered despite wanting to quit. Two people said that they almost didn’t show up to this workshop but that they were thankful they did. I responded by saying that I had also considered not teaching this workshop but I’m glad I did. I started crying because I was so grateful for the community support that helped everyone persevere.

On Day Two after lunch, Alejandra taught an episode on introductions speaking only in Spanish! (You can view the original episode in English or the translation.) Since I could read and listen to this episode in Spanish, note taking in Spanish was a lot easier. This really solidified in my mind how hard it is to translate and learn at the same time and why it is so important to have a library of lessons in Spanish. I decided to continue speaking in Spanish when I taught the last two episodes regarding The Carpentries teaching practices and operations. While I didn’t have a translated lesson to use, I have already one slideshow and given one talk about The Carpentries in Spanish, so I felt comfortable speaking about The Carpentries in Spanish.

During the final 20 minutes of the workshop, we had a roundtable discussion about what everyone was excited about moving forward. After two days of reading people’s thoughts in the Etherpad, it was great to have a face-to-face discussion and hear everyone’s voices. While everyone said something slightly different, the main theme is everyone wants to improve their local training programs by organizing and teaching Software Carpentry and Data Carpentry workshops.

Outlook

I think we’ve come a long way growing communities of people who are passionate about improving research and teaching all over the world. You can read more about the translation and lesson release in the Carpentries blog in English and Spanish. As with the lesson translations, everyone is enthusiastic about organizing more workshops and expanding the curricula. These will be a long-term community project. To get involved, check out our GitHub repository for Spanish translations or join the Carpentries Latin America mailing list.

I’ve also come along way since this started. In three years, my fluency in verbal and computing languages has grown. In 2015 I didn’t think I was talented enough to teach programming in Spanish, but by early 2018 I had gained the experience and expertise necessary. It required some perseverance, but I didn’t do it alone; many colleagues around the globe contributed support to help turn some of these ideas into a reality. I think it is a beautiful example of how having a growth mindset, grit, and community support is really important when we think about expanding the Carpentries into new communities.

Thanks

I want to thank Paula Andrea Martinez, Maria Florencia and Raniere Silva for comments on earlier versions of this post. Thanks to everyone who helped make all these events happen!

softwarecarpentry  datacarpentry  instructortraining 
</body> </html> <!DOCTYPE HTML> CarpentryCon West 2018
06 May 2018

CarpentryCon West 2018

A community gathering of Data, Software, and Library Carpenters in sunny Davis, CA. For details visit: http://ivory.idyll.org/dibsi/CarpentryConWest.html

Note: If you are looking for the international CarpentryCon event taking place in Dublin on 30 May - 1 June, 2018, please visit http://www.carpentrycon.org/.

We’re inviting Carpentries folks of all stripes — from new fans to veteran community-members, from all disciplines, near and far — to join us for CarpentryCon West! We’ve got housing and space for DIBSI 2018, our annual bioinformatics summer institute, so we’ve set aside Friday evening through Sunday morning, June 29-July 1, for a Carpentries gathering in sunny Davis, California. Things you can expect to find include:

What to expect

  • Lots of social time with a small, friendly Carpentries community!
  • Keynote address from Anelda van der Walt on Carpentries communities in Africa
  • Other keynotes (TBD!)
  • Discussions about our new Spanish curriculum
  • An introduction to Binder as an instructional tool and a hackyfest to binderize repositories
  • On-boarding and mentorship opportunities to help new and experienced instructors connect and become familiar with Carpentries curriculum
  • Check-out opportunities for new instructors! Attendance will be counted as your Discussion session requirement, and we will also offer Demo opportunities for anyone who needs it!
  • Un-conference style activities proposed by attendees

It’s also worth noting that we still have room at our Carpentries Instructor Training (with Anelda and Sher!) on June 25-26, and will be running a variety of Carpentries workshops on June 27-28. See DIBSI 2018 for more details!

Contibute your ideas!

Want to organize a meet-up or activity? We’re happy to facilitate! File an issue in our planning repo: https://github.com/dib-lab/CarpentryConWest18! Or, contact us at dibsi.training@gmail.com. We can help to arrange space and connect you with collaborators to start the planning process.

How to sign up!

Registration is $50. Housing is available from 6/29-7/2 for $225, which includes breakfast and dinner (but not lunch).

Please register by May 15th to guarantee your place at DIBSI West Coast Carpentry Con. If you’re coming from afar, you’ll need to register soon to obtain on-campus housing, which includes breakfast and dinner, as these spaces are limited.

Local registration (no housing needed) is here: https://registration.genomecenter.ucdavis.edu/events/WCCC_DIBSI_2018/

Out-of-town registration (includes housing)* is here; https://registration.genomecenter.ucdavis.edu/events/WCCC_with_Housing_DIBSI_2018/

* If you’ve already registered for another DIBSI housing block – Week 1 or the ANGUS 2-week workshop – please contact dibsi.training@gmail.com to request a registration link that accounts for overlap between the housing reservation blocks.

Additional needs

If you have any additional needs of any kind, please do not hesitate to ask! We will be adding information about local activities for children, nursing rooms, and ways we support people of all abilities. We welcome inquiries!

