Boise State’s Research Community Invited to a Hands-On Coding Workshop to Learn How to use Snakemake to Automate Data Analysis Pipelines
When: Wednesday, November 1
Where: Bergquist Lounge, Student Union Building
Time: 5:00 p.m. to 7:00 p.m.
Tell your friends (and your friends’ friends)!
Description: Many areas of natural and social science, as well as engineering, require data analysis that involves a series of transformations: filtering, aggregating, comparing to theoretical models, culminating in the visualization and communication of results. Because this process is rarely static, components of the analysis pipeline are subject to replacement and refinement, which makes reproducing computational results challenging. Legacy tools like GNU Make are useful for describing analyses as a directed network of transformations and prerequisites. Snakemake is a next-generation tool based on this concept and designed specifically for bioinformatics and other complex, computationally challenging analyses. This presentation will introduce a simple analysis, implement it in Snakemake, and discuss additional best practices for reproducible research.
NOTE: Some prior experience with the command line is assumed, and attendees are encouraged to follow along on their own computers.
About Byron Smith: Byron is a senior graduate student in the lab of Dr. Thomas Schmidt at the University of Michigan. He will be completing his PhD in Ecology & Evolutionary Biology during the summer of 2018. Byron attended a Software Carpentry workshop first as a learner, then as a teaching assistant, and was trained as an instructor in 2015. Since then, he has supported best practices for computation and analysis in the sciences by teaching workshops and contributing to lesson materials. Byron develops and uses bioinformatic tools and statistical models to integrate diverse data towards understanding complex microbial communities. His PhD research focuses on the ecology of starch fermentation by microbial communities in the gut.