Are you the publisher? Claim or contact us about this channel

Embed this content in your HTML


Report adult content:

click to rate:

Account: (login)

More Channels

Channel Catalog

Channel Description:

Data Carpentry is non-profit organization that develops and provides data skills training to researchers.

older | 1 | .... | 4 | 5 | (Page 6) | 7 | 8 | 9 | newer

    0 0

    Invitación a participar

    Las Carpentries, el Nodo Nacional de Bioinformática México (NNB), y la Sociedad Iberoamericana de Bioinformática (SoIBio) les invitan a participar en el proyecto Carpentry para América Latina.

    Las Carpentries han generado material para enseñar a investigadores y estudiantes, las habilidades computacionales necesarias para realizar su trabajo de manera eficiente. Actualmente, las carpentries cuentan con más de una docena de lecciones creadas con técnicas de pedagogía actual. Estas lecciones se han promovido en talleres en más de 37 países. Carpentry para América Latina tiene la intención de promover este movimiento con la comunidad hispana.

    Tenemos varias actividades en pie en las que todos están bienvenidos a participar:

    1. Traducción al español de las lecciones de Software Carpentry y Data Carpentry
    2. Revisión del material traducido
    3. Mantenimiento de las lecciones traducidas
    4. Si eres instructor de Carpentry, participa como instructor en los talleres Carpentry en español en Latino América.
    5. Si no eres instructor Carpentry, hablas español y quieres enseñar, participa para certificarte como instructor.
    6. Si eres trainer y hablas español, participa de las sesiones de demostración en español.
    7. Si quieres escribir un post en español sobre tu experiencia con las Carpentries, comunícate con nosotros.
    8. Si tienes otras sugerencias, todas son bienvenidas!

    ¡Únete a este esfuerzo! Escríbenos a y participa junto con nosotros.

    Para unirse a la lista de correo electrónico, visita!forum/latinoamerica

    Si estás interesado en mas información sobre los avances, visita


    Escrito por Heladia Salgado. Editador por Sue McClatchy and Paula Andrea Martinez

    Invitation to participate

    The Carpentries, the National Node of Bioinformatics Mexico (NNB) and the Ibero-American Society of Bioinformatics (SoIBio) invite you all to participate in the project Carpentry for Latin America.

    The Carpentries have lesson materials to teach researchers and students the computational skills necessary to perform their work. Currently, the Carpentries have more than a dozen lessons created with current pedagogy techniques. These lessons have promoted workshops in more than 37 countries. The project Carpentry for Latin America has the intention to promote this movement with the Spanish community.

    We have several current activities, including the following, where you are welcome to take part:

    1. Translating Software Carpentry and Data Carpentry lessons into Spanish
    2. Reviewing translated lessons
    3. Maintaining translated lessons
    4. Participating as an instructor in the Carpentry workshops in Spanish in Latin America if you are already a Carpentry instructor.
    5. Certifying yourself as an instructor if you are not a Carpentry instructor and you speak Spanish fluently.
    6. If you are a trainer and speak fluent Spanish, join the demo sessions in Spanish.
    7. If you would like to write a blog post about your experience with the Carpentries, get in touch with us.
    8. If you have any other suggestions, those are also welcome!

    Join in this effort! Write to and participate with us.

    To join the mailing list, visit!forum/latinoamerica

    If you are interested to learn about the updates, visit


    Written by Heladia Salgado. Edited by Sue McClatchy and Paula Andrea Martinez.

    0 0

    We are now requesting comments on plans related to The Carpentries!

    A blog post last week provided history and some context behind the planning still in progress for the eventual merger of Data Carpentry and Software Carpentry into a unified organization, tentatively called The Carpentries. An outline of the planned structure, roles, and responsibilities of The Carpentries is now available, and we request your feedback through a series of Requests for Comment and related GitHub issues by October 6, 2017.

    Requests for Comment (RFCs, also called Requests for Public Comment) are a tool used by government groups and other organizations to solicit feedback on planned actions which may affect a broad community. So far we have attempted to keep you apprised of the planning process, but want to incorporate community input into the unified vision and plan presented in the following topics:

    • RFC1 Organization and responsibilities of The Carpentries
    • RFC2 Board of Directors
    • RFC3 Membership Council (transition from current Software Carpentry Advisory Council)
    • RFC4 Staff
    • RCF5 Financial organisation
    • RFC6 Subcommittees and task forces
    • RFC7 Lesson Organizations

    Please head over to the GitHub repository and add your comments to relevant issues by October 6, 2017. If you prefer not to respond on GitHub, or would like to remain anonymous, you may respond to the RFCs using this Google Form.

    0 0

    As the Carpentry community continues to grow, our instructor training is increasingly in demand! In September, we welcomed 13 new Instructor Trainers who will help us to meet that need. We are now accepting applications for the next group of new Trainers. In this round, we welcome all applicants, but are particularly keen to recruit trainers who can work in Latin America, Africa, Australia and New Zealand. We would also like to recruit new Trainers who are fluent in Spanish.

    Carpentry Instructor Trainers run instructor training workshops, lead online teaching demonstrations, and engage with the community to discuss and guide the continuing development of the instructor training curriculum, the instructor checkout process, and downstream instructor support.

    We meet regularly to discuss our teaching experiences and to stay up to date on policies, procedures, and curriculum updates.

    The Trainers are an eclectic group. Some of us have formal training in pedagogy, some are experienced Carpentry instructors. Some run trainings as part of their jobs, and others pitch in during their own free time. We all share a commitment to propagating evidence-based practices in teaching and to helping new instructor trainees become familiar and comfortable with Carpentry practices and principles.

    Our Trainer agreement explains what is involved. It describes our expectations for anyone who aspires to become a Carpentry Instructor Trainer.

    The trainer training process consists of eight one-hour weekly virtual meetings (with a break for the December holidays). In these meetings we will discuss readings on pedagogy, largely drawn from our ‘textbook’, How Learning Works. We will also review the Carpentry Instructor Training curriculum, and discuss ways in which we can both teach and apply best practices to create a welcoming and effective class. After completing the meeting series, new Trainers will shadow part of an online instructor training event and a teaching demonstration session. Trainers-in-training also attend the regular monthly meetings of the Trainer community.

    This group of Trainers will start meeting in November. They will be eligible to teach instructor trainings by February, 2018.

