Teaching basic lab skills
for research computing

A Year to Build a Software and Data Carpentry Community at the University of Florida - The Impact of a Local Instructor Training Workshop on Building Computing Capacity

This January was the one year anniversary of our effort to bring regular Software Carpentry and Data Carpentry workshops to the University of Florida. These workshops are aimed at helping students, staff, and faculty gain the computing skills they need to be successful in our data-driven world. The Carpentries are international organizations that provide materials, instructor certification, and organization of multi-day workshops on basic software development and data analysis tools. In January 2016 a Software Carpentry instructor training workshop held at the University of Florida Informatics Institute provided the start of our efforts. Since then, instructors trained here as well as experienced instructors already in the UF community have held four workshops, reaching 98 participants, including 70 students, 14 staff and 11 faculty. The participants received training in programming languages like R and Python, version control with Git and GitHub, SQL database queries, OpenRefine, and Excel spreadsheets.


Graph of participants’ status at UF and word cloud of departments our participants hail from ( https://www.jasondavies.com/wordcloud/)

Such a robust and recurring workshop pattern is uncommon in the Carpentries community (but not unprecedented) and it is a result of the generosity and volunteerism of a combination of staff, faculty, students, and organizations at UF. Together we recognized that members of the UF community did not have enough opportunities to get hands-on experience with the software development and data analysis tools they need to be effective researchers, employees, and future job-seekers. In response, we have established a highly collaborative process for giving our fellow UF community members, whether they are students, staff, or faculty, this opportunity.

Our Year of Workshops

Though UF has a longer history with the Data and Software Carpentry communities, the start of this current program was an instructor training workshop held in January 2016 at the UF Informatics Institute (UFII). Dr. Ethan White provided funds (through a grant from the Gordon and Betty Moore Foundation) for UF to become a Software Carpentry Foundation affiliate member and to run an on-site training for instructors. Fourteen people from UF attended the 2016 workshop, 5 came from other Florida institutions, and 4 from elsewhere in the US and Canada. As a result of this workshop, 8 participants from UF became newly certified instructors for Software or Data Carpentry. Today there are a total of 10 active instructors at UF.

Several existing instructors, including Matthew Collins from the Advanced Computing and Information Systems Lab and Dr. François Michonneau from the Whitney Laboratory for Marine Bioscience, with the help of the newly trained instructors, then approached the director of the UF Informatics Institute, Dr. George Michailidis, for logistical support to run a Software Carpentry workshop in March 2016. While it was very successful, only 16 participants of 31 who signed up attended. We did not charge a registration fee, so we believe that many people simply did not show up when another commitment arose.

For our second workshop, held in August 2016 just before the start of the semester, Alethea Geiger from the UFII worked with the UF Conference Department to set up an account and a registration page that accepted credit card payments. We were able to charge a $30 registration fee which allowed us to pay for lunch during the workshop. This amount appears to strike a good balance between using a registration fee to encourage attendance and cover catering costs while not imposing serious financial hardship for participants with limited funding. However, the Conference Department web site did not let us smoothly deal with waitlists and capacity caps, and over the first weekend we had more than 35 people sign up for the workshop. In order to accommodate everyone, the Marston Science Library generously offered a larger room for the workshop. Everyone who registered attended this workshop.

In October 2016, we held our third workshop using the Data Carpentry curriculum. At this workshop we had the honor of having Dr. Kari L. Jordan as a participant. Dr. Jordan was recently hired as the Data Carpentry organization’s director of assessment and this was her first experience at a workshop. The registration process worked smoothly this time and were able to use the UFII conference room for the workshop and catering. Our most recent event was another Software Carpentry workshop held at the UFII in February 2017.

What it Takes

This group’s volunteered time as well as the coordination and support of three existing instructors and the logistics supplied by the Informatics Institute have made it possible to reliably host Carpentry workshops. It currently takes about 8 hours for the lead instructor to arrange instructors, helpers, and announcements and to respond to attendee questions. The staff at the UFII spend another 8 hours managing registration and preparing the catering. Instructors spend between 4 and 12 hours preparing to teach depending on whether they have taught the lesson before. Helpers who are already familiar with the content of the lessons usually don’t need further preparation but new helpers spend 4 to 8 hours reviewing lessons and software installation instructions. Combined, each workshop takes about 40 person-hours of preparation and over 80 person-hours to host. With the exception of the UFII staff, this time is all volunteered.

How do we keep people volunteering? There are a number of factors that go into maintaining volunteers’ motivation and momentum. We didn’t plan these in advance but now that we have them in place, we recognize them as the reasons we can continue to keep our community engaged and excited about putting on workshops.

  1. Instructor density - have enough instructors to get 3-6 people at each workshop without burdening anyone’s schedule
  2. Instructor cohesion - just like we suggest learners attend workshops with a buddy, instructors who come to the instructor training from the same department or discipline immediately make their own community of practice
  3. Instructor mentorship - a core group of senior instructors to guide initial workshops (note the plural) so new instructors can focus on the teaching experience without the logistical burdens
  4. Professional staff - find staff who organize workshops as part of their job to share the overhead of coordinating logistics
  5. Institution-level support - a single research lab or department doesn’t have enough people to do this on its own, doing it for the whole institution fits the needs of everyone and shares the work
  6. Follow-through - have supporting events and communities available for people to keep learning and keep their experience with the Carpentries fresh in their minds when it comes time to look for more instructors and helpers

Community Building After the Workshops

Some of the instructors have also been involved in creating and helping communities of learners on campus grow outside of workshops. Dr. Michonneau started a Meetup.com group for the Gainesville community focused on R. M. Collins is an advisor to the UF Data Science and Informatics student organization which holds about 12 evening workshops each semester focused on building data science skills for UF students. In spring 2017 Dr. Daniel Maxwell , Informatics Librarian for the Marston Science Library, re-invigorated the UF R Users mailing list and is holding weekly in-person drop-in sessions. These venues allow former workshop participants to continue learning the skills taught in the Carpentry workshops. They provide a space where participants can ask questions of and interact with their peers when they start using the tools taught in the workshops for their own research. This ongoing communal engagement is proving to be a key factor in making sure workshop participants continue to develop their abilities.

