Elmar Pruesse
HPC Lead Engineer at National Jewish Health
Denver, Colorado, Germany
Summary
🤩
Rockstar🎓
Top School
Top expert inComputational Genomics and Bioinformatics Workflow Development
Elmar Pruesse is an HPC Lead Engineer and bioinformatics scientist with 11 years of experience building robust, reproducible computational pipelines for genomics and high-performance clusters. Based in Denver with roots in Germany, he combines a PhD in bioinformatics and a strong CS background to bridge research-grade analysis and production engineering. He leads HPC infrastructure and workflow reliability at National Jewish Health while contributing upstream to major open-source projects like MultiQC, Snakemake, Bioconda and the future R package, improving reporting, packaging, and scheduler compatibility. His contributions often focus on practical interoperability—fixing edge-case bugs, adding assembly statistics and job-id-aware error handling, and adapting tools to LSF/OpenLava and macOS environments. Former postdoc and industry bioinformatician, he brings both academic rigor and hands-on DevOps instincts to accelerate reproducible science. Colleagues rely on him for quiet technical leadership that makes complex bioinformatics workflows resilient and easier to share.
11 years of coding experience
9 years of employment as a software developer
Doctor of Philosophy (Ph.D.) Bioinformatics, Doctor of Philosophy (Ph.D.) Bioinformatics at Max Planck Institute for Marine MicrobiologyDiplom-Informatiker (~Master of CS) Computer Science, Diplom-Informatiker (~Master of CS) Computer Science at University of BremenAbitur Math English, Abitur Math English at Altes Gymasium, BremenHigh School, High School at Fuqua School, Farmville, VA
English, German, Spanish
Github Skills (30)
data-visualizations10
rep10
python10
package-management10
r10
conda10
build-system10
data-visualisation10
bash10
hpc10
distributed-computing10
parallel-computing10
repr10
bioinformatics10
lsf10
Programming languages (19)
Github contributions (5)
bioconda/bioconda-recipes
Dec 2016 - Nov 2022
Conda recipes for the bioconda channel.
Role in this project:
Backend Developer
Backend DeveloperContributions:27 reviews, 1051 commits, 2321 PRs in 6 years
Contributions summary:Elmar primarily contributed to the bioconda-recipes repository by updating and rebuilding various bioinformatics software packages. Their work involved modifying build scripts (`build.sh`), patching source code, and adjusting configuration files to accommodate updated dependencies or build environments. The user's changes ensured that the packages compiled correctly and were compatible with the bioconda channel's requirements, including adapting to different operating systems like MacOS. The user also added and updated build scripts for new and updated tools.
recipescondabiocondabioinformaticspackage-management
snakemake/snakemake
Jul 2016 - Oct 2022
This is the development home of the workflow management system Snakemake. For general information, see
Role in this project:Backend & DevOps Engineer
Backend & DevOps EngineerContributions:5 reviews, 15 commits, 6 PRs in 6 years 4 months
Contributions summary:Elmar primarily contributed to bug fixes and enhancements within the Snakemake workflow management system. Their work involved resolving issues related to conda environments, cluster status updates, and temporary file handling. The user also focused on improving the system's robustness through optimizations, such as addressing command-line argument limitations, and contributing code for better error handling and the inclusion of job IDs in error messages. Further contributions include addressing operating system specific requirements and handling dependencies.
management-systemworkflow-management-systemgeneral-informationreproducibilitysnakemake
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