Code of Conduct

All contributions are expected to follow the Carpentries’ code of conduct.

softwarecarpentry  datacarpentry  postdoclife  DIBlab 
</body> </html> </a> <a href="/tags/family<!DOCTYPE HTML> How my father shaped my career before and after his death
12 Jun 2018

How my father shaped my career before and after his death

A Father's Day reflection

Father’s Day is this Sunday. For me, this holiday usually comes and goes without much thought. I don’t have kids. My mother isn’t married to some man I have to call a step-father. My father died at the age of 57 on October 6, 2007, two days before my 25 birthday. That means its been 9 years since I last called or visited my dad to wish Happy Father’s Day. I don’t usually get too sentimental around this holiday, but this week I stumbled upon some Mike Eisen tweets about his father’s death, and I’ve been working to organize meetings that are very friendly to scientists with children, and now I can’t stop thinking about how my father’s life and death have impacted my career.

This is not a biography of my father, nor is it a complete summary of how his life has impacted me, but it does touch upon how his profession and personal life affected some decisions I made regarding my education and research topics.

Rudy Martin Harris (RMH, same initials as me) started working at LeTourneau, Inc as a mechanical engineer immediately after graduating from college, and he worked right up until a few weeks before he died from a 5 month battle with skin cancer. LeTourneau manufactured “earthmoving equipment” like offshore drilling rigs and the biggest bulldozers you’ve ever seen, but my dad worked with computers to automate the manufacturing process. I think at one point there were 5 computers in our “patio room” (a patio that he converted into a 2nd living room pretty much all by himself). My father was a self-proclaimed workaholic; he’d spend all day at the office and then get back to work tinkering with computers til late at night. Eventually, he moved up the ladder to Vice President of Manufacturing, so he spent less time hacking away at computers and more time flying around to visit other manufacturing plants. I never wanted to explicitly follow in my father’s footsteps, but I do remember thinking that it would be really cool to work my way from an entry-level position all the way to the top to the President’s office.

The few times I visited my father at work, the only females I encountered were secretaries. I don’t know if anyone every explicitly said it, but I assumed engineering was a man’s job and that females weren’t allowed. I remember being shocked during my first semester of college to meet female students that that were enrolled in the aerospace and petroleum engineering programs. I was like, “how did you know that was a thing?” Sometimes I wonder where I would be now if my dad had gotten me a summer internship at his company or encouraged me to study engineering. Even though he didn’t groom to follow in his footsteps, I think I inherited his intellectual acumen, his desire for everything to be well organized and efficient, and his half introvert/half extrovert personality. I think I would have made a good engineer, but I’m finding awesome ways to apply those traits to scientific and social problems, so no hard feelings.

There was a time, however, that I did harbour very negative feelings toward my father. Over Christmas break when I was 14, my mom and dad got in the only fight I’m aware of them ever having, and he moved out. I was crushed. I didn’t understand how my father could leave me to go live with some other woman who was raising her grandchildren because her own kids were too incompetent to be good parents. At that age, I didn’t really understand what an affair was, but I hated the fact that he was spending his time and money on someone’s else kids rather than spending them on me. At first, I lashed out by not speaking to my father for a whole year. He would come to my volleyball games and take we water skiing on the weekend, but I literally would not utter a single word to him. I must have been insufferable. I eventually started talking to my dad again, but it wasn’t until my junior year in college that I would say we had a decent relationship. I graduate in 4.5 years and then spent a semester TAing. The day I was moving out of my apartment to go live abroad for a year, my dad called to say he had really aggressive skin cancer and that had spread throughout all nearly all his major organs. I went to see him once a month for the next 5 month, and he looked as if he aged 10 years between every visit.

A lot of doctors (PhDs and MDs) get involved with cancer research after a loved one dies of cancer. Not me. I had no desire to be an MD, and I was set on being a scientist. While living in Costa Rica, I learned how to collect marine samples by SCUBA diving and got pretty good a culturing marine microbes and extracting their DNA. I was looking for a research tech job when I found a position in a lab that was using DNA microarrays to study parental behavior and mating behavior. I was like, “This is a thing?!” I was definitely intrigued by the possibility of understanding what makes some individual good dads and faithful partners whereas others not so much, so I joined the lab. I learned a lot about how different levels of molecules like dopamine, oxytocin, prolactin, and testosterone in the brain can influence how decision making and social behaviors. It was all pretty fascinating and enlightening for a while, but I eventually got bored reading about the same genes, brain regions, evolutionary theories, nasals sprays that influence social behavior. More importantly, I felt like I learned enough about the biological forces that may have shaped my father’s personal life that I no longer need to devote my professional life to understanding the future, not the past.