    If you are interested in joining the Trainer community, please apply here! Applications will be open until October 17. If you have previously applied and are still interested, you may either re-apply (especially if anything relevant has changed) or just let us know that you are still interested.

    If you have any questions about the training process or the expectations for being a Trainer, please get in touch with Karen Word.

    0 0

    The inaugural Carpentries mentoring program was a great success, and we have used the feedback we received from both mentors and mentees to craft a new and improved mentoring experience in round two. The next round will run October 25th - January 10th.

    According to round one participants, the benefits of mentoring included greater understanding of the challenges new instructors face, more clarity about why we teach what we teach, getting timely responses to questions, and community engagement.

    Participants felt the program could be improved if mentoring groups had specific goals, and if we gave mentors more guidance on how to run mentoring sessions.

    We listened to that feedback and have made changes to the program. We are now offering curriculum-specific mentoring: both mentors and mentees can choose which tools they are most interested in discussing from the following list:

    • Git
    • Shell
    • Python
    • R
    • SQL

    Once a topic has been selected, participants can choose what aspect of mentoring they want for their chosen tool:

    • Lesson Maintenance
      • Contributing to current lesson development
      • Contributing to lesson maintenance
    • Teaching Workshops
      • Developing confidence and skill in teaching
      • Preparing to teach a specific lesson (e.g., Python)

    Additionally, we plan to offer mentoring on two big issues:

    Organizing Workshops

    • Logistics of organizing a workshop (e.g. marketing, registration)
    • Logistics of running a workshop (e.g. recruiting instructors, distributing tasks)
    • Community Building
      • Strategies to create and build local communities
      • Tried-and-true events that help foster local community development

    To help groups get organized we have provided sample mentoring program outlines to help groups use their time together productively.

    Interested in mentoring? We will hold two information sessions on Thursday, October 12th at 06:00 UTC and 21:00 UTC. Sign up to attend either information session on the etherpad.

    Applications for both mentors and mentees are open. The deadline to apply to participate in the program is October 18th.

    Share your excitement about mentoring via Twitter (@datacarpentry @swcarpentry @drkariljordan @cloudaus) with the hashtag #carpentriesmentoring.

    0 0

    Mentorship is an important part of the Carpentry experience. As Instructors, we both teach and mentor our Learners. We also mentor each other as Instructors, learning something new from each other every time we teach and interact with one another. The Mentoring Subcommittee offers guidance to new and continuing Instructors through weekly discussion sessions, where Instructors from the global Carpentry community gather to share their experiences and learn from each other. This is a fantastic opportunity to interact with other Carpentry Instructors from around the world.

    Many in the Carpentry community have expressed interest in having more extensive and longer-lasting opportunities for mentorship. Based on this, we ran a pilot version of a new Mentorship Program, starting in January 2017. Nearly 100 Carpentry Instructors participated in the program, with 58 Mentees and 34 Mentors in 18 small groups. Groups were put together based on a variety of factors, including common teaching interests and geographies. These groups met once a month to discuss topics of interest to the group members and to help Mentees prepare for their first workshop.

    In June 2017, we asked participants in the pilot program for their feedback. Participants said that they enjoyed the opportunity to share and learn from each others’ experiences and expertise. They also reported that the experience enabled them to get involved with the Carpentry community and to network with Carpentry Instructors at other institutions. When asked about negative aspects of the program, many participants reported difficulty scheduling meetings with their groups as well as a lack of focus and difficulty deciding topics to discuss with their groups. Many participants offered concrete suggestions on how the program could be improved, including:

    • offering more guidance to mentorship groups on what to do during the program
    • assigning groups specifically around common interests and goals
    • enabling more integration and communication among groups.

    As with any pilot program, one of the goals of this program was to identify aspects that could be improved, based on the shared experiences of the participants, so we are very grateful for the feedback we received.

    We listened to your feedback and have made changes to the program. We are now offering curriculum-specific mentoring: both mentors and mentees can choose which tools they are most interested in discussing from the following list:

    • Git
    • Shell
    • Python
    • R
    • SQL

    Additionally, groups will focus on either lesson maintenance, teaching workshops, organizing workshops, or community building. This program will run from October 25th to January 10th, 2018, and will culminate in a Virtual Showcase, in which groups will share their work with the broader Carpentry community.

    So far, 18 people have signed up to participate in this round of mentoring groups. Applications close October 18th, so don’t wait to apply to either be a mentor or mentee.

    Get involved by attending one of the information sessions being held October 12th at 06:00 UTC and 21:00 UTC. Sign up to attend on the etherpad. You can also join the conversation by tweeting to @datacarpentry and @swcarpentry using the hashtag #carpentriesmentoring.

    0 0
  • 10/09/17--17:00: Work Cycle Ganymede Wraps Up
  • We are wrapping up Cycle Ganymede. Here’s what we accomplished over the past six weeks and what we’re still working on. To help with any of these projects, please get in touch!

    Archiving Pre- and Post-Workshop Survey Data

    What did we do?

    During the previous work cycle, Data Carpentry launched new pre- and post-workshop surveys that included skills-based questions, and the ability for respondents to provide a unique identifier to facilitate future paired analyses. We archived the old survey data for Data Carpentry and created a draft RMarkdown report and plots for all of the data. Paula Andrea Martinez helped Kari Jordan with this. Because of the way the code is structured, there was no easy way to create a RMarkdown report that includes only selected plots. Hopefully, we will find a way round this for future reports.

    How can you help?

    If you’re interested in other visualizations or analyses of our data, please contribute! All our data and the code that generated this report is available for reuse. We would love to see people with other questions or ideas use the data in their work or contribute for future reports.

    Long-term Survey Report

    What did we do?

    The results of the Carpentries long-term survey are extremely compelling, and we want to share them with a broader community. Accordingly, a team led by Kari Jordan is working to draft a manuscript around our long-term survey results. Assessment will be the topic of our October 19 community call.

    How can you help?

    If you would like to know more about our assessment work, or if you would like to help out in some way, please join the October 19 call. If you have recently attended a workshop, please complete the survey. You can also join our Google Group on assessment.

    Instructor Training Curriculum Lesson Release

    What did we do?

    Trainers and instructors did a lot of work readying our instructor training curriculum for the release of a new version. Thanks to all who took part. The material has now been published. See it here.

