Fostering a Reproducible Research Culture

Jeremy Leipzig

3.19.15

RR in the Field

Why’s of Reproducibility

Sanity

Reuse

Redundancy

Evaluation

Reproducible interests

Sweave & knitr

Ties that bind

Why Snakemake?

Addresses Makefile weaknesses: Difficult to implement control flow

No cluster support

Inflexible wildcards

Too much reliance on sentinel files

No reporting mechanism

Keeps the good stuff: Implicit dependency resolution

Johannes Köster

Self-Reporting Workflows

The Future

Virtual Machine Container

Dockerized analyses?

Sweave

Snakemake

Container

Acknowledgements

BiG Deanne Taylor Batsal Devkota Noor Dawany Perry Evans Juan Perin Pichai Raman Ariella Sasson Hongbo Xie Zhe Zhang

TIU

Jeff Pennington

Byron Ruth

Kevin Murphy

DBHi

Bryan Wolf

Mark Porter