My Work with the Penn-CHOP Microbiome Program

Hereunder is a list of some of the more presentable (and open source) projects I've worked on as a developer with the Penn-CHOP Microbiome Program (PCMP). See also the new MicroBioCode website!
I've contributed to all these projects to varying degrees. A few I built from scratch, others I've updated and maintain, and to some I've just made minor additions. Use the buttons on each card to see my contributions (my GH username is Ulthran).

More Details

The PCMP is comprised of many labs across the University of Pennsylvania and the Children's Hospital of Philadelphia, each of which has some connection to the study of human or animal microbiomes. The software needs of these labs range from high (a core of PhD bioinformatians who need performant and reliable big data pipelines as well as the flexibility to perform fine grained exploratory analyses) to medium (mostly wet lab experiments that need follow up analysis with user-friendly and reproducible pipelines) to low (mostly wet lab and clinical work, lab members who like to live in spreadsheet land but might want a few tasks automated). It's my job as the developer for the PCMP (I'm the first and so far only pure developer for the program) to create, enhance, and maintain software for the labs in the program. If you have any unanswered questions about my work with the PCMP please reach out, I love talking about this stuff.

Metagenomics Pipelines

Most of the work I do with the PCMP involves getting sequencing data from one form and transforming it to another. Doing this in a way that is well documented, reproducible, and performant is critical for being able to publish the results of downstream analysis.

Statistical Packages

Some of the cleanest and most straightforward work I do is in helping researchers developing a new statistical method to create a well-packaged software solution to accompany publication. Easy to use and install statistical packages help drive citations for the paper.

Utility Libraries

Some methods just aren't worth publishing, whether they're too mundane or too unique to bother. But these methods still need to be reliable and easy to use internally.

Services

I've built and modified some services for tracking and storing sequencing data as it passes through the PCMP.

DevOps Tools

I've developed some tools for improving bioinformatics software development. A lot revolves around the Sunbeam ecosystem for new extensions and testing.