ICHS & UCSF Library team up to sponsor Software Carpentry workshops

In order for researchers to keep pace with the data deluge of modern science, they need to speak the language of computing. “In today’s tech-driven world, all trainees should now have the opportunity to learn basic programming skills,” says ICHS Director, Atul Butte; and to ensure the opportunity for researchers at UCSF to gain these skills, ICHS teamed up with the UCSF Library Data Science Initiative to offer a series of Software Carpentry workshops on campus.

Software Carpentry is a volunteer non-profit organization dedicated to teaching computing skills to researchers in science, engineering, medicine, and related disciplines since 1998. They recently offered two example-driven workshops at the UCSF Mission Bay campus, one focused on Python and one focused on R. Both workshops were held at capacity, with a waitlist as long as the attendees list – clearly exhibiting the need for such educational opportunities.

Both workshops introduced basic programming concepts such as variables, loops, and functions. They also covered some fundamentals in Unix, Git, and Github. One developer working at UCSF who TA’d the Python workshop, Geoffrey Boushey, was impressed with the Software Carpentry methodology, noting that “You can find good programming tutorials online, but setup and installation issues often prevent people from successfully running their first line of code. Software Carpentry did an unusually good job getting everyone across that initial hurdle.  At the end of the two day Python session, I felt that the workshop participants had the foundation to continue learning and contributing on their own.”

Over 200 students, staff, and postdocs have attended the six workshops offered during the past year; and feedback has been consistently positive, with over 90% of attendees saying they would recommend the course to a friend or colleague. The vast majority of participants also indicated that they took away new skills from the workshops that they could apply immediately to their research, which is the ultimate goal.

All Software Carpentry lesson materials are freely reusable under the Creative Commons – Attribution license, and the UCSF community is encouraged to make use of these materials. However, there is no substitute for practical experience when it comes to coding, so in addition to organizing these workshops, Ariel Deardorff at the UCSF Library is hosting working sessions for Python/R.

Individuals in both the research and medical practice communities on campus would benefit from a deeper knowledge of the complex data being generated in their field, and computation is the key. ICHS hopes to enhance the educational offerings at UCSF to include more data science and computing, and these workshops are just the beginning.