The report documents eight case studies, mostly in biology, in which research groups used coding agents such as Codex and Claude Code. The projects range from basic maintenance and targeted optimization to full rewrites in modern programming languages.
The eight projects span from simple build modernization to a full GPU-native rewrite. | Image: OpenAI
Coding agents delivered speedups of more than 60 times
One of the simpler projects involved modernizing cyvcf2, a Python library for reading genetic data. GPT-5.5 replaced its outdated build and installation process with a modern one.
The MHCflurry migration was far more involved. MHCflurry is an immunology model that predicts which targets immune cells will recognize. Claude Code and Codex alternated between the roles of developer and reviewer while porting about 10,000 lines of code from TensorFlow to PyTorch.
