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Kevin Osborn edited this page Jul 20, 2016 · 13 revisions

Status updates on project

We have an ongoing series of meetings needs updating.

We have created a number of sample programs using the GA4GH API.

Please insert regular status updates below this line such that the latest status is at the top. Always include the date!

2016, July 20 : Metadata functionality added

The reference server now supports Metadata functionality.

  • added 'info' field to dataset
  • added 'name' and 'gene_symbol' to feature and featureSearch

2016, June 23 : Changes to date

The reference server now uses Protocol Buffers rather than Avro. Client applications will need to be rebuilt to the new schemas and use the protobuf json serialization libraries to be compatible with this version of the server.

2016, May 10 : Functionality complete to date

The implementation team has completed the "Genomic Anlysis" milestone. There is now a GA4GH reference server running in a Microsoft Azure VM that serves up the 1000 Genomes data set. The server can be accessed at 1kgemomes.ga4gh.org. We have added some extra links on the landing page as well:

  • Swagger interactive API documentation
  • iPython notebook on programming against the client API
  • sample visualization application
  • help email address

In addition to the 1KGenome server the team has also reconfigured the way files are organized behind the server to simplify the structural requirements.

2016, March 23: Milestones presented to the DWG

The implementation for the reference server presented a set of milestones to the the DWG. The link to the presentation can be found in the meeting invite but the first milestone "Genomic Analysis" will provide get and post functionality for the API in the following areas:

  • References
  • Reads
  • Variants
  • Variant Annotations
  • Sequence Annotations

It will not include support for the following (these will come with a later milestone)

  • Protocol Buffers
  • Metadata capabilities for BioSample and Individual
  • RNA
  • Genotypes to Phenotypes
  • Data streaming

The milestone will also include setting up an externally accessible reference server that will be set up to serve out the 1000 Genome data set. This server will be running in an Azure VM (hopefully a container) and will access the data via cloud data access methods.

Due Date : 2016, April 25

Next milestone will transition over to using protocol buffers. More on that as we get closer.

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