Silas Kieser
Senior Research Assistant at University of Bern
Vevey, Vaud, Switzerland
Summary
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Rockstar🎓
Top SchoolSilas Kieser is a senior research assistant and metagenome researcher with 11 years of experience bridging bioinformatics research and software engineering. Trained at EPFL and now pursuing a PhD in Biomathematics/Bioinformatics, he has deep expertise in exploratory analysis of high-throughput sequencing data (single-cell RNA-seq, Hi-C, metagenomics) and has autonomously built production-ready analysis pipelines. His master's work at Nestlé linking pediatric microbiota to intestinal disorders led to a published manuscript and speaks to his ability to take projects from hypothesis to publication. On GitHub he contributes to Bioconda packaging and DevOps for widely used bioinformatics tools, showing practical experience in software distribution and reproducible research. Based in Vevey, Switzerland, he balances rigorous computational skills (Python, R, bash, C++) with hands-on contributions that improve tool accessibility for the community.
11 years of coding experience
Doctor of Philosophy - PhD, Biomathematics, Bioinformatics, and Computational Biology, Doctor of Philosophy - PhD, Biomathematics, Bioinformatics, and Computational Biology at University of GenevaEngineer's degree, Bioengineering and Biocomputation, Engineer's degree, Bioengineering and Biocomputation at Ecole polytechnique fédérale de LausanneBachelor of Science (B.Sc.), Bioengineering and Biocomputation, Bachelor of Science (B.Sc.), Bioengineering and Biocomputation at EPFL (École polytechnique fédérale de Lausanne)
German, French, English, Italian
Stackoverflow
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Github Skills (12)
bioinformatics10
conda10
bash10
package-management10
build-automation10
scripting9
shell9
script9
sh9
python8
docker6
dockers6
Programming languages (22)
Github contributions (5)
bioconda/bioconda-recipes
Dec 2018 - Oct 2022
Conda recipes for the bioconda channel.
Role in this project:
DevOps Engineer & Package Maintainer
DevOps Engineer & Package MaintainerContributions:62 reviews, 66 commits, 125 PRs in 3 years 10 months
Contributions summary:Silas primarily contributed to maintaining and updating conda recipes for the bioconda channel. They modified build scripts for various bioinformatics tools like `cat`, `metagenome-atlas`, and `magpurify`, often involving changes to installation processes and dependencies. Significant effort was dedicated to integrating and updating software packages such as `busco` and `kofamscan`. The user also made general infrastructure improvements and dependency updates.
recipescondabiocondabioinformaticspackage-management
metagenome-atlas/supp_data_atlas
Apr 2019 - Sep 2023
Contributions:3 pushes, 2 branches in 4 years 6 months
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