Brad Chapman
Principal Data Science Architect
Somerville, Massachusetts, United States
Summary
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Rockstar🎓
Top School
Top expert inComputational Genomics and Bioinformatics Workflow Development
Brad Chapman is a Principal Data Science Architect with 25 years of experience building scalable bioinformatics tools, infrastructure, and reproducible workflows for academia and industry. Based in Somerville, MA, he combines a PhD in Plant Biology with deep engineering chops—contributing to flagship open-source projects like Biopython, IPython/ipyparallel, and MultiQC while packaging and deploying tools via Bioconda and CloudBioLinux. At Ginkgo Bioworks he translates complex biological problems into robust data pipelines and CWL-compatible workflows, drawing on prior leadership at Harvard and MGH. His strengths lie at the intersection of back-end development, DevOps, and scientific rigor: improving parser robustness, Docker/CWL integrations, and workflow engine reliability. Not obvious from job titles alone, he remains an active hands-on contributor who has implemented SQLite/BioSQL support, improved heartbeat and logging for parallel systems, and added nuanced parsing and plotting features for CNV and coverage analyses.
25 years of coding experience
14 years of employment as a software developer
University of GeorgiaBachelor of Science (BS) Plant Molecular Biology, Bachelor of Science (BS) Plant Molecular Biology at Michigan State University
Stackoverflow
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Github Skills (65)
variants10
python10
package-management10
bash10
ipython10
data-parsing10
gatk10
parallel-computing10
fabric10
reporting-services10
pandas10
dockers10
numpy10
workflow-description-language10
mu10
Programming languages (24)
Github contributions (5)
bcbio/bcbio-nextgen
Jul 2010 - Jan 2020
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Role in this project:
Back-end Developer & Bioinformatics Analyst
Back-end Developer & Bioinformatics AnalystContributions:5009 commits, 207 PRs, 2670 pushes in 9 years 7 months
Contributions summary:Brad primarily contributed to the bcbio-nextgen bioinformatics pipeline, focusing on enhancing and extending its capabilities. They implemented code changes to handle issues with colons in sample/batch names, improved documentation for CWL functionalities, and implemented features related to variant calling and data standardization. Furthermore, the user addressed build and performance issues, contributing to the stability and usability of the pipeline.
scalablecallingrnaseqvariant-callinggenomics
chapmanb/cloudbiolinux
Dec 2008 - Mar 2020
CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
Role in this project:Back-end & DevOps Engineer
Back-end & DevOps EngineerContributions:1752 commits, 68 PRs, 510 pushes in 11 years 5 months
Contributions summary:Brad's contributions centered around configuring and automating the installation of bioinformatics tools and related dependencies on a Linux system. They worked on creating installation scripts for several programs, including FreeNX, and automated the setting of environmental variables to facilitate their use. The user also handled the creation and configuration of anaconda environments and their associated dependencies. Their work demonstrates a focus on streamlining the infrastructure for a reproducible and easy-to-use environment.
analysesmachinesbioinformaticsconfigurebiological
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