Timothy O'donnell
Member Of The Technical Staff at Open Athena
Cambridge, Massachusetts, United States
Summary
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Rockstar🎓
Top SchoolTimothy O'donnell is a computational biologist and Member of the Technical Staff at Open Athena with 12 years blending software engineering, machine learning, and immunology to advance therapeutic discovery. He built and deployed production-grade bioinformatics tools—most notably the Openvax suite used in Phase I cancer vaccine trials—and has a PhD in Immunology from Mount Sinai. Timothy consults with biotechs and research groups, helping teams apply deep learning for structural biology and personalized therapies, and contributed infrastructure and data-handling fixes to the openfold reproduction of AlphaFold2. Comfortable across lab and production environments, he pairs hands-on ML/DevOps work with high-throughput immune profiling expertise (PhIP-seq, immunopeptidomics). Based in Cambridge, MA, he brings a rare combination of academic rigor and practical engineering that accelerates translational projects.
12 years of coding experience
15 years of employment as a software developer
Bachelor of Science (B.Sc.), Mathematics and Computer Science, Bachelor of Science (B.Sc.), Mathematics and Computer Science at Brown UniversityDoctor of Philosophy - PhD, Immunology, Doctor of Philosophy - PhD, Immunology at Icahn School of Medicine at Mount Sinai
Github Skills (8)
pytorch10
python10
bash9
cuda9
mlops8
numpy8
dockers7
docker7
Programming languages (11)
Github contributions (5)
aqlaboratory/openfold
Aug 2022 - Aug 2022
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
Role in this project:
DevOps Engineer & ML Engineer
DevOps Engineer & ML EngineerContributions:9 commits, 2 PRs, 3 comments in 18 days
Contributions summary:Timothy primarily focused on improving the repository's infrastructure and data handling. They modified scripts to correctly download and unzip data resources, enhancing the data preparation pipeline. Furthermore, the user addressed CUDA-related errors and numpy deprecation warnings, indicating involvement in the project's machine learning components and their execution environment. The changes streamlined dependencies and prepared the project for further development.
gpupytorchprotein-structurealphafold2
openvax/mhcflurry
Apr 2016 - Jun 2022
Peptide-MHC I binding affinity prediction
Contributions:31 releases, 11 reviews, 1692 commits in 6 years 2 months
bindingpredictionaffinitymhcpeptide
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