Damien Goutte-gattat
Research Software Engineer at German BioImaging - Gesellschaft für Mikroskopie und Bildanalyse e.V.
London, England, United Kingdom
Summary
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Rockstar🎓
Top SchoolDamien Goutte-gattat is a Research Software Engineer with 14 years of experience at the intersection of biology, ontologies, and open-source tooling, currently based in London and working with German BioImaging. With a PhD in Molecular Biology, he has led ontology engineering and tooling at Cambridge—co-editing major resources like the Drosophila Anatomy Ontology, Uberon and the Cell Ontology—and built the Ontology Development Kit and SSSOM-Java reference implementation. He pairs deep domain knowledge in genetics and microscopy with pragmatic software skills, contributing parsers and QA improvements to widely used bioinformatics projects such as Biopython and enhancing the Protégé desktop experience including arm64 macOS packaging. Damien’s work blends research-grade reproducibility and automation (ImageJ plugins, curation pipelines) with long-standing open-source stewardship, and he runs an independent forge for his projects. Colleagues describe him as a quietly productive engineer who surfaces practical fixes for subtle data and deployment edge cases.
14 years of coding experience
13 years of employment as a software developer
Doctor of Philosophy - PhD Molecular Biology, Doctor of Philosophy - PhD Molecular Biology at Université Grenoble Alpes
Stackoverflow
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Github Skills (14)
unit-testing10
bioinformatics10
javas10
biopython10
sequence-alignment10
parsing10
python10
file-parsing10
java10
file-format10
file-parser10
testing10
macos8
build-automation8
Programming languages (17)
Github contributions (5)
protegeproject/protege
Jul 2021 - Jan 2023
Protege Desktop
Role in this project:
Full-stack Developer
Full-stack DeveloperContributions:6 releases, 3 reviews, 29 commits in 1 year 6 months
Contributions summary:Damien primarily contributed to the Protégé Desktop project by enhancing its functionality and improving its build and deployment processes. They focused on improving the user experience by restoring a tab-triggered auto-completion feature and fixing an issue related to highlighting OWL entities. Moreover, the user added support for the arm64 architecture for the macOS package, including simplification of the build layout, and updated various launcher scripts. They also addressed a security issue related to the Rio TriX parser.
semanticsknowledge-graphelectronowlobo
biopython/biopython
Aug 2019 - Jan 2023
Official git repository for Biopython (originally converted from CVS)
Role in this project:Back-end Developer & QA Engineer
Back-end Developer & QA EngineerContributions:8 reviews, 25 commits, 7 PRs in 3 years 6 months
Contributions summary:Damien contributed to the Biopython project by implementing new parsers and writers for the "xdna", SnapGene, and Gene Construction Kit (GCK) file formats. They also added test cases to ensure the correct functionality of the new parsers, including handling edge cases and potential data loss scenarios during writing. The user further integrated these new formats within the existing SeqIO framework, and also made improvements to the existing modules.
git-repositoryphylogeneticspythondnagenomics
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