Data Carpentries Workshops 2025
The Institute for Modeling Collaboration and Innovation hosts Data Carpentries workshops each semester to improve data literacy and reproducible science. The Carpentries teaches foundational computational and data science skills to researchers worldwide. The spring workshop, Genomics in Unix and R, is quickly approaching but there is still space for participants to join. Attendees may register for U of I credit (CRN 79405 or 79403) or take the workshops without academic credit.
Course Title: Data Carpentries: Data Wrangling and Processing for Genomics (1 credit)
Course numbers: AVS 524-01 (CRN 79405) or BCB 524-01 (CRN 79403)
Instructors: James Van Leuven (I), Jeremiah Chapleski (I)
April 8-24, T/Th, 3:15-5:45pm
Course Description: Data Carpentries aims to teach researchers basic concepts, skills, and tools for working with data to get more done in less time, and with less pain. This hands-on workshop will cover basic concepts and tools, including best practices for the organization of bioinformatics projects and data, use of command-line utilities, use of command-line tools (shell and R) to analyze sequence quality and perform variant calling, connecting to and using high-performance computing services, and visualizing genomic data. The course is aimed at graduate students and other researchers but is open to all interested students. While the course is designed for learners who have no prior experience with the tools covered in the workshop, some familiarity with biological concepts (DNA, mutation, population variation) is useful. Participants must bring a laptop with a MacOSX, Linux, or Windows operating system (not a tablet, Chromebook, etc.) on which they have administrative privileges. For more information see https://j-chapleski.github.io/2025-04-08-IMCI-data_carpentries/.
Schedule:
Apr 8: Introductions, overview of sequencing platforms, data formats, and analysis tools
Apr 10: File manipulations in shell, cloud computing, installing command-line programs
Apr 15: Read mapping to reference genomes, processing output files
Apr 17: Read mapping to reference genomes, processing output files
Apr 22: Shell scripting and data wrangling in R
Apr 24: Plotting output data in R, understanding data quality
