Introduction to Shell, Git and R

BIDS Software Carpentry Workshop


June 11, 2018 to June 12, 2018
9:15am to 5:00pm
190 Doe Library
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Full details, the schedule and syllabus, and a link to register are available at the Introduction to Shell, Git and R Workshop website.

Software Carpentry and Data Carpentry aim to teach researchers basic research computing skills in hands-on workshops that cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. The course is aimed at graduate students and other researchers at UC Berkeley. Participants from outside the university are welcome to join as long as the Eventbrite permits, for reasons of capacity.  The goal of the workshop is to provide learners new to these tools with a basis for further exploration. 

Instructors: Diya Das, Rebecca Barter, Richard Barnes
Helpers: Jenna Baughman, Caroline Cypranowska

Contact: Diya Das (


Diya Das

BIDS Alum – BIDS Data Science Fellow

Diya Das completed her BIDS Data Science Fellowship in May 2019 and is now an Informatics Analyst II in Development Sciences Informatics at Genentech. At UC Berkeley, she was a postdoctoral researcher in the lab of John Ngai, where she studied regeneration in the olfactory epithelium, the tissue responsible for our sense of smell. She analyzed how olfactory stem cells contribute to both steady-state differentiation and injury-induced regeneration using single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin sequencing (ATAC-seq) and other genomics techniques. Her first co-authored paper, a collaboration between biologists, computer scientists, and statisticians, demonstrated the paths by which adult stem cells choose between neuronal and non-neuronal fates. Her second co-authored paper addressed how these stem cells mediate tissue regeneration after severe chemical injury. She's also contributed to methods papers for the analysis of scRNA-seq data (available here and here). 

Diya also facilitated opportunities for fellow researchers to develop their data science skills by coordinating the BIDS Software/Data Carpentry workshops (she was a Software Carpentry instructor and lesson maintainer), and organizing The Hacker Within, a weekly meeting for demonstration of scientific computing tools. She also led the Career Paths & Alternative Metrics Working Group (chaired by BIDS Senior Fellow Henry Brady), which addresses the career paths available to data scientists within academia.

Diya was formerly the Co-Director and Development Lead of Beyond Academia, a grad student and postdoc-run group whose mission is to encourage career exploration and help their peers nurture skills necessary to be competitive in their future careers. She was also an organizer of the 2017 CDIPS Data Science Workshop, which helped grad students and postdocs explore data science careers via mentored team projects, lectures, skills-based workshops, and company visits. 

Rebecca Barter

BIDS Alum – BIDS Data Science Fellow

Rebecca was a BIDS Data Science Fellow in the Department of Statistics at UC Berkeley, jointly advised by Professors Bin Yu and Jasjeet Sekhon. She spent her undergraduate years at The University of Sydney in Australia, from which she graduated in 2013 with a bachelor of science (advanced) and received the University Medal in Statistics. She worked problems in applied statistics related to data visualization (e.g. her R package, superheat, for developing beautiful and customizable heatmaps) and applications in health, such as in the utilization and exploration of observational electronic medical records.  Rebecca is currently co-authoring a book, The Elements of Data Science: A Perspective from Applied Statistics and Machine Learning, with her advisor, Bin Yu.  She was also interested in the process of communicating and learning best practices in data science via discussion, teaching, and writing.

Richard Barnes

PhD Student, Energy & Resources Group
University of California, Berkeley

Richard Barnes is a PhD student with the Energy & Resources Group and a Master's student with EECS. He develops and applies high-performance computational and mathematical techniques to better understand the complex interface of society and the environment. His major areas of research include continent-scale geomorphological modeling and ecoevolutionary game theory.