Thomas Holder
Senior Scientific Software Developer at AQEMIA
Paris, Ile-de-France
Summary
🤩
Rockstar🎓
Top SchoolThomas Holder is a Senior Scientific Software Developer with 17 years of experience blending computational structural biology and pragmatic software engineering, currently based in Paris and working at Aqemia. He has a strong track record in molecular visualization and bioinformatics—most notably long-term contributions to the open-source PyMOL project and robustness and typing work in Biopython. Thomas excels in Python and C++, cross-platform Linux desktops, CI/deployment (Anaconda Cloud, AppVeyor/CircleCI), and test frameworks like pytest and Catch2, routinely turning domain science into production-quality tools. His background spans academia (Max Planck) to industry (Schrödinger, Leukocare, Rentschler), where he combined molecular modelling, data science, and team-building in cross-functional scrum environments. An understated but telling detail: he pairs deep technical contributions with hands-on user training and community moderation, reflecting both developer craftsmanship and stewardship of scientific software ecosystems.
17 years of coding experience
19 years of employment as a software developer
Master of Science (M.Sc.), Bioinformatics, Master of Science (M.Sc.), Bioinformatics at University of TübingenBig Nerd Ranch
German, English
Stackoverflow
41reputation
0reached
1answer
0questions
Github Skills (25)
unit-testing10
maintenance10
visualization10
c-language10
python10
visual10
biopython10
visualize10
bioinformatics10
cprogramming-language10
visualizations10
3d-graphics9
pdb9
error-handling9
typehinting9
Programming languages (15)
Github contributions (5)
schrodinger/pymol-open-source
Nov 2012 - Dec 2022
Open-source foundation of the user-sponsored PyMOL molecular visualization system.
Role in this project:
Software Developer (with a focus on Molecular Visualization)
Software Developer (with a focus on Molecular Visualization)Contributions:8 reviews, 840 commits, 47 PRs in 10 years 2 months
Contributions summary:Thomas's commits primarily focused on enhancing and refining the PyMOL molecular visualization system. They implemented new features like a ring selection operator ("byring"), a centroid-based distance mode ("distance mode=4"), and loop-like cartoon styles ("cartoon dash"), indicating contributions to core functionalities. Additionally, they made improvements to data loading, MOL2 export, and error handling, showcasing an understanding of the software's internal workings and user experience.
pythonmolecularfoundationpymolmolecular-visualization
Pymol-Scripts/Pymol-script-repo
Dec 2011 - Nov 2022
Collected scripts for Pymol
Role in this project:Back-end Developer
Back-end DeveloperContributions:13 reviews, 134 commits, 32 PRs in 11 years
Contributions summary:Thomas's primary contribution appears to be the addition of features and improvements to a Python-based PyMol script repository. The user implemented a dropdown menu for unit selection in a rendering plugin. Further commits show merges from the upstream master branch and contributions to an autodock plugin. The user's work has improved the functionality and capabilities of the PyMol scripts in the repository.
scriptpythonpython-scriptspymol
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