Fabian Egli
Bioinformatician
Zurich, Zurich, Switzerland
Summary
🤩
Rockstar🎓
Top SchoolFabian Egli is a bioinformatician with 11 years' experience applying machine learning and software engineering to proteomics and computational biology across ETH Zürich, DTU and Balgrist Campus. He combines hands-on Python package development, web deployment (Flask/nginx), and data science with domain expertise in positional proteomics and degradomics, and has taught wet-lab methods alongside computational analyses. An active open-source contributor, he improved tooling for the widely used nf-core community and strengthened Biopython’s test suite and QA—work that highlights his focus on robust, reproducible scientific software. Based in Zurich, he brings a rare blend of experimental insight and backend/devops craftsmanship that helps translate complex biological workflows into reliable, maintainable pipelines.
11 years of coding experience
9 years of employment as a software developer
Master’s Degree, Cell/Cellular and Molecular Biology, Master of Science in Biologie, Master’s Degree, Cell/Cellular and Molecular Biology, Master of Science in Biologie at Eidgenössische Technische Hochschule ZürichLife Science Zurich Graduate School Molecular and Translational Biomedicine
English, German, German, French
Github Skills (16)
unit-testing10
bioinformatics10
biopython10
precommit10
python10
pre-commit-hook10
testing10
nextflow9
maintenance8
linter8
code-cleanup8
phylogenetics8
sequence-alignment7
cicd7
dockers7
Programming languages (18)
Github contributions (5)
nf-core/tools
Apr 2022 - Jan 2023
Python package with helper tools for the nf-core community.
Role in this project:
Backend & DevOps Engineer
Backend & DevOps EngineerContributions:158 reviews, 353 commits, 123 PRs in 9 months
Contributions summary:Fabian primarily focused on maintaining and improving the nf-core tools repository, a Python package for the nf-core community. Their contributions involved fixing bugs related to Nextflow configuration file parsing, specifically addressing issues with DAG file suffixes. The user also worked on streamlining the module update process, including refactoring code and implementing patch file generation. Furthermore, they made enhancements to the project by adopting and improving the code style through pre-commit hooks.
nf-corelinterpythonpipelinelinting
biopython/biopython
Jun 2021 - Aug 2022
Official git repository for Biopython (originally converted from CVS)
Role in this project:QA Engineer / Test Automation Engineer
QA Engineer / Test Automation EngineerContributions:20 reviews, 9 commits, 15 PRs in 1 year 2 months
Contributions summary:Fabian primarily contributed to the testing framework and test suite of the Biopython library. They added tests for Uniprot features, including description, evidence, and status qualifiers, verifying the correct parsing and representation of these features. The commits involved modifying existing test files and updating the NEWS and CONTRIB files to reflect the changes. Furthermore, the user fixed an issue related to calculating the height of clades in UPGMA trees, and added tests for them.
git-repositoryphylogeneticspythondnagenomics
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