Benedict Paten
Associate Director
San Francisco Bay Area United States
Summary
🤩
Rockstar🎓
Top SchoolBenedict Paten is an Associate Director and professor in the UCSC Genomics Institute with 16 years of experience at the intersection of computational biology and software engineering. He combines deep academic training (PhD in Computational Biology from Cambridge) with hands-on backend development and test automation, contributing to scalable workflow engines like Toil that power large bioinformatics pipelines. At UCSC he advances research software, mentors teams, and drives reproducible, production-ready solutions for genomics. Notably, his open-source work includes fixing nuanced job-graph and serialization bugs and implementing mechanisms to pass return values across workflow targets—small technical changes that materially improve reliability in complex pipelines.
16 years of coding experience
8 years of employment as a software developer
Doctor of Philosophy (PhD) Computational Biology, Doctor of Philosophy (PhD) Computational Biology at University of CambridgeUniversity of California Santa CruzUniversity College London
Github Skills (5)
workflow-management10
python10
job-scheduling10
testing10
file-management9
Programming languages (10)
Github contributions (5)
DataBiosphere/toil
May 2015 - Jul 2020
A WDL, CWL and Python API supporting easy-to-use workflow engine. It is scalable, efficient and cross-platform (Linux/macOS).
Role in this project:
Back-end Developer & Test Automation Engineer
Back-end Developer & Test Automation EngineerContributions:169 commits, 65 PRs, 131 pushes in 5 years 3 months
Contributions summary:Benedict contributed to adding tests for the codebase, including a test for the static declaration of targets within the Toil workflow. The user implemented a mechanism for passing return values from a target's run function to child and follow-on targets using a mapping system. The code changes reveal an involvement in fixing bugs related to job graph connectivity, service job serialization, and ensuring that file writes are properly synchronized.
linuxmacospythonwdlworkflow-engine
benedictpaten/jobTree
Jan 2011 - Apr 2015
Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)
Contributions:242 commits, 5 PRs, 7 pushes in 4 years 3 months
python
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