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Welcome to the biocommons!

The biocommons is a community of that fosters pre-competitive collaboration on interoperable and high-quality bioinformatics open source software and data, primarily for sequence variant interpretation. Code is released under Apache License v2 and data are released under the Creative Commons CC-BY 4.0 license.

Projects

Released

  • bioutils provides common tools and lookup tables used primarily by the hgvs and uta packages
  • eutils simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
  • hgvs Python library to parse, format, validate, normalize, and map sequence variants.
  • SeqRepo non-redundant, compressed, journalled, file-based storage for biological sequences
  • seqreo-rest-service OpenAPI-based REST interface to biological sequences and sequence metadata
  • UTA Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources and versions, multiple genomic references, and multiple alignment methods, particularly splign (NCBI) and (blat) (UCSC)

Incubating

  • anyvar Proof-of-Concept variation translation, validation, and registration service

Governance

  • Mission: Why we exist (or longer executive summary?)
  • Culture: How we treat each other respectfully
  • Governance: How we organize to promote effective collaboration
  • Practices and Tools: How we get stuff done coherently
  • Architecture and Coding Guidelines: How we build interoperable tools with consistent behavior
  • Community: How you can get involved, learn, use, and contribute joyfully

You're Invited!

The biocommons project began as an umbrella project for open source software that was released by Invitae. Biocommons software was subsequently used by groups at ClinGen, Color, GA4GH, GenomOncology, and many other institutions. In order to ensure that existing projects continue to meet the needs of the community, and to provide a forum for related new software, the biocommons project is being restructured in order to clarify governance, code of conduct, contribution policies, and coding guidelines. See the reboot preview pages for more information.