If you are looking for other science-themed Father’s Day related reads, Titus Brown, Mike Eisen, and Jonathan Eisen have all blogged about the life and death of their father and how it impacted their careers. Titus’s father was a well-known physicist who died in 2013 after failing to recover from an illness. Gerry Brown mentored over 100 graduate students! Who knows if Titus will officially mentor that many (he’s only at 10), but he has unofficially mentored hundreds through his Data Intensive Biology Summer Institute. Mike and Jonathan’s father, a respected scientist at NIH, took his own life in 1987. Mike writes about how he will never stop trying to figure responded the stress of work with suicide, and I can’t help but wonder if this doesn’t explain why he is often very critical of the NIH. To honor their father, Jonathan went on a mission to make all their father’s paper publicly available. On a lighter note, Jeremy Fox compared his own work ethic to that of his father and paternal grandfather who owned a local grocery store in a small town.

family  academia  science 
</body> </html> " class="button special small">family<!DOCTYPE HTML> How my father shaped my career before and after his death
12 Jun 2018

How my father shaped my career before and after his death

A Father's Day reflection

Father’s Day is this Sunday. For me, this holiday usually comes and goes without much thought. I don’t have kids. My mother isn’t married to some man I have to call a step-father. My father died at the age of 57 on October 6, 2007, two days before my 25 birthday. That means its been 9 years since I last called or visited my dad to wish Happy Father’s Day. I don’t usually get too sentimental around this holiday, but this week I stumbled upon some Mike Eisen tweets about his father’s death, and I’ve been working to organize meetings that are very friendly to scientists with children, and now I can’t stop thinking about how my father’s life and death have impacted my career.

This is not a biography of my father, nor is it a complete summary of how his life has impacted me, but it does touch upon how his profession and personal life affected some decisions I made regarding my education and research topics.

Rudy Martin Harris (RMH, same initials as me) started working at LeTourneau, Inc as a mechanical engineer immediately after graduating from college, and he worked right up until a few weeks before he died from a 5 month battle with skin cancer. LeTourneau manufactured “earthmoving equipment” like offshore drilling rigs and the biggest bulldozers you’ve ever seen, but my dad worked with computers to automate the manufacturing process. I think at one point there were 5 computers in our “patio room” (a patio that he converted into a 2nd living room pretty much all by himself). My father was a self-proclaimed workaholic; he’d spend all day at the office and then get back to work tinkering with computers til late at night. Eventually, he moved up the ladder to Vice President of Manufacturing, so he spent less time hacking away at computers and more time flying around to visit other manufacturing plants. I never wanted to explicitly follow in my father’s footsteps, but I do remember thinking that it would be really cool to work my way from an entry-level position all the way to the top to the President’s office.

The few times I visited my father at work, the only females I encountered were secretaries. I don’t know if anyone every explicitly said it, but I assumed engineering was a man’s job and that females weren’t allowed. I remember being shocked during my first semester of college to meet female students that that were enrolled in the aerospace and petroleum engineering programs. I was like, “how did you know that was a thing?” Sometimes I wonder where I would be now if my dad had gotten me a summer internship at his company or encouraged me to study engineering. Even though he didn’t groom to follow in his footsteps, I think I inherited his intellectual acumen, his desire for everything to be well organized and efficient, and his half introvert/half extrovert personality. I think I would have made a good engineer, but I’m finding awesome ways to apply those traits to scientific and social problems, so no hard feelings.

There was a time, however, that I did harbour very negative feelings toward my father. Over Christmas break when I was 14, my mom and dad got in the only fight I’m aware of them ever having, and he moved out. I was crushed. I didn’t understand how my father could leave me to go live with some other woman who was raising her grandchildren because her own kids were too incompetent to be good parents. At that age, I didn’t really understand what an affair was, but I hated the fact that he was spending his time and money on someone’s else kids rather than spending them on me. At first, I lashed out by not speaking to my father for a whole year. He would come to my volleyball games and take we water skiing on the weekend, but I literally would not utter a single word to him. I must have been insufferable. I eventually started talking to my dad again, but it wasn’t until my junior year in college that I would say we had a decent relationship. I graduate in 4.5 years and then spent a semester TAing. The day I was moving out of my apartment to go live abroad for a year, my dad called to say he had really aggressive skin cancer and that had spread throughout all nearly all his major organs. I went to see him once a month for the next 5 month, and he looked as if he aged 10 years between every visit.

A lot of doctors (PhDs and MDs) get involved with cancer research after a loved one dies of cancer. Not me. I had no desire to be an MD, and I was set on being a scientist. While living in Costa Rica, I learned how to collect marine samples by SCUBA diving and got pretty good a culturing marine microbes and extracting their DNA. I was looking for a research tech job when I found a position in a lab that was using DNA microarrays to study parental behavior and mating behavior. I was like, “This is a thing?!” I was definitely intrigued by the possibility of understanding what makes some individual good dads and faithful partners whereas others not so much, so I joined the lab. I learned a lot about how different levels of molecules like dopamine, oxytocin, prolactin, and testosterone in the brain can influence how decision making and social behaviors. It was all pretty fascinating and enlightening for a while, but I eventually got bored reading about the same genes, brain regions, evolutionary theories, nasals sprays that influence social behavior. More importantly, I felt like I learned enough about the biological forces that may have shaped my father’s personal life that I no longer need to devote my professional life to understanding the future, not the past.