    How can you help?

    If you are a Trainer teaching this material, please let us know if you find any errors or omissions by raising an issue on the GitHub repository. We would also value more general feedback.

    Genomics Lesson Update

    What did we do?

    Many new and current Maintainers, as well as other members of our community, worked long and hard at both an Issue Bonanza and Bug BBQ to prepare the Genomics Lesson for release. Because of the number of outstanding issues and pull requests that need to be resolved, the release has been postponed to early November. A huge thank you to everyone who has been taking part in this release! You can see some of the milestones here, here and here. In the Genomics curricula, we are also piloting a new approach involving a curriculum committee and more maintainers, and using a ‘Looks Good to Me’ model. Thanks to everyone who has been involved in this pilot model. There are still some things to figure out, and we will be updating this with a maintainers report, to see if this is a general model we can use for other curriculum.

    How can you help?

    We would welcome assistance with both resolving issues and reviewing the outstanding pull requests. Please contact Erin Becker if you can help.

    FAQ Update

    What did we do?

    As we prepare for a joint Carpentries, we plan to standardize information and procedures across both organizations. During this cycle, the existing website FAQs were moved into HelpScout, during which time they were also updated and tagged (some with multiple tags). Some new FAQs were created as well. The website for the updated FAQs is, and it is keyword-searchable.

    How can you help?

    Looking for the answer to something but can’t find it? Reading through the FAQs and notice something that should be updated or edited? Please let us know so we can update it or add it to the knowledge base.

    What else?

    During this cycle, all Software and Data Carpentry staff travelled to in Davis, California for a two-day, in-person meeting. Read about what we achieved there.

    0 0

    This is an open invitation to our community members to share their knowledge.

    We have a global community working in many different disciplines using a vast range of tools. On our blog, we would like to tap into that community experience and then share that hard-won knowledge.

    This kind of information could help people new to a discipline, or might inspire others to try out a tool they have never used before.

    Time wasted or time saved?

    As with all learning, there is an opportunity cost; time spent learning new tools is time stolen from essential research.

    So the first decision might be whether you can spare the time to learn something new, though that might not be the hardest decision. After all, if a tool pays off in increased efficiency and time savings down the track, then that time is definitely well spent.

    But which tool should you pick? For what purpose?

    This is where experience in a discipline is so valuable. After all, anyone working with statistics can probably make a great case for R.

    We would like to hear from community members willing to share their experiences.

    Posts on My Workflow from senior researchers in a discipline would be a fantastic resource for newcomers.

    Posts about My Favorite Tool and Why I Love it would help others decide whether to put in the time to master it.

    You may be thinking “I am way, way too busy” to do this so we want to make it easy for you. We have a form with some prompts for you to fill in. Just a few short lines are all we need, and we will do the rest.

    Worried you have made errors in the form after submitting it? Anxious you have omitted something important? We will let you review the post before it goes out.

    So what are you waiting for? Please tell us your story today!

    0 0

    What concrete changes are people implementing in their computational research practices as a result of completing a Carpentries workshop?

    Our long term survey report shows that two-day Software or Data Carpentry workshops are effective for increasing skills and confidence, and the adoption of reproducible research perspectives. We see gains in our survey measures for learners’ motivation to continue their learning, change in reproducible research behavior, and frequency of use of computational skills and tools. We find this very exciting, especially since a recent general survey of bootcamps and short-format trainings reports no measurable impact on skill development or research productivity.

    Software and Data Carpentry have taught workshops to over 27,000 learners in 35 countries around the world. Post-workshop survey reports for Software Carpentry and Data Carpentry have consistently shown that people like the workshops, that they know more about importing data sets into R and Python to work with data, write functions, and initialize repositories in git, and that they think they can apply skills immediately to their work.

    Our focus has always been on long term change, including:

    • Improving learners’ confidence and motivation to use computational tools,
    • Changing behaviors around reproducible research and effective computational work, and
    • Increasing the frequency and types of computing skills used. Therefore, we launched our first long-term assessment survey in March 2017 to gather quantitative evidence about specific behaviors our learners have adopted and continue to embody six months or more after completing a Carpentries workshop.

    Assessment specialists on staff and in the community developed an instrument, based on existing instruments, for collecting information regarding learners confidence and motivation to use the tools they learned, and behaviors they adopted after attending a Carpentries workshop. We focused on assessing learner confidence, motivation and adoption of good research practices, rather than learners’ skills in particular tools, as these elements represent the primary goals of our workshops. Confidence and motivation are important factors for learners to have to continue their learning. They also promote community building, a significant focus area of the Carpentries.

    The final survey instrument included items for self-reported behaviors around good data management practices, change in confidence in the tools they learned, and other ways the workshop may have impacted learners (ex. Improved research productivity). Over 530 people who took a Software or Data Carpentry workshop 6 months or more ago, responded to our long-term survey. These results show that workshop learners had a positive impression of the workshop and the majority felt their skills and perspectives have changed as a result of the workshop. results show that these two-day impactful workshops are effective for increasing skills and confidence. The impact of these workshops is also apparent in respondents coding practices. A majority of respondents (70%) reported having improved their coding practices, by using programing languages like R or Python or the command line to automate repetitive tasks, by reusing code for other purposes, or by and using databases to manage large data sets. Respondents have continued their learning and incorporated use of these tools into their weekly or daily work. Additionally, fifty-four percent of respondents have made their analyses more reproducible as a result of completing a Carpentries workshop by reusing code and making their data and analyses available on public repositories.

    Not only do these two-day coding workshops increase researcher’s daily programming usage, sixty-five percent of respondents have gained confidence in working with data and open source tools as a result of completing the workshop. The long-term assessment data showed a decline in the percentage of respondents that ‘have not been using these tools’ (-11.1%), and an increase in the percentage of those who now use the tools on daily basis (14.5%).

    Highlights from our long-term survey

    The majority of our respondents:

    • Gained confidence in the tools that were covered during their workshop (85.3%).
    • Reported improving their coding practices (63.1%).

    Respondents also substantially increased their frequency of use of programing languages (R, Python, etc.), databases (Access, SQL, etc.), version control software and/or the Unix shell, incorporating these tools into their regular workflows. Nineteen percent of respondents transitioned from using these tools once a month or less to weekly or daily use per the figure below.

    alt text

    Learners perceive the workshop had an impact on their confidence, as well as their productivity, reproducibility and coding. Interestingly, people also felt that the workshops had a positive impact on their career as a whole, and some received recognition for their work.

