To cite BioCompute, please use:

  1. Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations
  2. Enabling precision medicine via standard communication of HTS provenance, analysis, and results
  3. Bioinformatics tools developed to support BioCompute Objects

Table of contents

BCO Portal
Platform Specific Tools
BCO Community
BCO Documentation
Software Packages
BCO Registry
BCO Aggregator
BCO Cheat Sheet
References


Publicly available resources developed by the BioCompute community include:

BCO Portal

The BCO Portal is a form based creation tool for generating BioCompute Objects. The BCO Portal contains built-in linting and conformance against the current BioCompute specification. The BCO Portal includes a database of created BCOs. Unless specified in the embargo field, BCOs in the database are viewable to the general public.

Platform Specific Tools

HIVE BCO App

The High-throughput Integrated Virtual Environment (HIVE) for genome analysis and the widely used, open source Galaxy project both have platform specific tools for generating BioCompute Objects from workflows. Both of these can be found on our home page.

Cancer Genomics Cloud BCO App

The Cancer Genomics Cloud (CGC) has a powerful tool built into the CGC platform to capture and export a workflow as a BioCompute Object.

Galaxy BCO Extension

The Galaxy BCO API Extension enables Galaxy users to the export of Galaxy “workflow invocations” (i.e. realizations of a computational pipeline) in BCO format.

BCO Community

  • The BCO Gitter has spaces for general discussion, technical development, BCO implementation, and networking.

BCO Documentation

Software Packages

  • The R package biocompute can create, validate, and export BioCompute Objects. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard. A checksum validator and a JSON schema validator are provided. Also supports exporting BioCompute Objects as JSON, PDF, HTML, or Word documents, and exporting to cloud-based platforms.

BCO Registry

  • The BioCompute consortium maintains a database of registered authorities. Registered authorities are able to assign their own IDs in the object_id field, such as gwu000001.

BCO Aggregator (under construction)

  • The BioCompute consortium maintains a database of submitted BCOs. The database acts as a mirror that generates checksums for validation.

BCO “Cheat Sheet”

References

  1. 2791-2020 IEEE Standard
    The official IEEE standard, known as IEEE 2791-2020.

  2. Repository
    The open source repository referenced by the standard. Three formats of the publication are available.

  3. Semantic Versioning
    BioCompute versioning is based on semantic versioning, but does not use the “major” value in “major.minor.patch” (e.g. 2.4.11).

    • Use “minor” increments for additions (e.g. the addition of a “reviewedBy” block).
    • Use “patch” for minor fixes (e.g. editorial spelling corrections).
    • There is no “major” increment in BCO versioning. A BCO is a record of a specific instance of an analysis, so major changes result in a new BCO.
  4. Provenance Ontology
    Contributor roles in a BCO are explicitly defined according to the Prov-O standard, and include roles for reviewing a BCO, creating the content in a BCO, and for authoring the BCO itself.

  5. JSON Schema
    BioCompute is based heavily on the JSON Schema media type. Definitions and format within the BCO Schema adhere to “draft-handrews-json-schema-02.”