If you are looking for other science-themed Father’s Day related reads, Titus Brown, Mike Eisen, and Jonathan Eisen have all blogged about the life and death of their father and how it impacted their careers. Titus’s father was a well-known physicist who died in 2013 after failing to recover from an illness. Gerry Brown mentored over 100 graduate students! Who knows if Titus will officially mentor that many (he’s only at 10), but he has unofficially mentored hundreds through his Data Intensive Biology Summer Institute. Mike and Jonathan’s father, a respected scientist at NIH, took his own life in 1987. Mike writes about how he will never stop trying to figure responded the stress of work with suicide, and I can’t help but wonder if this doesn’t explain why he is often very critical of the NIH. To honor their father, Jonathan went on a mission to make all their father’s paper publicly available. On a lighter note, Jeremy Fox compared his own work ethic to that of his father and paternal grandfather who owned a local grocery store in a small town.

family  academia  science 
</body> </html> </a> <a href="/tags/academia<!DOCTYPE HTML> How my father shaped my career before and after his death
12 Jun 2018

How my father shaped my career before and after his death

A Father's Day reflection

Father’s Day is this Sunday. For me, this holiday usually comes and goes without much thought. I don’t have kids. My mother isn’t married to some man I have to call a step-father. My father died at the age of 57 on October 6, 2007, two days before my 25 birthday. That means its been 9 years since I last called or visited my dad to wish Happy Father’s Day. I don’t usually get too sentimental around this holiday, but this week I stumbled upon some Mike Eisen tweets about his father’s death, and I’ve been working to organize meetings that are very friendly to scientists with children, and now I can’t stop thinking about how my father’s life and death have impacted my career.

This is not a biography of my father, nor is it a complete summary of how his life has impacted me, but it does touch upon how his profession and personal life affected some decisions I made regarding my education and research topics.

Rudy Martin Harris (RMH, same initials as me) started working at LeTourneau, Inc as a mechanical engineer immediately after graduating from college, and he worked right up until a few weeks before he died from a 5 month battle with skin cancer. LeTourneau manufactured “earthmoving equipment” like offshore drilling rigs and the biggest bulldozers you’ve ever seen, but my dad worked with computers to automate the manufacturing process. I think at one point there were 5 computers in our “patio room” (a patio that he converted into a 2nd living room pretty much all by himself). My father was a self-proclaimed workaholic; he’d spend all day at the office and then get back to work tinkering with computers til late at night. Eventually, he moved up the ladder to Vice President of Manufacturing, so he spent less time hacking away at computers and more time flying around to visit other manufacturing plants. I never wanted to explicitly follow in my father’s footsteps, but I do remember thinking that it would be really cool to work my way from an entry-level position all the way to the top to the President’s office.

The few times I visited my father at work, the only females I encountered were secretaries. I don’t know if anyone every explicitly said it, but I assumed engineering was a man’s job and that females weren’t allowed. I remember being shocked during my first semester of college to meet female students that that were enrolled in the aerospace and petroleum engineering programs. I was like, “how did you know that was a thing?” Sometimes I wonder where I would be now if my dad had gotten me a summer internship at his company or encouraged me to study engineering. Even though he didn’t groom to follow in his footsteps, I think I inherited his intellectual acumen, his desire for everything to be well organized and efficient, and his half introvert/half extrovert personality. I think I would have made a good engineer, but I’m finding awesome ways to apply those traits to scientific and social problems, so no hard feelings.

There was a time, however, that I did harbour very negative feelings toward my father. Over Christmas break when I was 14, my mom and dad got in the only fight I’m aware of them ever having, and he moved out. I was crushed. I didn’t understand how my father could leave me to go live with some other woman who was raising her grandchildren because her own kids were too incompetent to be good parents. At that age, I didn’t really understand what an affair was, but I hated the fact that he was spending his time and money on someone’s else kids rather than spending them on me. At first, I lashed out by not speaking to my father for a whole year. He would come to my volleyball games and take we water skiing on the weekend, but I literally would not utter a single word to him. I must have been insufferable. I eventually started talking to my dad again, but it wasn’t until my junior year in college that I would say we had a decent relationship. I graduate in 4.5 years and then spent a semester TAing. The day I was moving out of my apartment to go live abroad for a year, my dad called to say he had really aggressive skin cancer and that had spread throughout all nearly all his major organs. I went to see him once a month for the next 5 month, and he looked as if he aged 10 years between every visit.

A lot of doctors (PhDs and MDs) get involved with cancer research after a loved one dies of cancer. Not me. I had no desire to be an MD, and I was set on being a scientist. While living in Costa Rica, I learned how to collect marine samples by SCUBA diving and got pretty good a culturing marine microbes and extracting their DNA. I was looking for a research tech job when I found a position in a lab that was using DNA microarrays to study parental behavior and mating behavior. I was like, “This is a thing?!” I was definitely intrigued by the possibility of understanding what makes some individual good dads and faithful partners whereas others not so much, so I joined the lab. I learned a lot about how different levels of molecules like dopamine, oxytocin, prolactin, and testosterone in the brain can influence how decision making and social behaviors. It was all pretty fascinating and enlightening for a while, but I eventually got bored reading about the same genes, brain regions, evolutionary theories, nasals sprays that influence social behavior. More importantly, I felt like I learned enough about the biological forces that may have shaped my father’s personal life that I no longer need to devote my professional life to understanding the future, not the past.

