Welcome to the bycon
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 one (BeaconPlus) is a general version easily adaptible for individual use cases.
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.