Matthew Berkeley
Software Developer at SIB Swiss Institute of Bioinformatics
Geneva, Geneva, Switzerland
Summary
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Rockstar🎓
Top SchoolMatthew Berkeley is a senior software and platform engineer based in Geneva with nine years of experience building scientific software and production platforms. He leads development of BUSCO, a widely used genome-completeness tool with over 17,000 citations, and has delivered interactive front-end dashboards and ML analyses to make genomic pipelines more actionable. His background in astrophysics and a PhD in Physics underpins strong expertise in large-scale data processing, Bayesian analysis, and high-performance Python code applied to multi-terabyte datasets. Matthew has practical experience across the stack—from automation and build/release engineering for major open-source bioinformatics recipes to Vue.js and Plotly visualizations—and has contributed automation improvements to the prominent bioconda-recipes repository. He blends experimental lab work and CAD/design experience from cryogenic and antenna characterization projects with production software practices, giving him a rare combination of hands-on hardware intuition and scalable software engineering. Colleagues rely on him to translate complex scientific requirements into reproducible, maintainable tools used by genomics and astrophysics communities worldwide.
9 years of coding experience
5 years of employment as a software developer
Master of Science (MSc), Space Studies, Master of Science (MSc), Space Studies at International Space UniversityBachelor of Arts (B.A.), Physics and Astrophysics, Bachelor of Arts (B.A.), Physics and Astrophysics at Trinity College, DublinDoctor of Philosophy - PhD, Physics, Doctor of Philosophy - PhD, Physics at The Catholic University of America
Irish, German, French
Stackoverflow
2,065reputation
168kreached
67answers
32questions
python
top-5%
Github Skills (13)
bioinformatics10
conda10
package-management10
python9
bash9
floating-point6
docker6
pdb6
tensorflow-datasets6
tensorflow6
multidimensional-arrays6
numpy6
dockers6
Programming languages (4)
Github contributions (5)
bioconda/bioconda-recipes
Jan 2020 - Dec 2022
Conda recipes for the bioconda channel.
Role in this project:
Automation Engineer / Build & Release Engineer
Automation Engineer / Build & Release EngineerContributions:33 reviews, 8 commits, 40 PRs in 2 years 11 months
Contributions summary:Matthew primarily contributed to the automation and build processes of the bioconda recipes. Their work involved updating and modifying recipes, specifically for the BUSCO bioinformatics tool. They made changes to build scripts, run test scripts, and configuration files related to the software package. The user's contributions also included updating versions, cleaning up recipes, and integrating new versions of software packages within the repository.
recipescondabiocondabioinformaticspackage-management
berkelem/WISEmapper
Feb 2018 - May 2022
Create full sky maps using the data from the four mid-infrared bands of the WISE telescope.
Contributions:916 commits, 3 PRs, 829 pushes in 4 years 4 months
skyplanetmidwisecarbon-emissions
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