Introduction to Genomics Data Wrangling

BIDS Data Carpentry Workshop


August 6, 2018 to August 7, 2018
9:00am 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 Genomics Data Wrangling​​ 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: Caroline Cypranowska, Diya Das
Helpers: Jenna Baughman, Drew Hart, Dennis Sun

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. 

Caroline Cypranowska

PhD Student, Molecular and Cell Biology Department, UC Berkeley

Caroline Cypranowska is a PhD student in the Molecular and Cell Biology department in the lab of Ehud Isacoff. She uses functional genomics methods to study how motor neurons send and receive signals, using the fruit fly as her model organism. Caroline’s appreciation for computational biology and data science began during her previous work in the lab of Ahmet Yildiz, where she studied how molecular motors move cellular cargoes. Recognizing that programming and data science has helped her transition between diverse projects, Caroline volunteers with The Hacker Within to help others develop skills relating to data visualization, data science, and computation.