    The figure below shows what impact the workshop respondents’ attended had on several factors, including career, confidence, and continuous learning. Respondents were asked to rate their level of agreement (1-Strongly disagree to 5-Strongly agree) with the statements below. The x-axis labels for the figure are in bold, and correspond to the statement following.

    • Reproducible: I have made my analyses more reproducible as a result of completing the workshop.
    • Recognition: I have received professional recognition for my work as a result of using the tools I learned at the workshop.
    • Productivity: My research productivity has improved as a result of completing the workshop.
    • Motivation: I have been motivated to seek more knowledge about the tools I learned at the workshop.
    • Confidence: I have gained confidence in working with data as a result of completing the workshop.
    • Coding: I have improved my coding practices as a result of completing the workshop.
    • Career: I have used skills I learned at the workshop to advance my career.

    alt text

    The figure shows that respondents agree or strongly agree about gaining confidence in working with data (85.3%), making their analyses more reproducible (69.4%), and receiving professional recognition for their work (64.7%) all as a result of attending a Software or Data Carpentry workshop.

    From this figure we also see that there are opportunities to improve. Motivation to seek more knowledge seems unchanging, likely because learners who attend our workshops are already motivated. Perhaps these learners remain enthusiastic, having high pre-workshop motivation scores, rather than a decrease in motivation post-workshop. We’d also like to see a shift in positive trend for learners using the skills they learned to advance their career, which is why we are implementing round two of the Carpentries Mentoring Program this fall.

    Interested in reading more? The full report is available, and it provides more detailed information about the motivation behind this survey, respondent demographics, and growth opportunities. Take a look at the report. We will continue to conduct this assessment at 6 month intervals to capture feedback from people who took workshops 6 months or more ago. Additionally, assessment will be the focus of our October community call. Bring your thoughts to the community call October 19th!

    The surveys used in this work, anonmyized data and R scripts for generating the figures are available in our assessment repository. This report was made possible by community input from Ben Marwick, Belinda Weaver, Naupaka Zimmerman, Jason Williams, Tracy Teal, Erin Becker, Jonah Duckles, Beth Duckles, Elizabeth Wickes. We thank you all so much for your contributions to the code in this report and development of our long-term survey!

    If you have other questions about the data or results, please use the data, re-analyze the results or ask your own questions!

    What strikes you? Comment below, and tweet us your thoughts @datacarpentry @swcarpentry and @drkariljordan using the hashtag #carpentriesassessment.

    Thanks to the Gordon and Betty Moore Data Driven Discovery initiative for support of Data Carpentry and these assessment efforts.

    0 0

    As most of you know, Software Carpentry and Data Carpentry are merging into a new organization, provisionally called “The Carpentries”. This new organization will officially begin on January 1, 2018, with a hugely talented staff and dedicated community already in place.

    This is an exciting time, and we are looking for people who want to help direct the new organization by being an elected member of the Board of Directors of The Carpentries. The board will include both appointed and elected members in order to balance community engagement with needed expertise in leading a growing non-profit organization. For more information about the responsibilities and composition of the board, see this issue, part of the merger RFC.

    Who can run and vote?

    Following current SCF bylaws current Carpentries members may vote and serve on the Board. Election or appointment to the board is currently limited to members.

    The membership is made up of:

    • Every qualified instructor who has taught at least two Software or Data Carpentry workshops in the past two calendar years.
    • Anyone who has done 30 days or more work for the Carpentries in the past calendar year.
    • Anyone who has, in the opinion of the Steering Committee, made a significant contribution in the past year.
    • The signatory for a Silver, Gold or Platinum Member Organization

    If you’re not sure if you’re a member, log in to AMY and see if records show that you have taught in the last two years. If you need records updated or have any questions, please email If you have taught workshops that aren’t registered, please include a link to those workshops. We’ll also be sending out an email to each instructor with their status.

    How do I stand for election?

    In order to stand for election we request that you write a blog post that introduces yourself to the community. The post:

    • must be about 500 words and can be written in any format (question and answer, paragraph etc.)
    • must be titled “2018 Election: Your Name”
    • must be submitted by December 1, 2017

    You can submit your post as a pull request to either the SWC website repository, the DC website repository or by email. In the post, you should explain:

    • your previous involvement with The Carpentries
    • what you would do as a member of the Board of Directors to contribute to the growth and success of the community

    The post from last year’s SWC elections contains examples.

    Candidates will be given the opportunity to share their thoughts with our community, including ideas for continued involvement, at our two community meetings on November 16, 2017.

    Timeline for election:

    • October 23: nominations open
    • November 16: nominees can introduce themselves on community calls
    • December 1: nominations close
    • December 4-8: community votes on candidates

    0 0
  • 10/24/17--17:00: My Favorite Tool is Git
  • I love Git and GitHub.

    I only use them for work I care about. Examples include lesson development for R workshops, my recent performance review packet, and collaborative projects on species distribution modeling. Oh, and Software Carpentry workshop websites (obviously).

    Why I like Git:

    The version control system and the companion remote host system (GitHub or Bitbucket or CloudForge, etc.) provide a great versioning and collaboration platform, the highlights of which have been enumerated many times over and in such depth that I won’t talk about them here.

    The reason I like this dynamic duo is that it reinforces best practices. I should say that using version control won’t necessarily make you 100% compliant with everyone’s idea of best practices, but with a little consideration of a workflow, it can go a long way. Here is why:

    1. Reproducibility: By ignoring my output folder in pretty much all my Git repositories, it forces all figures & analyses to be completely reproducible from materials that are in the folders that are tracked.

    2. Offsite backup: Rather than lugging my aging laptop to and fro, pull-add-commit-push allows me to preserve my work in a location accessible from any internet-enabled terminal. This has the added benefit of protecting against natural disasters and the inevitable bricked hard drive (mark my words, death, taxes, and a failed HD are the only certainties in life now).

    3. Sharing: Sure, some of what I currently work on is not ready to be released, so I use the private repository option. But when I am ready to share my code and data, it’s literally one to two mouseclicks and my work is open for re-use by the community. The visibility of platforms like GitHub and Bitbucket make work that much more discoverable.

