Gert Hulselmans
Bioinformatician
Leuven, Flemish Brabant, Belgium
Summary
🤩
Rockstar🎓
Top SchoolGert Hulselmans is a bioinformatician with 13 years of experience combining computational biology research at KU Leuven and VIB with hands-on software engineering. He specializes in back-end data engineering for bioinformatics pipelines, improving data parsing, storage and performance across projects like pySCENIC and Biopython. Gert is an active open-source contributor to high-profile repos—helping extend Polars’ CSV/pyarrow compatibility and enhancing container builds in Apptainer—bringing production-grade robustness to scientific tooling. His work spans improving file-format interoperability (gzipped and non-UTF8 CSVs, Parquet support) to subtle bug fixes and documentation that smooth researcher workflows. Based in Leuven, he pairs a biomedical sciences background with low-level engineering chops gained from early volunteer work on the Parted Magic Linux distro. Colleagues rely on him for pragmatic, reproducible solutions that bridge research needs and scalable software.
13 years of coding experience
6 years of employment as a software developer
Master's degree, Biomedical Sciences, General, Master's degree, Biomedical Sciences, General at KU Leuven
English, Dutch
Github Skills (26)
csv-parse10
python10
pyarrow10
data-engineering10
data-manipulation10
pandas10
linux10
build-system10
biopython10
sequence-alignment10
containerization10
data-structure10
excel-dna10
go10
csv-parsing10
Programming languages (29)
Github contributions (5)
aertslab/pySCENIC
Oct 2018 - Nov 2022
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:2 releases, 61 commits, 1 PR in 4 years 1 month
Contributions summary:Gert primarily focused on improving the codebase related to data storage and database management, as the commits show modifications to the ranking database implementations. They refactored code to remove dependencies, such as feather-format, and replaced them with direct implementations, and improved code for loading data into pandas dataframes. The user's work also included changes to filenames and database names, as well as fixes related to data processing within the pipeline. Furthermore, they added support for Parquet databases.
gene-regulatory-networkpythoninferregulatorybioinformatics
pola-rs/polars
May 2021 - Jan 2023
Dataframes powered by a multithreaded, vectorized query engine, written in Rust
Role in this project:Back-end Developer & Data Engineer
Back-end Developer & Data EngineerContributions:85 reviews, 108 commits, 134 PRs in 1 year 8 months
Contributions summary:Gert contributed to the `polars` repository by implementing features related to the CSV parsing and data manipulation functionalities, including the ability to read gzipped CSV files and converting data from various formats. They also improved the library's compatibility with pyarrow, adding support for features such as column and projection selection and added support for non-UTF-8 encoded CSV files. Furthermore, the user addressed several bugs related to data loading and data type conversions, and improved performance for getitem operations.
polarsdataframespythondataframerust
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