My Profile Photo

Pascal Sturmfels


Studying computer science at University of Michigan; interests include machine learning in medicine, approximation algorithms, and iOS development.


The Lair

Sleuth Reproducibility is critical to experimental results. To this end, many RNA-seq papers archive their data in the Sequence Read Archive. This data is theoretically enough to reproduce the results of the original paper; doing so is intractable due to the computational power required to process the results and the computational biology background needed to select the right computational tools.

The Lair is a system and website that the Pachter Lab and I made to address this problem: It hosts interactive re-analyses of publicly available RNA-seq data. The development of this system work was published in an article in BMC Bioinformatics.

The reason the Lair is so powerful is that the re-analyses of papers are performed automatically by a back-end Snakemake build-system that uses kallisto and sleuth. The website allows anyone to inspect the results of RNA-seq experiments without needing computing power or extensive knowledge of alignment/analysis tools.

You can take a look at the Lair repo to see the source for the website. I designed the website, as well as the majority of the back-end system behind it.

The workflow of the back-end system is diagramed below: Lair Workflow