    4. Documentation: Everybody’s favorite part of software development is … not likely writing documentation (granted there are some of you out there). Because good documentation is imperative for re-use and evaluation, the little reminders from GitHub (“Help people interested in this repository understand your project by adding a README”) further encourage best practices for open research. The support for markdown rendering on GitHub makes it especially nice for writing professional-looking documentation of your work.

    Sure, I struggled struggle sometimes with Git syntax and concepts, but 98% of the time I only use four commands (pull-add-commit-push, remember?) and the Git/GitHub combo reduces the time I spend developing, preserving, and sharing the work I do.

    – Jeff Oliver, Data Science Specialist, Tucson, Arizona

    Have a favorite tool of your own? Please tell us about it!

    0 0
  • 10/29/17--17:00: People's Favourite Tools
  • A big thank you to everyone who has responded so far to the call for short posts about their favourite tools.

    So far we have had Paula Martinez on R, Jeff Oliver sharing his love of Git and GitHub, Kellie Ottoboni talking up IPython, and Thomas Arildsen on how the Jupyter Notebook facilitates his teaching. Juliane Schneider has now weighed in on the wonders of OpenRefine.

    Expect more posts as people contribute further favourites. Even if your tool has already been mentioned, we would still welcome a post about it, as your use of the tool may be different.

    Have you got a favourite tool you would like to tell us about? Please use this form to add a bit of detail and we will do the rest. You can read the background to these posts here.

    0 0

    In April 2017, Data Carpentry began to pilot a survey that includes skills-based questions. Check out the blog post about our assessment strategy, and the work involved leading up to this effort.

    The survey includes the following statement:

        Please enter a unique identifier as follows: Number of siblings (as numeric) + First two letters of the city you were       
        born in (lowercase) + First three letters of your current street (lowercase). This identifier will be confidential to 
        you and will help us pair your results with the post-assessment.
        Example: If I have 4 siblings, was born in Arlington, and live on Creekwater Street, my unique identifier would be 

    This unique identifier is asked of respondents so that our staff can run paired analyses of the pre- and post-survey results to measure significant gains post-workshop.

    In addition to the unique identifier, the survey includes skills-based questions. One example of a survey question is:

        ggplot is an R package that is used to build plots from data in a dataframe. If ‘df’ is your dataframe and has 
        columns x and y, which of the following lines of code will produce a plot of x versus y?
          A: ggplot <- df
          B: ggplot(df)
          C: ggplot(df, aes(x, y))
          D: ggplot(df, aes(x, y)) + geom_point()
          E. None of the above will work.

    Our goal in including skills-based questions was to determine whether learners were leaving our workshops having specific skills working with data.

    Feedback from some of the instructors has been that this survey has given some of our learners anxiety about our workshops. Though language around the purpose of the unique identifier was included, some learners felt the questions they were being asked were intrusive, and that the skills-based questions are intimidating.

    Therefore, a call for a survey focus group went out on discuss and the virtual assessment network to take a closer look at this survey, and what changes should be made to make it more inclusive.

    Lead by Kari L. Jordan, the focus group included Stephen Childs, Alycia Crall, Reshama Shaikh, Aleksandra Nenadic, Karen Word, and Louisa Bells. These individuals have expertise in data science assessment and evaluation.

    The focus group’s first meeting was Friday, October 20th 2017. The primary goal of this meeting was to determine how we could assign unique identifiers to our learners and still have their data remain anonymous. Additionally, we discussed the need to collect demographic information, and how to accomplish that in an inclusive way.

    In terms of unique identifiers, an idea was to ask learners to provide their personal e-mail address as their unique identifier. Issues were raised around learners not remembering which e-mail address they gave, and that by providing their e-mail address their responses would not be anonymous. The idea of having SurveyMonkey create unique survey links for participants was discussed, but this would not be feasible because our survey links are embedded into the workshop website template. SurveyMonkey does offer the ability to create custom variables however, this will add more manual work for staff and workshop hosts. A graphic was also discussed as an option for unique identifiers, however, we are concerned that learners may not remember what graphic they chose. We are still searching for a solution, so if you have ideas please get in touch.

    U.S. based workshop participants are asked demographic questions (race/ethnicity, gender, etc.) Collecting this type of information can be challenging, and we want to be sure we are asking demographic questions in an inclusive manner. Thus language around our gender question was improved so that respondents can select which gender identity they most identify with.

    Additionally, learners are encouraged to contact their workshop host if they need support for any accessibility requirements that would improve their experience at the workshop.

    Lastly, instead of asking learners to select their race, we ask, “How would you describe yourself?” Learners are prompted to select from several groups.

    During our second meeting (October 25th) we discussed the skills-based questions that are included on Data Carpentry’s pre- and post-workshop surveys. The consensus was that our community is more concerned with measuring learner’s confidence and motivation to use the tools, therefore, the skills-based questions were removed from the surveys.

    We welcome feedback from the community about the adjustments we have made to our surveys. If you have feedback or ideas, please submit an issue on the Carpentries/assessment repo. Tweet us your thoughts at @datacarpentry and @drkariljordan using the hashtag #carpentriesassessment. Get in touch if you’d like to be involved in this conversation.

    0 0
  • 11/02/17--17:00: Pack Your Bags for Dublin!
  • The Carpentries are excited to announce that the 2018 CarpentryCon will take place from 30 May - 1 June, 2018 at University College Dublin (UCD).

    Yes, we are going to Ireland for the inaugural CarpentryCon!

    A huge thank you to UCD for their bid - we are confident that this will be a fantastic venue.

    We are also grateful to all the other community members who proposed bids to host CarpentryCon. All were compelling, and it was very hard to select one from so many fantastic options.

    However, Dublin is a great fit for many things we want:

    • It is a busy travel hub, which should offer lots of easy connections and opportunities for cheap fares.
    • It is a mid-point between Europe and the USA and Canada, and easy to connect to from the southern hemisphere too.
    • As a popular tourism destination, it is well-placed to offer a wide range of budget-priced accommodation options.
    • Lots of tech companies operate there - we will tap them for sponsorship.
    • The host has great experience running this kind of event.