UF’s Impact on the Carpentry Community

UF has a long history and deep connections to the Carpentries. Data Carpentry was originally imagined during the 2013 COLLAB-IT meeting between the IT members of iDigBio (a large NSF-sponsored project centered at UF) and the other NSF biocenters. The attendees of this two-day workshop found that one important need shared by the biocenters was a training program for researchers, focused on the novice, to develop software skills and data literacy for analyzing their data. Some attendees were involved with Software Carpentry and decided to develop a curriculum based on Software Carpentry’s teaching principles. Dr. White, as well as iDigBio staff including Deborah Paul, Dr. Michonneau, and M. Collins were instructors, helpers, and attendees at the prototype Data Carpentry workshop held in May 2014 at NESCENT facility at Duke University. The second official Data Carpentry workshop was put on by the iDigBio project right here at UF.

Since this first engagement with the Carpentries, many other members of the UF community have participated in Software and Data Carpentry workshops across the country. Not all have participated in this most recent effort to run workshops here on campus and some have moved on to other institutions but they have all contributed to UF being a valued organization in the Carpentries community.

In addition to building its own workshop infrastructure, UF is helping to advance the Carpentry programs in the US and globally. Dr. White is a founding Data Carpentry steering committee member, a member of the Software Carpentry Advisory Council, and has developed a semester-long course based on Data Carpentry materials that he has taught twice as WIS6934 through the Department of Wildlife Ecology. Through the iDigBio project and support from Dr. White, M. Collins and D. Paul have taught workshops in Nairobi, Kenya and Santa Clara, Costa Rica before the Biodiversity Information Standards conferences in 2015 and 2016. M. Collins has also served as a mentor to instructors trained during the South African instructor training and along with D. Paul has more recently become a member of the formal Carpentry mentorship program providing on-going support to new instructors across the country.

Going Forward

The success of our group has been the result of the serendipitous meeting of interested UF community members, an existing international teaching community, and informal funding and infrastructure support. We are now looking for a way to formalize UF’s commitment to building capacity in informatics skills for its staff, students, and faculty through an on-going structure.

To start this process, a consortium of labs and institutes at the University of Florida have combined resources to sponsor a joint Gold Partnership with Software and Data Carpentry going forward. The UF partners are Dr. White’s lab, the UF Biodiversity Institute (via Dr. Pamela Soltis), iDigBio (via Dr. Soltis), and the UF Informatics Institute (via Dr. Michailidis). This partnership will provide annual instructor training opportunities to grow the instructor community

To continue the rest of the key parts of our success, we still need:

  1. A UF department or institute to adopt the goal of informatics capacity building for the UF community.
  2. An individual to be given the task of coordinating this goal across UF.
  3. Continuous funding and resources to provide for a pipeline of people capable of meeting this goal.

We believe UF has a unique opportunity to create a sustainable effort that cuts across individual departments and research labs. While existing on-book courses and department-specific programs are available, we have shown that there is need for hands-on, community-led informatics skill development for everyone on campus regardless of affiliation or discipline. By approaching this need at the university level we can maintain the critical mass of expertise and motivation to make our staff more productive, our students more employable, and our faculty’s research more innovative.

Acknowledgements

The following people have been active members of the UF instructor community and have volunteered their time in the past year by participating as instructors or helpers during the recent workshops:

Erica Christensen (*) - Ernest Lab, WEC
Matthew Collins - Advanced Computing and Information Systems Lab, ECE
Dave Harris (*) - White Lab, WEC
Allison Jai O’Dell (*) - George A Smathers Libraries
Sergio Marconi (*) - White Lab, WEC
François Michonneau - Martindale Lab, Whitney Laboratory for Marine Bioscience
Elise Morrison (*) - Soil and Water Sciences, IFAS
Deborah Paul (*) - Institute for Digital Information, Florida State University
Kristina Riemer (*) - White Lab, WEC
Henry Senyondo (*) - White Lab, WEC
Miao Sun - Soltis Lab, FLMNH
Brian Stucky (*) - Guralnick Lab, FLMNH
Shawn Taylor (*) - White Lab, WEC

(*) Trained at the January 2016 UF instructor training workshop

The following entities have contributed material support to our workshops or the Carpentries communities:

Advanced Computing and Information Systems Lab, Electrical and Computer Engineering
Earnst Lab, Wildlife Ecology and Conservation
Soltis Lab, Florida Museum of Natural History
University of Florida Biodiversity Institute
University of Florida Informatics Institute
White Lab, Wildlife Ecology and Conservation

We would also like to thank the incredible support provided by Alethea Geiger, Flora Marynak, and Deb Campbell at the UF Informatics Institute. They have managed the space, catering, registration, and financial aspects of our workshops for us and their services are the main reason we can provide so many workshops.

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