John Eppley
Senior Software Engineer at University of Hawaii at Manoa
Davis, California, United States
Summary
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Rockstar🎓
Top SchoolJohn Eppley is a senior software engineer based in Davis, CA with 12 years of focused experience building bioinformatics and metagenomics systems and high-performance computing pipelines. He has a long research-to-production arc spanning UC Berkeley and MIT to his current role at the University of Hawaii, combining deep domain knowledge in computational biology with pragmatic software engineering. A regular contributor to the Snakemake workflow project, he has improved IO benchmarking, checkpoint diagnostics, and remote file access performance—skills that translate to reliable, scalable analysis workflows. Trained in physics and bioengineering, he brings a quantitative mindset to designing robust, test-covered systems that bridge research and operational bioinformatics.
12 years of coding experience
6 years of employment as a software developer
Bioengineering, Bioengineering at University of California, BerkeleyBS, Physics, BS, Physics at Haverford CollegePhysics, Mathematics, Physics, Mathematics at Rice University
Stackoverflow
561reputation
36kreached
25answers
0questions
Github Skills (23)
rep10
pytest10
python10
testing10
repr10
fileio10
file-handling10
file-processing10
workflow-management10
file-access10
debug9
debugging9
ftp9
performance-optimization9
sftp9
Programming languages (8)
Github contributions (5)
snakemake/snakemake
Nov 2018 - Jul 2021
This is the development home of the workflow management system Snakemake. For general information, see
Role in this project:
Back-end Developer
Back-end DeveloperContributions:3 reviews, 8 commits, 14 PRs in 2 years 8 months
Contributions summary:John primarily contributed to bug fixes and improvements within the Snakemake workflow management system. They addressed issues related to IO counting in the benchmark, expanded error messages for checkpoint functionality, and optimized the cleanup process of the workflow directory. Additionally, the user implemented connection pooling for SFTP and FTP, demonstrating an understanding of remote file access optimization. They also addressed several specific issues by providing bug fixes and tests.
management-systemworkflow-management-systemgeneral-informationreproducibilitysnakemake
jmeppley/du_histogram
Jul 2017 - Feb 2020
Contributions:2 releases, 12 pushes, 2 branches in 2 years 6 months
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