    What we hope to do for attendees

    • It is important that this be an inclusive event, so we aim to keep registration costs low. We will announce price ranges for registration soon.
    • We also hope to be able to provide travel scholarships to facilitate attendance from those who might not otherwise be able to come. Stay tuned for announcements.
    • To help attendees who need to provide evidence of speaking or presenting in order to get funding for travel, we will offer at least one session where attendees can share how they have incorporated Carpentry techniques into their own research and teaching, and/or how they have grown their local Carpentry community. Contributions may be either talks or posters. Details soon.

    We would like to get some rough estimate of how many people might want to attend. Please fill in this short, anonymous form that will help us gauge the level of community interest in CarpentryCon2018.

    What can you expect from CarpentryCon?

    CarpentryCon will focus on three main themes:

    Community Building

    We will bring members of the Carpentry community together with people sharing similar interests from around the globe. Unlike most conferences, our format will be “come and learn”.

    Sharing Knowledge

    Community leaders will offer sessions on teaching methods, curriculum development, community organization, and leadership skills so we can grow our next generation of community leaders and champions.


    Participants will be able to come together informally to meet peers and community leaders and to share stories about challenges and successes.

    What else?

    CarpentryCon2018 planning will now ramp up in earnest. Keep an eye on our blog, Twitter and Facebook channels for announcements and updates. The CarpentryCon repo also has a lot of information. Want to get tweeting? Use the hashtag #CarpentryCon2018.

    0 0

    Post from the University of California Curation Center of the California Digital Library

    In today’s data-driven, online and highly interconnected world, librarians are key to supporting diverse information needs and leading best practices to work with and manage data. For librarians to be effective in a rapidly evolving information landscape, training and professional development opportunities in both computational and data skills must be available and accessible.

    Over the past couple years, an international Library Carpentry (LC) movement has begun that seeks to emulate the success of the Carpentries — both the Data Carpentry and Software Carpentry initiatives — in providing librarians with the critical computational and data skills they need to serve their stakeholders and user communities, as well as streamline repetitive workflows and use best data practices within the library. This Library Carpentry community has already developed initial curriculum and taught more than 40 workshops around the world.

    We are excited to announce that California Digital Library (CDL) has been awarded project grant funds from IMLS to further advance the scope, adoption, and impact of Library Carpentry across the US. CDL’s 2-year project will be conducted by their digital curation team, University of California Curation Center (UC3), and will focus on these main activities:

    1. development and updates of core training modules optimized for the librarian community and based on Carpentries pedagogy
    2. regionally-organized training opportunities for librarians, leading to an expanding cohort of certified instructors available to train fellow librarians in critical skills and tools, such as the command line, OpenRefine, Python, R, SQL, and research data management
    3. community outreach to raise awareness of Library Carpentry and promote the development of a broad, engaged community of support to sustain the movement and to advance LC integration within the newly forming Carpentries organization

    Why Library Carpentry?

    Library Carpentry leverages the success of the Carpentries pedagogy, which is based on providing a goal-oriented, hands-on, trial-and-error approach to learning computational skills, and extends it to meet the specific needs of librarians.

    It is often difficult to figure out what skills to learn or how to get started learning them. In Library Carpentry, we identify the fundamental skills needed for librarians and develop and teach these skills in hands-on, interactive workshops. Workshops are designed for people with little to no prior computational experience, and they work with data relevant to librarians (so that librarians are working with data most applicable to their own work). Workshops are also friendly learning environments with the sole aim of empowering people to use computational skills effectively and with more confidence.

    How does this relate to the Carpentries?

    Two sister organizations, Software Carpentry and Data Carpentry, have focused on teaching computational best practices. The ‘separate but collaborative’ organizational structure allowed both groups to build a shared community of instructors with more than 1000 certified instructors and 47 current Member Organizations around the world. However, as Software Carpentry and Data Carpentry grew and developed, this ‘separate but collaborative’ organizational structure did not scale. As a result, the governing committees of both Software Carpentry and Data Carpentry recognized that as more mature organizations they can be most effective under a unified governance model.

    On August 30, 2017, the Software Carpentry and Data Carpentry Steering Committees met jointly and approved the following two motions, which together form a strong commitment to continue moving forward with a merger. As part of this merger, the new “Carpentries” organization will look to increase its reach into additional sectors and communities. The nascent Library Carpentry community has recently met to decide they aim to join as a full-fledged ‘Carpentry’ in the coming year.

    This grant will help LC solidify approaches to learning and community building, while also bringing resources to the table as we embark on future integration of LC within the merged Carpentries organization.

    How does the Carpentries model work?

    In the Carpentries model, instructors are trained and certified in the Carpentries way of teaching, using educational pedagogy, and are asked to commit to offering workshops in their regions and reworking/improving and maintaining lessons. These instructors teach two-day, hands-on workshops on the foundational skills to manage and work effectively with data. The goal is to become practitioners while in the workshop and then continue learning through online and in-person community interaction outside the classroom.

    With the “train-the-trainer” model, the Carpentries are built to create learning networks and capacity for training through active communities and shared, collaborative lessons. They have used this model to scale with parallel approaches of developing lessons, offering workshops, and expanding the community. The LC community has also used this model and our grant project aims to extend this further.

    Next Steps

    As an immediate next step, CDL has begun recruiting for a Library Carpentry Project Coordinator. This will be a 2-year and grant funded position. You can apply at the UC Office of the President website. Due date is November 31, 2017.

    While this position will report to CDL’s Director of University of California Curation Center (UC3), this position will focus on extending LC activities in the USA and working globally to gain capacity and reach for the Library Carpentry community and Carpentries staff.

    For more information on this project, please feel free to contact CDL’s UC3 team at You can also follow UC3 on Twitter at @UC3CDL). To learn more about Library Carpentry, you can visit and follow on Twitter at @LibCarpentry.

    We look forward to these next steps for Library Carpentry and a growing network of data savvy librarians.

    0 0

    Software and Data Carpentry are currently accepting applications to join the lesson Maintainer team. Carpentry Maintainers work with the community to make sure that lessons stay up-to-date, accurate, functional and cohesive. Maintainers monitor their lesson repository, make sure that PRs and Issues are addressed in a timely manner, and participate in the lesson development cycle including lesson releases. They endeavor to be welcoming and supportive of contributions from all members of the community.

    More detailed information about what Maintainers do can be found here. Please review this document, paying attention to the time commitment involved, before submitting your application. New Maintainers will be invited to join the existing Maintainer group as we develop formal guidelines and training documentation for onboarding new Maintainers.