If you are looking for other science-themed Father’s Day related reads, Titus Brown, Mike Eisen, and Jonathan Eisen have all blogged about the life and death of their father and how it impacted their careers. Titus’s father was a well-known physicist who died in 2013 after failing to recover from an illness. Gerry Brown mentored over 100 graduate students! Who knows if Titus will officially mentor that many (he’s only at 10), but he has unofficially mentored hundreds through his Data Intensive Biology Summer Institute. Mike and Jonathan’s father, a respected scientist at NIH, took his own life in 1987. Mike writes about how he will never stop trying to figure responded the stress of work with suicide, and I can’t help but wonder if this doesn’t explain why he is often very critical of the NIH. To honor their father, Jonathan went on a mission to make all their father’s paper publicly available. On a lighter note, Jeremy Fox compared his own work ethic to that of his father and paternal grandfather who owned a local grocery store in a small town.

family  academia  science 
</body> </html> " class="button special small">academia<!DOCTYPE HTML> How my father shaped my career before and after his death
12 Jun 2018

How my father shaped my career before and after his death

A Father's Day reflection

Father’s Day is this Sunday. For me, this holiday usually comes and goes without much thought. I don’t have kids. My mother isn’t married to some man I have to call a step-father. My father died at the age of 57 on October 6, 2007, two days before my 25 birthday. That means its been 9 years since I last called or visited my dad to wish Happy Father’s Day. I don’t usually get too sentimental around this holiday, but this week I stumbled upon some Mike Eisen tweets about his father’s death, and I’ve been working to organize meetings that are very friendly to scientists with children, and now I can’t stop thinking about how my father’s life and death have impacted my career.

This is not a biography of my father, nor is it a complete summary of how his life has impacted me, but it does touch upon how his profession and personal life affected some decisions I made regarding my education and research topics.

Rudy Martin Harris (RMH, same initials as me) started working at LeTourneau, Inc as a mechanical engineer immediately after graduating from college, and he worked right up until a few weeks before he died from a 5 month battle with skin cancer. LeTourneau manufactured “earthmoving equipment” like offshore drilling rigs and the biggest bulldozers you’ve ever seen, but my dad worked with computers to automate the manufacturing process. I think at one point there were 5 computers in our “patio room” (a patio that he converted into a 2nd living room pretty much all by himself). My father was a self-proclaimed workaholic; he’d spend all day at the office and then get back to work tinkering with computers til late at night. Eventually, he moved up the ladder to Vice President of Manufacturing, so he spent less time hacking away at computers and more time flying around to visit other manufacturing plants. I never wanted to explicitly follow in my father’s footsteps, but I do remember thinking that it would be really cool to work my way from an entry-level position all the way to the top to the President’s office.

The few times I visited my father at work, the only females I encountered were secretaries. I don’t know if anyone every explicitly said it, but I assumed engineering was a man’s job and that females weren’t allowed. I remember being shocked during my first semester of college to meet female students that that were enrolled in the aerospace and petroleum engineering programs. I was like, “how did you know that was a thing?” Sometimes I wonder where I would be now if my dad had gotten me a summer internship at his company or encouraged me to study engineering. Even though he didn’t groom to follow in his footsteps, I think I inherited his intellectual acumen, his desire for everything to be well organized and efficient, and his half introvert/half extrovert personality. I think I would have made a good engineer, but I’m finding awesome ways to apply those traits to scientific and social problems, so no hard feelings.

There was a time, however, that I did harbour very negative feelings toward my father. Over Christmas break when I was 14, my mom and dad got in the only fight I’m aware of them ever having, and he moved out. I was crushed. I didn’t understand how my father could leave me to go live with some other woman who was raising her grandchildren because her own kids were too incompetent to be good parents. At that age, I didn’t really understand what an affair was, but I hated the fact that he was spending his time and money on someone’s else kids rather than spending them on me. At first, I lashed out by not speaking to my father for a whole year. He would come to my volleyball games and take we water skiing on the weekend, but I literally would not utter a single word to him. I must have been insufferable. I eventually started talking to my dad again, but it wasn’t until my junior year in college that I would say we had a decent relationship. I graduate in 4.5 years and then spent a semester TAing. The day I was moving out of my apartment to go live abroad for a year, my dad called to say he had really aggressive skin cancer and that had spread throughout all nearly all his major organs. I went to see him once a month for the next 5 month, and he looked as if he aged 10 years between every visit.

