Introduction to Snakemake The seminar introduces Snakemake, a reproducible research software favored for its user-friendly interface and scalability. Attendees are encouraged to clone the repository containing presentation materials and example workflows while setting up Miniconda for code execution.
Personal Journey into Bioinformatics After graduating from MIT, the speaker worked as a bioinformatician at At Vitro in Boston where they created an analysis pipeline using Snakemake. The speaker's early experiences with bugs led them to collaborate closely with Johannes Custer, who later offered them a postdoc position after becoming a professor.
What is Snakemake? Snakemake is designed for creating scalable workflows that can run jobs in parallel across multiple cores or clusters. It has gained popularity within the bioinformatics community due to its clean syntax and interoperability with Python—making it easy for users familiar with Python programming.
Inspiration Behind Workflow Management Inspired by GNU Make, which manages dependencies between files during compilation processes, Snakemake automates workflow management through declarative rules specifying input-output relationships without requiring complex coding structures like traditional imperative languages do.