biocommons's Projects
Organization-wide GitHub configuration
[in development] Proof-of-Concept variation translation, validation, and registration service
Declares/reserves "biocommons" for namespace packages only; see other repos for specific functionality
Template for new biocommons packages, and source of configuration for periodic updates to derived packages
biocommons website
non-redundant, compressed, journalled, file-based storage for biological sequences
provides common tools and lookup tables used primarily by the hgvs and uta packages
Parent images used by biocommons
simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
Hackathon 2023 projects and planning.
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
automated evaluation suite to assess tools that manipulate HGVS formatted variants
Verify that the supported installation method ('pip install --upgrade setuptools; pip install hgvs') works.
biocommons logos and logo-generation code
Makefile (of all things) to space-efficiently mirror selected NCBI resources
OpenAPI-based REST interface to biological sequences and sequence metadata
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
C-based Needleman-Wunsch and Smith-Waterman alignment algorithms with a Python interface.