Fredrik Boulund
Head Of Bioinformatics At The Center For Translational Microbiome Research (CTMR)
Stockholm County, Sweden
Summary
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Rockstar🎓
Top SchoolFredrik Boulund is Head of Bioinformatics at the Center for Translational Microbiome Research in Stockholm, bringing 11 years of experience designing and running shotgun metagenomics workflows and coordinating data management for translational microbiome projects. He combines deep academic training (PhD in Bioinformatics) with hands-on systems skills—Python, Linux administration and workflow tooling—to translate high-throughput sequencing and proteomics methods into robust analysis pipelines. Fredrik has led rapid operational scale-ups, notably converting a microbiome lab into a national-scale SARS-CoV-2 diagnostics facility during the pandemic, reflecting strong operational and cross-organizational leadership. He contributes to prominent open-source bioinformatics projects like MultiQC and Snakemake, adding reproducibility and Pathlib compatibility improvements that make pipelines more flexible and auditable. As a co-founder of a diagnostics company and a seasoned method developer, he blends entrepreneurial drive with a track record of finding novel antibiotic resistance genes and advancing proteomics-based infection diagnostics. Known for pragmatic engineering of reproducible workflows, he often surfaces practical improvements—like refactoring visual outputs into clearer tables—that improve usability for diverse lab teams.
10 years of coding experience
7 years of employment as a software developer
Leadership logistics food handling tactics, Leadership logistics food handling tactics at Lv6, Swedish Armed ForcesLeadership, Leadership at Halmstad UniversityDoctor of Philosophy (Ph.D.) Bioinformatics, Doctor of Philosophy (Ph.D.) Bioinformatics at Chalmers University of Technology
English, Swedish, Danish, French, German
Stackoverflow
23reputation
1kreached
0answers
1question
Github Skills (16)
bioinformatics10
workflow-management10
analyse10
pathlib10
snakemake10
python10
reporting-services10
mu10
testing9
repr9
data-visualisation9
data-visualization9
data-visualizations9
rep9
popen6
Programming languages (16)
Github contributions (5)
MultiQC/MultiQC
Nov 2016 - Nov 2019
Aggregate results from bioinformatics analyses across many samples into a single report.
Role in this project:
Backend Developer
Backend DeveloperContributions:25 commits, 9 PRs, 62 comments in 3 years
Contributions summary:Fredrik primarily contributed to the development of a new module, "prokka," for the bioinformatics tool MultiQC. This involved writing Python code to parse and integrate data from Prokka annotation pipelines into MultiQC reports. The user also made minor code adjustments, including removing unnecessary imports and modifying docstrings, and refactored the output from a barplot to a table. Further contributions involved adding BBMap module functionality.
multiqcpythonpypianalysesbioconda
snakemake/snakemake
Apr 2018 - Oct 2018
This is the development home of the workflow management system Snakemake. For general information, see
Role in this project:Back-end Developer
Back-end DeveloperContributions:13 commits, 8 comments, 3 issues in 5 months
Contributions summary:Fredrik primarily focused on enhancing the Snakemake workflow management system by adding and improving Pathlib compatibility. They modified existing code to convert file paths from `Path` objects to strings, ensuring compatibility. The user also added tests specifically for Pathlib, demonstrating a commitment to thoroughness. This work indicates a focus on improving the system's usability and flexibility in handling file paths.
management-systemworkflow-management-systemgeneral-informationreproducibilitysnakemake
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