    You can apply to become a Maintainer here.

    New Maintainers will be mentored in the maintenance process to help them understand the current structure of the lessons, how that structure has arisen, any open topics of discussion around major changes to the lessons, and Git and GitHub mechanics.

    Applications will be open through Wednesday, November 22, 2017 at 6am UTC. Use this link to see the deadline in your local time.

    Please get in touch with Erin Becker ( if you have any questions. Thank you for your interest in joining the Maintainer team!

    0 0

    We ran a 16S metagenomics workshop based on Data Carpentry materials at the North-West University, South Africa, from 24-27 October. A combination of lessons from Data Carpentry, as well as specific workflows for 16S data analysis, were used. We modified most of the lessons according to our main (critical) lesson’s dataset that we were using for 16S analysis. The following topics were covered: spreadsheet organization, shell, 16S analyses on HPC (using Shi7, NINJA and QIIME), R genomics and specific plots of 16S data in R. We extended the workshop to three full days to fit in all the lessons and decided on an additional half-day where attendees would have the opportunity to work on their own data. Twenty-three participants attended the whole workshop.


    Here is a breakdown of the lessons, with successes and challenges mentioned for each:

    • Bianca Peterson made an R presentation of Data Carpentry’s Data Organization in Spreadsheets Ecology lesson to guide Leani Bothma, who was teaching for the first time as a newly trained instructor. This saved some time, which we then used for the shell lesson. Total teaching time: 1 hour.

    • We used the Shell Genomics lesson of Data Carpentry as is, and only modified the output according to our HPC. Tomasz Sanko, also a newly trained instructor, taught this lesson at a very reasonable pace, but couldn’t get through the whole lesson. Feedback shows that learners still need a little more time on the Unix lesson, which is crucial for the next lesson where they analyse 16S data on the HPC. At least 90 additional minutes are needed for this lesson, thus totalling 4.5 hours teaching time.

    • One full day for 16S analysis was perfect: we finished in time even with some troubleshooting along the way. This 16S workflow was written by Tonya Ward (Knights Lab, University of Minnesota) and all the required software was installed on our HPC prior to the workshop. The support from IT was amazing - they made sure that an ethernet cable was available for each participant to ensure continued connectivity while working on the HPC. Total teaching time: 6 hours.

    • The R lesson (R genomics from Data Carpentry that we modified according to the metadata/mapping file that we used for the 16S analysis) was taught by qualified instructor Caroline Ajilogba Fadeke. This was her first time teaching. Not all the data in this mapping file is real - some variables were made up in order to do plotting (this lesson can certainly be improved by adding more variables). Time allocation seemed to be perfect, the pace was not fast at all, and almost everybody kept up with the instructor. Total teaching time: 4.5 hours.

    • In the following R session, learners used output files generated by QIIME to make a variety of visualizations in R. Andries van der Walt, also a newly-trained instructor, taught this microbial community analysis in R lesson, which he wrote. Participants got stuck on typos, even though everything on the screen was correct and they had the lesson in a browser. They seemed to fall behind and looked quite tired, since it was the third full day of the workshop. He recapped everything the next day, and people said that they understood. There were many interruptions during his lesson on day 4 (sorry again Andries!): HPC talk, finishing the last section of the Unix lesson (piping and script writing), taking a group photo, and a quick thank you from Professor Carlos Bezuidenhout (who contributed funds towards this workshop). Our HPC people talked to participants regarding registering for an HPC user account and showed them how the scheduler works. Participants appreciated this, even though it wasn’t part of our formal schedule. Luckily, Tonya had a workflow and script ready for drawing diversity plots in R (for this specific dataset that was analysed) and thus had participants running the script while she was explaining all the commands and arguments. They didn’t seem to mind, since they were familiar with R syntax by now, and actually appreciated the time taken for interpretation of the results. Unfortunately, we didn’t have enough time to cover the other plot types in Andries’s workflow, but participants said that they will have a look at those after the workshop.


    The modified lessons (around the single example dataset) seemed to work much better. The cognitive load was greatly reduced, and they could really get to know the data since they were working on it from the first day. Participants didn’t mind an extended workshop - they actually appreciated it. After the workshop, several participants used what they learned during the workshop, and analysed their own data.

    Word of thanks

    We would like to thank Boeta Pretorius (NWU IT Director), Adelle Lotter (Acting director: NWU Academic and Office Solutions) and Professor Carlos Bezuidenhout (Microbiology department) for their support and for sponsoring the workshop. We would also like to thank the NWU IT team, Riaan Stavast, Thabo Molambo, Hannes Kriel, Martin Dreyer, and especially Ciellie Jansen van Vuuren, for going the extra mile to ensure all software were loaded and working on the HPC and for providing additional support in terms of internet access throughout the workshop.

    0 0

    How would you like to work first-hand on developing our ever growing instructor pool? A Mentoring Subcommittee Co-Chair position has just opened!

    The leader serving in this year-long position (December 2017- December 2018) will share duties with the co-chair of the mentoring subcommittee, with a commitment averaging 1.5 hours/week.

    The expectations of the mentoring subcommittee co-chairs are to host the monthly mentoring subcommittee meetings, facilitate opportunities for building connections across our community to better serve our instructors, and to manage the weekly instructor discussion sessions hosted on this etherpad.

    If you would like to be considered, please fill out this short google form by December 4th. The current mentoring subcommittee co-chairs will select a new co-chair from the applicant pool with input from the Carpentries staff liaison, and other members of the Carpentries community.

    Apply Here


    • Host one of the two monthly mentoring subcommittee meetings (The co-chair will host the other.)
    • Attend one debriefing meeting per month with the co-chair (usually soon after the monthly meeting).
    • Commit to an average of 1.5 hours per week (usually ~2 hours/week during the week of hosting the mentoring subcommittee meetings).
    • When possible, help host or co-host instructor discussions.
    • Communicate challenges and opportunities with Carpentries staff liaison.

    Transition Timeline:

    1 year position (December 2017 - December 2018)

    • Mentored by both co-chairs of the subcommittee (Jamie & Marian) for the first month.
    • Until February 2018, work closely with the co-chair (Marian).


