All decks
  • Fachprojekt: Reproduzierbare Datenanalyse mit Snakemake

  • Reproducible data analysis with Snakemake

    Data analyses usually entail the application of many command line tools or scripts to transform, filter, aggregate or plot data and results. With ever increasing amounts of data being collected in science, reproducible and scalable automatic workflow management becomes increasingly important. Snakemake is a workflow management system, consisting of a text-based workflow specification language and a scalable execution environment, that allows the parallelized execution of workflows on workstations, compute servers, clusters and the cloud without modification of the workflow definition. Since its publication, Snakemake has been widely adopted and was used to build analysis workflows for a variety of high impact publications. With about thousands of homepage visits per month, it has a large and stable user community. This talk will show how Snakemake can be used to easily document, execute, and reproduce data analyses.

  • Snakemake Tutorial

    Tutorial slides that complement https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html

  • Snakemake in short

  • Snakemake lightning talk

    GCCBOSC 2018

  • Snakemake live demo

    GCCBOSC 2018

  • Snakemake Poster GCCBOSC 2018

  • Poster Rust-Bio 2018

  • Snakemake

    SPHN Workflow Interoperability Workshop

  • The road to reproducibility - Snakemake in 2017

    Keynote at Snakemake Day 2017 in Amsterdam (https://snakemake-days.github.io)

  • Snakemake+Bioconda (short)

    Short introduction to reproducibilty with Snakemake and Bioconda

  • Workflow and tool management

    Keynote at AEBC 2017

  • Reproducible and scalable data analysis with Snakemake

    Non-CS introduction to Snakemake and Bioconda at Forschungszentrum Jülich.

  • Snakemake Tutorial

    Tutorial slides

  • A Bayesian model for single cell gene expression analysis with MERFISH data

    Talk at CWI Scientific Meeting, Dec 9, 2016

  • Reproducible and scalable data analysis with Snakemake

    Snakemake introduction at CWI

  • Wege aus der in-silico Reproduzierbarkeitskrise

    Keynote at Helmholz workshop "Nachhaltige Softwareentwiklung"

  • Rust-Bio

    Invited talk about Rust-Bio at the Mozilla Rust Bay Area Meeting.

  • Snakemake and Bioconda: A Tutorial

    Non-CS introduction to Snakemake and Bioconda by Alex

  • Genotyping somatic insertions and deletions

    PROSIC talk for HiTSeq 2016

  • Bioconda

    Presentation of Bioconda for DTL

  • Snakemake and Bioconda

    Non-CS introduction to Snakemake and Bioconda at Leeselab.

  • A Bayesian model for gene expression analysis with MERFISH data

  • Introduction to Snakemake

    AbVitro visit 2016

  • Introduction to Snakemake

    Presented at the Broad Institute, Boston, October 2015

  • Snakemake Tutorial

    Tutorial slides for GCB 2015