Jared Lumpe
Senior Bioinformatics Engineer
San Francisco, California, United States
Summary
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Rockstar🎓
Top SchoolJared Lumpe is a Senior Bioinformatics Engineer in San Francisco with 11 years of experience building production-ready computational biology software and pipelines. He specializes in Python-based bioinformatics, having developed GAMBIT—a pathogen identification tool used by public health labs and published in PLoS One—and now leads pipeline design and infrastructure work for multiplexed PCR assays at Cepheid. Jared brings a strong engineering discipline to bioinformatics, introducing automated testing practices (including a unit testing framework for Snakemake) and improving maintainability across team codebases. He also contributes to open-source scientific software, notably improving SymPy’s code generation internals, demonstrating attention to correctness in complex symbolic tooling. Colleagues rely on him to bridge rigorous research methods (ensemble modeling, optimal experimental design) with reproducible, deployable software for diagnostics.
11 years of coding experience
8 years of employment as a software developer
Bachelor of Science (BS) Cellular and Molecular Biology, Bachelor of Science (BS) Cellular and Molecular Biology at Santa Clara UniversityMaster's degree Biological and Medical Informatics, Master's degree Biological and Medical Informatics at University of California, San Francisco
Github Skills (12)
computer-algebra10
code-generation10
python10
computer-algebra-system10
data-structure9
math9
algorithm9
data-structures9
mathematics9
algorithms9
testing8
pytest8
Programming languages (19)
Github contributions (5)
sympy/sympy
Jun 2018 - Nov 2018
A computer algebra system written in pure Python
Role in this project:
Back-end Developer
Back-end DeveloperContributions:18 commits, 5 PRs, 18 comments in 5 months
Contributions summary:Jared primarily contributed to the `sympy/sympy` repository by modifying and enhancing the code generation modules. Their work involved accounting for free symbols within `codegen.ast.CodeBlock` and ensuring the correct handling of assignment types. Further contributions included refactoring the `ast.Token` class and associated documentation, as well as improving the `CodeBlock.cse()` method to prevent conflicts with existing symbols. These changes directly improved the functionality, correctness, and maintainability of the code generation capabilities of SymPy.
mathpythonsciencecomputer-algebra-systemalgebra
jlumpe/pycyt-old
Sep 2015 - Nov 2022
Contributions:71 pushes, 11 branches, 9 issues in 7 years 2 months
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