    • Collaborate with dedicated members of our community to mentor instructors and create a strong network.
    • Assist with improving and creating new resources for our instructor and mentoring communities.
    • Meet many other amazing Software and Data Carpentry instructors and instructors-in-training.
    • Gain and practice skills in community organization.
    • Learn more about how the Carpentries function as an organization.

    0 0
  • 11/20/17--16:00: Genomics Lesson Release
  • Thanks to a Herculean effort from our Maintainers, the long-awaited Data Carpentry Genomics lessons have now been published on Zenodo! These lessons were originally developed through a hackathon in 2014, and have gone through several major rounds of revision since then. We had an Issue Bonanza in August and a Bug BBQ in September, with contributions from dozens of community members.

    These contributions were critical to transforming the initial lesson drafts into a polished version, ready for teaching by any Carpentry instructor with a Genomics background. As with our previous lesson release, every contributor is an author, so thank you to all who have been involved!

    Extra thanks to Anita Schürch, Fotis Psomopoulos, Tracy Teal, and Amanda Charbonneau for their quick response time to pull requests and issues and their eagle-eyed proofreading. Also a special thank you to all of the Genomics Maintainers, who put in a huge effort to reorganize and clean up these lessons over the past several months.

    Overview of the Genomics Data Carpentry workshop
    This workshop teaches data management and analysis for genomics research including: best practices for organization of bioinformatics projects and data, use of command line utilities, use of command line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing.

    Please note that the R Genomics Lesson has not yet been released, as the Maintainers for that lesson are working on a major overhaul and re-focusing of those materials. If you are interested in being involved with that re-design, please check out the repo.

    Thanks again to everyone for helping get these lessons ready for teaching! We’re looking forward to seeing many more Genomics workshops happening soon and hearing back from you all about your experiences teaching these materials.

    0 0
  • 11/20/17--16:00: Meet the Candidates
  • Eight nominations have come in so far for the 2018 Steering Committee of the new, merged Carpentries.

    The nominees so far are:

    There is still time to put your name forward. Nominations will close on 1 December.

    If you are not sure if you are eligible to stand for election, or to vote in the election, please check out this blog post which has all the logistics.

    0 0

    Data Carpentry workshop, 1-3 November, 2017


    Conducting the first Data Carpentry workshop by members of NWUMafikeng campus and teaching my (Caroline Ajilogba) first workshop was a great task with support from NWU and our mentor, Anelda van der Walt. The support from the co-instructors Martin Dreyer (NWU Potchefstroom) and Amy Hodge (Stanford University), and from helper Bennett Kankuzi (NWU Mafikeng) was great. Other helpers from the R study group at Mafikeng’s NWU campus, like Olubukola Aremu and Ayansina Ayangbenro, were available to enhance the workshop.

    This workshop was planned for 2.5 days, with spreadsheets, OpenRefine, and the Intro to R on the first day; the remainder of the R lesson on the second day; and SQL on the last half day.

    The day before the workshop, Caroline and Bennett met to make sure nothing was left behind only to find out on the first day of the workshop that the venue had not been included on the workshop web site. Thanks to Martin and Amy who helped to salvage the situation and quickly updated the website, while Caroline sent e-mail to as many participants as she could who had sent messages to her requesting the venue.

    Another interesting issue was the attendance register which was not available immediately but was also sorted before the workshop started on the first day. I must really say thank you to the organizers especially in making the connecting plugs, the stickies and also the badges available. Thank you so much.

    The caterers were on time and participants were learning in a good atmosphere as some of them commented that it was a plus to come for a workshop and be taught and also given tea breaks and lunches.

    Ist November 2017

    The first day was great, as participants trooped in with enthusiasm and were being helped to settle down and have their software installed. Though the installation had its hitches here and there, I think that was great as we had to find solutions to how to handle the hitches and that for me was ‘learning’!!!

    We waited nearly an hour for everyone to arrive the first day so that we could do data downloads and OpenRefine installation together. This took quite some time, as there were many issues with the install, including quite a few who had trouble with the required Java installation. Because of this and a later fire alarm and power outage, we were very short on time for teaching on the first day.

    The instructors did a great job with the spreadsheet (Martin) and OpenRefine (Amy) lessons. Students later indicated they felt it was rushed, but when asked repeatedly if they had questions or wanted things repeated, they would say all was fine. We were supposed to cover the first part of R on the first day, but did not have time for that because of the delays.

    Because of these issues, it seemed the point of the spreadsheet and OpenRefine lessons and their importance to the overall workflow and subsequent use of R seemed to get lost on the learners. The modules make sense in this order, as it is the same as someone’s own workflow might be, but seems sometimes difficult to connect for the learners. More emphasis should be placed on making these connections. For example, from the worksheet where the raw data is can be better organized, to using OpenRefine where more cleaning up is done, to loading it into R where data is analyzed and other databases are used.

    Comments at the end of this day generally indicated that people were enjoying the workshop but that much of it was just too fast.

    2nd November 2017

    This morning was started with installation of R and RStudio. More of the students came with this software already installed, and many came early to do the installations, so that we were able to start right on time at 9am. Caroline started on a good note with R, but since we could not start off R on the first day, she thought she could be a bit fast after laying the foundation. When it was time to use data in R, she saw that for some it was fun, while others were trying to catch up. Since we planned to cover SQL on the third day, Caroline thought she had to go fast in order to cover everything in that one day. We also had technical difficulties on this day with the room technology, as the school’s desktop she was using kept shutting down and wiping everything so that she would have to reload RStudio, reinstall packages, create data frames, etc.

    Again, comments on the second day indicated enthusiasm for R, but that it was going too fast. We never had anyone say that we were going too slowly. At this point, we still had the ggplot lesson to do and had decided that we would continue with R on the last half day and skip the SQL lesson altogether. Caroline did an excellent job responding to comments from day 2 that she slow down, and day 3 seemed to finally hit the right pace for these students.

    3rd November 2017

    The third day was better than I expected as participants were still ready to work, though some had told me they were travelling early Friday morning and were not available. The workshop concluded with enthusiasm from participants about being part of the study group.

    We did not have any engagement from people on the etherpad at this workshop, and even some reluctance to use the sticky notes. Often only one or two people would put up a sticky but when helpers walked around, many more people actually needed and accepted help. Several students were doing well and consistently helping the learners sitting next to them.

older | 1 | .... | 4 | 5 | (Page 6) | 7 | 8 | 9 | newer