A lot of doctors (PhDs and MDs) get involved with cancer research after a loved one dies of cancer. Not me. I had no desire to be an MD, and I was set on being a scientist. While living in Costa Rica, I learned how to collect marine samples by SCUBA diving and got pretty good a culturing marine microbes and extracting their DNA. I was looking for a research tech job when I found a position in a lab that was using DNA microarrays to study parental behavior and mating behavior. I was like, “This is a thing?!” I was definitely intrigued by the possibility of understanding what makes some individual good dads and faithful partners whereas others not so much, so I joined the lab. I learned a lot about how different levels of molecules like dopamine, oxytocin, prolactin, and testosterone in the brain can influence how decision making and social behaviors. It was all pretty fascinating and enlightening for a while, but I eventually got bored reading about the same genes, brain regions, evolutionary theories, nasals sprays that influence social behavior. More importantly, I felt like I learned enough about the biological forces that may have shaped my father’s personal life that I no longer need to devote my professional life to understanding the future, not the past.

If you are looking for other science-themed Father’s Day related reads, Titus Brown, Mike Eisen, and Jonathan Eisen have all blogged about the life and death of their father and how it impacted their careers. Titus’s father was a well-known physicist who died in 2013 after failing to recover from an illness. Gerry Brown mentored over 100 graduate students! Who knows if Titus will officially mentor that many (he’s only at 10), but he has unofficially mentored hundreds through his Data Intensive Biology Summer Institute. Mike and Jonathan’s father, a respected scientist at NIH, took his own life in 1987. Mike writes about how he will never stop trying to figure responded the stress of work with suicide, and I can’t help but wonder if this doesn’t explain why he is often very critical of the NIH. To honor their father, Jonathan went on a mission to make all their father’s paper publicly available. On a lighter note, Jeremy Fox compared his own work ethic to that of his father and paternal grandfather who owned a local grocery store in a small town.

family  academia  science 
</body> </html> </a> <a href="/tags/instructortraining<!DOCTYPE HTML> Three years in the making for Instructor training in Latin America
24 Aug 2018

Three years in the making for Instructor training in Latin America

Building global communities of Spanish-speaking Carpentry instructors and lesson developers

This month I (Rayna Harris) co-taught a remote The Carpentries Instructor Training Workshop for 25 Spanish-speaking trainees in six countries in Latin America. It was awesome! One thing that made this workshop so special for me is that it has been three-plus years in the making. So, I thought I would tell the story, from my perspective, about all the things that came into play to make this workshop a reality.

The early days of The Carpentries workshops in Spanish

In 2016, Greg Wilson introduced me to Selene Fernandez-Valverde to discuss a Software Carpentry meets Spanish-speaking bioinformatics endeavour. Back then my Spanish was eight years out of practice and I was still learning to program. I didn’t think I had the expertise to teach programming in Spanish. Sue McClatchy had more expertise and practice, but it is still difficult for a native English speaker to live-translate a lesson from English to Spanish while live coding in front of a classroom.

This observation led to two simultaneous efforts: support a community-wide effort for collaborative lesson translation and provide instructor training for Spanish speaking instructors. That is exactly what many staff and volunteers have done over the past three years.

Spanish translations hacakathon and lesson maintenance

In November 2017, I went to Germany to attend OpenCon and worked on translating Software Carpentry lessons into Spanish with Paula Andrea Martinez. Our hackathon session has been immortalized in the promotional materials for OpenCon2018.

In December 2017, I finished my PhD, and I decided to go visit all the awesome open-science advocates that I met at OpenCon in Buenos Aires. I met Juli Aranco from Buenos Aires and we organized a lesson translation hackathon where we made huge progress on the Git and R lessons. We also ran a one-day Software Carpentry Workshop using those translated lessons. It was a huge success. The translated UNIX lesson was flawless. The translated Git lesson ran long but was good. Everyone brought snacks to share. All attendees and four of the five instructors were female. It was a great day.

The release of three stable Spanish translations meant that we needed lesson maintainers. So, while living in Buenos Aires, I also co-taught Carpentry Maintainer training in Spanish! I couldn’t have done this without Erin Becker, Ivan Gonzalez, and François Michonneau. Living in Argentina gave them the confidence to speak in Spanish about programming. I also immersed myself in the maintainer role, and my Git and GitHub skill levels skyrocketed. I can pretty much do all things Git now.

Instructor Training workshops for Puerto Rico and Argentina

Back in March 2017, Sue and I travelled to Puerto Rico to run instructor training in English that coincided with a Data Carpentry Replicathon (hackathon for replicating scientific results) taught by Tracy Teal, Phillip Brooks and a few others. We conducted the course in English, but we chatted in Spanish over coffee breaks and at parties. It was very cool. We hosted a few virtual bilingual demos and discussions after the workshop and that was fun but we lost momentum.

The real momentum for me for instructor training came from being introduced to the R Ladies Buenos Aires community in February 2018. Paola Prieto (one my co-instructors for the pilot The Carpentries workshop in Spanish) invited me to give a talk at their group meeting, so I decided to talk The Carpentries and reproducible research with R in Spanish! Everyone was really enthusiastic, so I started working to incorporate them into the instructor training program.

In June 2018, Sue taught a workshop at Jackson lab with about 20 people, but I Zoomed in with two RLadies from Argentina, Laura Acion and Maria Florencia. They did their practice teaching using R Gapminder Spanish lesson. I’m proud to say that Laura and Maria have already completed their instructor training, and the three of us are continuing to work together via RLadies Buenos Aires and the LatinR conference!

