Martin Rippin
Bioinformatician System Developer
Stockholm, Sweden
Summary
🤩
Rockstar🎓
Top SchoolMartin Rippin is a seasoned bioinformatician and systems developer with 15 years of experience building reproducible, automated pipelines and production-grade infrastructure for research and diagnostics. Based in Stockholm, he combines deep domain expertise in genomics workflows (Snakemake, Nextflow, WDL/Cromwell) with hands-on DevOps—Docker, Kubernetes, Ansible, Slurm—and backend work in Go and Python to deliver integrated solutions. He contributes to prominent open-source bioinformatics projects (notably Snakemake, Cutadapt, pysam and Bioconda), focusing on robustness, Python 3 modernization, and packaging that makes tools reliably deployable in clinical and research settings. Comfortable spanning lab methods and code, he brings a PhD-level understanding of biology together with practical system integration skills to turn complex sequencing workflows into maintainable, automated services.
15 years of coding experience
4 years of employment as a software developer
Biology, Biology at University Centre in SvalbardKTH Royal Institute of TechnologyBiotechnology, 1.0 (excellent), Biotechnology, 1.0 (excellent) at Uppsala universitetDoctor of Philosophy (PhD), Biology, 0.0 (summa cum laude), Doctor of Philosophy (PhD), Biology, 0.0 (summa cum laude) at Universität zu KölnDiplom-Ingenieur (Dipl.Ing.), Biotechnology, 1.5 (excellent), Diplom-Ingenieur (Dipl.Ing.), Biotechnology, 1.5 (excellent) at Technische Universität Berlin
German, English, Swedish, French, Norwegian
Github Skills (29)
algorithm10
algorithms10
debug10
snakemake10
python10
package-management10
testing10
bash10
conda10
build-automation10
cython10
bioinformatics10
workflow-management10
back-end-development9
makefile9
Programming languages (23)
Github contributions (5)
marcelm/cutadapt
Sep 2010 - Jan 2023
Cutadapt removes adapter sequences from sequencing reads
Role in this project:
Back-end Developer
Back-end DeveloperContributions:3 releases, 17 reviews, 1982 commits in 12 years 6 months
Contributions summary:Martin's contributions focused on modifying and enhancing the `cutadapt` library, a tool for removing adapter sequences from sequencing reads. They made improvements to the core algorithm, and added features by modifying the underlying code. The changes are primarily focused on the core functionality of the code.
sequencepythonbiocondafastasequencing
pysam-developers/pysam
Nov 2011 - Oct 2022
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
Role in this project:Backend Developer & DevOps Engineer
Backend Developer & DevOps EngineerContributions:10 reviews, 78 commits, 20 PRs in 11 years
Contributions summary:Martin primarily focused on modernizing the codebase and making it compatible with Python 3. This included refactoring code to avoid deprecated features like `PyString_FromStringAndSize` and `PyFile`, and ensuring proper string handling with Python 3's `bytes` and `str` types. Additionally, the user made improvements to the build process and corrected indentation issues to improve readability and compatibility.
bcftoolsapipythonbcfpowers
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