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Libraries and CEHG co-sponsor Software Carpentry workshop

On July 23rd and 24th, 2015, Stanford's Center for Computational, Evolutionary and Human Genomics (CEHG) and Data Management Services co-sponsored a Software Carpentry Workshop on Stanford University campus. Software Carpentry is a non-profit volunteer organization focused on teaching researchers core computing skills for getting more done in less time and with less pain. The workshop had twenty-one participants, including graduate students, postdocs, and faculty, who all gathered in the teaching corner of the Branner Earth Sciences Library for two intense days of learning.

The instructors, Jennifer Shelton and Byron Smith – along with several helpers – guided the participants through a series of interconnected modules that covered topics such as:

  • Using the Unix shell and automating repetitive tasks
  • Programming and scientific computing in Python
  • Growing a program in a modular, testable way
  • Validating and testing software
  • Creating reproducible research workflows
  • Using Git and GitHub version control to track and share work efficiently

All instruction was done via live coding, with short tutorials alternating with practical exercises. The focus on hands-on-the-keyboard learning and frequent challenge questions to test the participants’ mastery of the material helped ensure an effective workshop that equipped the participants with many new skills that they can apply in their own research immediately. The participants also left the workshop with a much stronger basis for taking advantage of online resources for further learning.

The workshop was made possible through generous support from the University Libraries and CEHG, and the majority of participants were from CEHG-affiliated labs. Because many biologists were never trained to handle the enormous datasets that have become typical in genomics research, the Software Carpentry workshop offered a valuable opportunity to help lay the basis for more productive work practices.

Many thanks go to Amy Hodge at the Branner Earth Sciences Library for co-organizing the workshop, and to the instructors Jennifer Shelton and Byron Smith as well as the teaching assistants who all volunteered their time to help make this workshop a success.

About the Author

This post was contributed by Nina Overgaard Therkildsen, a postdoc in Steve Palumbi’s lab at Hopkins Marine Station (starting as an assistant professor at Cornell University in January 2016). Her research focuses on local adaptation and contemporary evolution in marine fish.