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Welcome to the bycon and beaconPlus project documentation

Bycon - a Python-based environment for the Beacon v2 genomics API

The bycon project - at least at its current stage - is a mix of Progenetix (i.e. GA4GH object model derived, MongoDB implemented) - data management, and the implementation of middleware & server for the Beacon API.

Some features and pecularities of the bycon solution are:

  • A single install can host multiple beacons and multiple datasets and those can be intersected.
  • bycon handles Beacon queries with full model aggregation; it does not matter which endpoint and response entity are combined with what type of filter or variant parameter since always all entities are evaluated and the response is aggregated. A single query can include parameters for an individual's sex, the histoloical diagnosis of a biosample, an experimental platform and genomic variation parameters and the response can deliver biosamples, individuals ... matching all those parameters.
  • With its origin in the Progenetix resource ("beaconized" since 2016) bycon provides strong support for copy number variation data, including additional services such as CNV frequency plots for matched results or various file export formats beyond the standard JSON response.
  • We provide several front-end projects of which the basic (BeaconPlus) is a general version and since 12/2024 is being distributed as part of the bycon package.

Bycon Code

The bycon code is maintained in the progenetix/bycon repository. Some additional utility scripts & functions can be found in the byconaut repository but are so not (well) documented & may contain deprecated or "internal use" code.

More information about the original use Progenetix case can be found on the project's documentation site.

For more information about bycon installation and use please see installation and track the changes for updates (or getting insights into the developments leading to the current state).

Notes about Previous Development

The bycon package was started during the development of the Beacon v2 specification with the aims to a) test and demonstrate features of the emerging specification in a real-world use case while b) serving the needs of the Progenetix oncogenomic resource. Many of the recent changes are aimed at disentangling the code base from this specific use case.

An earlier version of the Progenetix && Beacon "BeaconPlus" stack had been provided through the Perl based PGX project.