The first bilingual Instructor Training workshop for Latin America

Finally, in August 2018 we make it to the thing that people have been waiting for, a fully distributed online instructor training with participants in Argentina, Colombia, Costa Rica, Educador, Mexico and Peru. This was really a global event with four co-trainers and helpers (me, Sue McClatchy, Greg Wilson, Alejandra Gonzalez-Beltran, Paula Andrea Martinez). We were located in Canada, the USA, the UK, and Belgium. Everyone but Greg spoke Spanish to some degree. The students were encouraged to ask questions or make comments in either English or Spanish, so the Etherpad supported a really bilingual mix of stories and notes.

On Day One, Sue and I taught the lessons completely in English. While all the attendees acknowledged that the workshop would be taught in English, I knew some didn’t understand as well as the others. So, while Sue talked, I live translated what she was saying into Spanish in the Etherpad. Paula and some of the attendees were kind enough to help out to improve the notes. For me, the best part of day one was the episode on mindset and grit. I asked the attendees to share a recent time when they persevered despite wanting to quit. Two people said that they almost didn’t show up to this workshop but that they were thankful they did. I responded by saying that I had also considered not teaching this workshop but I’m glad I did. I started crying because I was so grateful for the community support that helped everyone persevere.

On Day Two after lunch, Alejandra taught an episode on introductions speaking only in Spanish! (You can view the original episode in English or the translation.) Since I could read and listen to this episode in Spanish, note taking in Spanish was a lot easier. This really solidified in my mind how hard it is to translate and learn at the same time and why it is so important to have a library of lessons in Spanish. I decided to continue speaking in Spanish when I taught the last two episodes regarding The Carpentries teaching practices and operations. While I didn’t have a translated lesson to use, I have already one slideshow and given one talk about The Carpentries in Spanish, so I felt comfortable speaking about The Carpentries in Spanish.

During the final 20 minutes of the workshop, we had a roundtable discussion about what everyone was excited about moving forward. After two days of reading people’s thoughts in the Etherpad, it was great to have a face-to-face discussion and hear everyone’s voices. While everyone said something slightly different, the main theme is everyone wants to improve their local training programs by organizing and teaching Software Carpentry and Data Carpentry workshops.

Outlook

I think we’ve come a long way growing communities of people who are passionate about improving research and teaching all over the world. You can read more about the translation and lesson release in the Carpentries blog in English and Spanish. As with the lesson translations, everyone is enthusiastic about organizing more workshops and expanding the curricula. These will be a long-term community project. To get involved, check out our GitHub repository for Spanish translations or join the Carpentries Latin America mailing list.

I’ve also come along way since this started. In three years, my fluency in verbal and computing languages has grown. In 2015 I didn’t think I was talented enough to teach programming in Spanish, but by early 2018 I had gained the experience and expertise necessary. It required some perseverance, but I didn’t do it alone; many colleagues around the globe contributed support to help turn some of these ideas into a reality. I think it is a beautiful example of how having a growth mindset, grit, and community support is really important when we think about expanding the Carpentries into new communities.

Thanks

I want to thank Paula Andrea Martinez, Maria Florencia and Raniere Silva for comments on earlier versions of this post. Thanks to everyone who helped make all these events happen!

softwarecarpentry  datacarpentry  instructortraining 
</body> </html> " class="button special small">instructortraining<!DOCTYPE HTML> Three years in the making for Instructor training in Latin America
24 Aug 2018

Three years in the making for Instructor training in Latin America

Building global communities of Spanish-speaking Carpentry instructors and lesson developers

This month I (Rayna Harris) co-taught a remote The Carpentries Instructor Training Workshop for 25 Spanish-speaking trainees in six countries in Latin America. It was awesome! One thing that made this workshop so special for me is that it has been three-plus years in the making. So, I thought I would tell the story, from my perspective, about all the things that came into play to make this workshop a reality.

The early days of The Carpentries workshops in Spanish

In 2016, Greg Wilson introduced me to Selene Fernandez-Valverde to discuss a Software Carpentry meets Spanish-speaking bioinformatics endeavour. Back then my Spanish was eight years out of practice and I was still learning to program. I didn’t think I had the expertise to teach programming in Spanish. Sue McClatchy had more expertise and practice, but it is still difficult for a native English speaker to live-translate a lesson from English to Spanish while live coding in front of a classroom.

This observation led to two simultaneous efforts: support a community-wide effort for collaborative lesson translation and provide instructor training for Spanish speaking instructors. That is exactly what many staff and volunteers have done over the past three years.

Spanish translations hacakathon and lesson maintenance

In November 2017, I went to Germany to attend OpenCon and worked on translating Software Carpentry lessons into Spanish with Paula Andrea Martinez. Our hackathon session has been immortalized in the promotional materials for OpenCon2018.

In December 2017, I finished my PhD, and I decided to go visit all the awesome open-science advocates that I met at OpenCon in Buenos Aires. I met Juli Aranco from Buenos Aires and we organized a lesson translation hackathon where we made huge progress on the Git and R lessons. We also ran a one-day Software Carpentry Workshop using those translated lessons. It was a huge success. The translated UNIX lesson was flawless. The translated Git lesson ran long but was good. Everyone brought snacks to share. All attendees and four of the five instructors were female. It was a great day.

