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.
26 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
package-management10
python10
bash10
ipython10
data-parsing10
gatk10
parallel-computing10
fabric10
reporting-services10
pandas10
dockers10
numpy10
workflow-description-language10
mu10
Programming languages (28)
Github contributions (5)
chapmanb/bcbb
Dec 2008 - Nov 2021
Incubator for useful bioinformatics code, primarily in Python and R
Role in this project:
Back-end Developer
Back-end DeveloperContributions:1216 commits, 18 PRs, 133 pushes in 13 years 1 month
Contributions summary:Brad contributed to the development of the bcbio-nextgen pipeline, adding functionality for processing and managing sequencing data. Their work involved implementing features for quality control, processing sample data, and generating reports. Additionally, the user was involved with improvements for aligning and genotyping code, demonstrating expertise in bioinformatics workflows. The user's work indicates familiarity with GATK and other related tools to perform advanced operations.
bioinformaticspython
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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