About this site and course

Author

Jelmer Poelstra

Published

February 19, 2024

This is the GitHub website for the course Practical Computing Skills for Omics Data (PLNTPTH 6193), a 2-credit Independent Studies course at Ohio State University during the Spring semester of 2024.

The course is taught by by Jelmer Poelstra from OSU’s Molecular and Cellular Imaging Center (MCIC) for the Department of Plant Pathology.

Course description

As datasets have rapidly grown larger in biology, coding has been recognized as an increasingly important skill for biologists. This is especially true in “omics” research with data from e.g. genomics and transcriptomics, which usually cannot be analyzed on a desktop computer, where most software has a command-line interface, and where workflows can include many steps that need to be coordinated.

In this course, students will gain hands-on experience with a set of general and versatile tools for data-intensive research. The course will focus on foundational skills such as working in the Unix shell and writing shell scripts, installing software, and submitting jobs at a compute cluster (the Ohio Supercomputer Center), and building flexible, automated workflows. Additionally, the course will cover reproducibly organizing, documenting, and version-controlling research projects. Taken together, this course will allow students to reproduce their own research, and enable others to reproduce their research, with as little as a single command.

More information

Topics taught

  • Unix shell basics and tools
  • Shell scripting
  • Computing at OSC with Slurm batch jobs and Conda software management
  • Version control with Git and GitHub
  • Project documentation with Markdown and project organization
  • Reproducible workflows with Nextflow

Course books

CarmenCanvas website

If you are a student in this course, you should also refer to the CarmenCanvas site for this course.

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