The release of three stable Spanish translations meant that we needed lesson maintainers. So, while living in Buenos Aires, I also co-taught Carpentry Maintainer training in Spanish! I couldn’t have done this without Erin Becker, Ivan Gonzalez, and François Michonneau. Living in Argentina gave them the confidence to speak in Spanish about programming. I also immersed myself in the maintainer role, and my Git and GitHub skill levels skyrocketed. I can pretty much do all things Git now.

Instructor Training workshops for Puerto Rico and Argentina

Back in March 2017, Sue and I travelled to Puerto Rico to run instructor training in English that coincided with a Data Carpentry Replicathon (hackathon for replicating scientific results) taught by Tracy Teal, Phillip Brooks and a few others. We conducted the course in English, but we chatted in Spanish over coffee breaks and at parties. It was very cool. We hosted a few virtual bilingual demos and discussions after the workshop and that was fun but we lost momentum.

The real momentum for me for instructor training came from being introduced to the R Ladies Buenos Aires community in February 2018. Paola Prieto (one my co-instructors for the pilot The Carpentries workshop in Spanish) invited me to give a talk at their group meeting, so I decided to talk The Carpentries and reproducible research with R in Spanish! Everyone was really enthusiastic, so I started working to incorporate them into the instructor training program.

In June 2018, Sue taught a workshop at Jackson lab with about 20 people, but I Zoomed in with two RLadies from Argentina, Laura Acion and Maria Florencia. They did their practice teaching using R Gapminder Spanish lesson. I’m proud to say that Laura and Maria have already completed their instructor training, and the three of us are continuing to work together via RLadies Buenos Aires and the LatinR conference!

The first bilingual Instructor Training workshop for Latin America

Finally, in August 2018 we make it to the thing that people have been waiting for, a fully distributed online instructor training with participants in Argentina, Colombia, Costa Rica, Educador, Mexico and Peru. This was really a global event with four co-trainers and helpers (me, Sue McClatchy, Greg Wilson, Alejandra Gonzalez-Beltran, Paula Andrea Martinez). We were located in Canada, the USA, the UK, and Belgium. Everyone but Greg spoke Spanish to some degree. The students were encouraged to ask questions or make comments in either English or Spanish, so the Etherpad supported a really bilingual mix of stories and notes.

On Day One, Sue and I taught the lessons completely in English. While all the attendees acknowledged that the workshop would be taught in English, I knew some didn’t understand as well as the others. So, while Sue talked, I live translated what she was saying into Spanish in the Etherpad. Paula and some of the attendees were kind enough to help out to improve the notes. For me, the best part of day one was the episode on mindset and grit. I asked the attendees to share a recent time when they persevered despite wanting to quit. Two people said that they almost didn’t show up to this workshop but that they were thankful they did. I responded by saying that I had also considered not teaching this workshop but I’m glad I did. I started crying because I was so grateful for the community support that helped everyone persevere.

On Day Two after lunch, Alejandra taught an episode on introductions speaking only in Spanish! (You can view the original episode in English or the translation.) Since I could read and listen to this episode in Spanish, note taking in Spanish was a lot easier. This really solidified in my mind how hard it is to translate and learn at the same time and why it is so important to have a library of lessons in Spanish. I decided to continue speaking in Spanish when I taught the last two episodes regarding The Carpentries teaching practices and operations. While I didn’t have a translated lesson to use, I have already one slideshow and given one talk about The Carpentries in Spanish, so I felt comfortable speaking about The Carpentries in Spanish.

During the final 20 minutes of the workshop, we had a roundtable discussion about what everyone was excited about moving forward. After two days of reading people’s thoughts in the Etherpad, it was great to have a face-to-face discussion and hear everyone’s voices. While everyone said something slightly different, the main theme is everyone wants to improve their local training programs by organizing and teaching Software Carpentry and Data Carpentry workshops.

Outlook

I think we’ve come a long way growing communities of people who are passionate about improving research and teaching all over the world. You can read more about the translation and lesson release in the Carpentries blog in English and Spanish. As with the lesson translations, everyone is enthusiastic about organizing more workshops and expanding the curricula. These will be a long-term community project. To get involved, check out our GitHub repository for Spanish translations or join the Carpentries Latin America mailing list.

I’ve also come along way since this started. In three years, my fluency in verbal and computing languages has grown. In 2015 I didn’t think I was talented enough to teach programming in Spanish, but by early 2018 I had gained the experience and expertise necessary. It required some perseverance, but I didn’t do it alone; many colleagues around the globe contributed support to help turn some of these ideas into a reality. I think it is a beautiful example of how having a growth mindset, grit, and community support is really important when we think about expanding the Carpentries into new communities.

Thanks

I want to thank Paula Andrea Martinez, Maria Florencia and Raniere Silva for comments on earlier versions of this post. Thanks to everyone who helped make all these events happen!

softwarecarpentry  datacarpentry  instructortraining 
</body> </html> </a>
</section> </div>