J Caporaso
Professor at Cymis Benefit Corporation
Flagstaff, Arizona, United States
Summary
🤩
Rockstar🎓
Top SchoolJ Caporaso is a Professor and computational biologist with 18 years of experience building widely used microbiome data science infrastructure, best known as a lead developer and PI on the QIIME 2 platform. He bridges academia and industry as faculty at Northern Arizona University and TGen North and as Chief Science Officer at Cymis, translating microbiome technologies into clinical and product contexts. Trained with a Ph.D. in biochemistry and dual undergraduate degrees in computer science and biochemistry, he blends deep wet-lab understanding with production-grade Python engineering. His open-source impact includes foundational contributions to QIIME 1/2 and practical enhancements to IPython’s display system, reflecting a knack for making complex bioinformatics tools accessible and reproducible. Based in Flagstaff, he repeatedly ships robust tooling that supports multi-omics workflows and clinical applications—work that often hides the substantial engineering required to make research software trusted in practice.
18 years of coding experience
10 years of employment as a software developer
Ph.D., Biochemistry, Computational Biology, Ph.D., Biochemistry, Computational Biology at University of Colorado AnschutzB.A., Biochemistry, B.A., Biochemistry at University of Colorado Boulder
English, French
Github Skills (19)
notebook10
develop10
python10
testing10
work-flow10
ipython10
workflow-engine10
workflow-automation10
web-framework10
documentation10
jupyter9
command-line-interface9
markdown9
command-line9
markdown-it9
Programming languages (17)
Github contributions (5)
biocore/qiime
Aug 2009 - Dec 2022
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Role in this project:
Back-end Developer & Technical Writer
Back-end Developer & Technical WriterContributions:5 releases, 2 reviews, 2993 commits in 13 years 6 months
Contributions summary:J's contributions primarily focused on refining the codebase for the QIIME software repository. They addressed bugs related to parameter processing and the selection of data types. The user also updated the documentation and added examples, which improves the usability of the code and the comprehensibility of the software features.
qiimemicrobiomeanalysis
rachis-org/rachis
Jan 2016 - Dec 2022
Rachis Framework (Formerly Known as QIIME 2 Framework (Q2F))
Role in this project:Back-end Developer
Back-end DeveloperContributions:3 releases, 26 reviews, 46 commits in 6 years 11 months
Contributions summary:J primarily contributed to the core framework of QIIME 2. Their work includes implementing the initial QIIME 2 framework, fixing bugs, and adding features like view type annotation handling to markdown workflows. They also made changes to the SDK and execution modules, improving functionality. Furthermore, the user contributed to testing and documenting these features, indicating involvement across multiple facets of the project's development.
qiime
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