Simon Bray
Research Software Engineer at Gain Therapeutics
Bath, England, United Kingdom
Summary
🤩
Rockstar🎓
Top SchoolSimon Bray is a research software engineer and computational chemist with eight years’ experience building reproducible bioinformatics and cheminformatics workflows, currently applying fragment-based virtual screening at Gain Therapeutics using the Galaxy platform. He combines a DSc in computational chemistry with hands-on engineering—authoring Galaxy tool wrappers, contributing back-end tests to the flagship Galaxy project, and automating Bioconda packaging for bioinformatics tools. His work spans production workflow design, tool development (RDKit/OpenBabel integrations), and technical training, reflecting both research rigor and platform-level reliability. Based in Bath, UK, he maintains an active open-source presence (GitHub and ORCID) and brings a pragmatically scientific perspective to drug discovery pipelines.
8 years of coding experience
3 years of employment as a software developer
Doctor of Science, Computational chemistry, Doctor of Science, Computational chemistry at Albert-Ludwigs-Universität Freiburg (Albert Ludwig University of Freiburg)
Github Skills (30)
package-management10
python10
seq10
rdkit10
bash10
conda10
sc10
trainings10
cheminformatics10
build-automation10
rna-seq10
bioinformatics10
unit-test10
metagenomics10
documentation10
Programming languages (12)
Github contributions (5)
galaxyproject/training-material
Mar 2019 - Oct 2022
A collection of Galaxy-related training material
Role in this project:
Technical Writer
Technical WriterContributions:37 reviews, 133 commits, 42 PRs in 3 years 7 months
Contributions summary:Simon contributed to the `galaxyproject/training-material` repository by updating and adding content to the training materials. The commits focused on topics related to single-cell RNA sequencing (scRNA-seq), cheminformatics, and metagenomics, as well as general documentation updates and improvements. The changes included formatting, structural improvements, and the addition of new file types, contributing to the repository's educational value and usability. The user also updated clipboard related JavaScript, which might be indirectly used by the tutorials.
chip-seqmetagenomicsrnaseqtraining-materialusegalaxy
bgruening/galaxytools
Apr 2019 - May 2022
:microscope::books: Galaxy Tool wrappers
Role in this project:Back-end Developer & Bioinformatics Tools Developer
Back-end Developer & Bioinformatics Tools DeveloperContributions:21 reviews, 202 commits, 106 PRs in 3 years 1 month
Contributions summary:Simon's commits primarily involve updates and modifications to Python scripts within the "chemicaltoolbox" directory, specifically related to cheminformatics tools. The changes include enhancements to the fragmenter/merger and openbabel tools, and a new tool for converting PDBQT to SDF. The user demonstrated skills in processing and manipulating chemical structures and data using tools such as openbabel and RDKit. They also contributed to the autodock_vina and chembl tools.
cheminformaticsmicroscopegalaxyprojgalaxygalaxy-tool
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