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Nov. 1 Coding Workshop: Snakemake, a Tool for Computationally Challenging Analyses

By: Cienna Madrid   Published 7:28 am / October 31, 2017

Join the Department of Research Computing in a hands-on coding workshop for Snakemake, a next-generation tool designed specifically for bioinformatics and other complex, computationally challenging analyses.

The workshop will be held from 5-7 p.m. Wednesday, Nov. 1, in the Student Union Bergquist Lounge. Attendees are asked to bring their laptops. This event is free and open to the public, however, some prior experience with the command line is assumed, and attendees are encouraged to follow along on their own computers. Free pizza will be provided.

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.

Byron Smith, a software carpentry instructor and doctoral candidate from the Department of Ecology and Evolutionary Biology at the University of Michigan, will lead the workshop. Smith develops and uses bioinformatic tools and statistical models to integrate diverse data towards understanding complex microbial communities. His doctoral research focuses on the ecology of starch fermentation by microbial communities in the gut.

About the CLUSTER community meetings: The CLUSTER (Computational Learning Using Scientific Tools to Educate Researchers) community meetings are offered to provide all of Boise State’s research community a campus-wide forum for learning about computationally enabled research.