Pygr is a hypergraph database in Python with applications in bioinformatics written by Christopher Lee, a faculty member at UCLA. There's a 30 minute video of talk about Pygr and a bunch of other resources on the Lee Lab website and Lee's thinking bioinformatics blog.
Thesis: Hypergraphs are a general model for bioinformatics and Python’s core models are already a good model of Bioinformatics Data
Pygr aims to show that these Pythonic patterns are a general and scalable solution for bioinformatics.
- Sequence: protein and nucleic acid sequences
- Mapping / Graphs: alignment, annotation
- Attributes: schema, i.e. relations between data
- Namespace (import): the ontology of all bioinformatics data
The general idea is not entirely different from the data types behind Gaggle, especially in the emphasis on basic data structures without a heavy semantic component.
Dr. Lee is also writing a textbook on probabilistic inference.