Author Archives: Christopher Taylor

App-ready databases from Python with SQLModel and FastAPI

Python is ubiquitous for those of us coming into programming from academic research backgrounds, both for generating scientific data and for analysing it. Of course, modern data-driven research only thrives when data is FAIR (findable, accessible, interoperable, and reusable) and traditional relational databases and APIs for interacting with them are a tried-and-true method of ensuring FAIRness. (And in the age of machine learning, the machines need things to be FAIR arguably even more than we do…)

“But I’m a data scientist/computational chemist/bioinformatician!” you protest. “I just (ab)use databases using Python, I don’t make them for someone else to use!” Understandable, but the barrier to entry may be much lower than you think, thanks to two related Python libraries: SQLModel and FastAPI. These powerful tools by developer Sebastián Ramírez (@tiangolo on GitHub) work in concert to make relational databases and APIs much easier to implement for Python natives. Let’s see how they can help…

Continue reading

SAbDab2: The structural antibody database in the age of machine learning 

Henriette L. Capel, Odysseas Vavourakis, Benjamin H. Williams, Christopher R. Taylor, and Charlotte M. Deane

The Structural Antibody Database 

The Structural Antibody Database (SAbDab) [1] is a publicly available repository of experimentally determined antibody structures, first released in 2013. Explicit support for single-domain antibodies was added in 2021, with SAbDab-nano [2]. Detailed annotations and consistent maintenance have made SAbDab a central resource supporting important advances in the field. SAbDab has been used to study antibody-antigen interactions, including SARS-CoV-2; to predict antibody structure; to design antibodies de-novo; and to investigate antibody flexibility. 

Continue reading