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Google Summer of Code 2011

The Open Bio Foundation is a mentoring organisation for Google Summer of Code 2011. As an OBF project, BioDAS contributors would be pleased to act as mentors for students wishing to work on DAS software. A couple of ideas for projects are listed below.

Potential students are also encouraged to submit their own project ideas, and the mentors below would be happy to discuss the possibilities.

Redesign of the DAS Registry

The DAS Registry plays a pivotal role in the DAS ecosystem. It is a central repository of DAS server metadata, allowing both humans and software applications to discover and interact with the myriad DAS data sources available. We believe that by offering specific functionality, the Registry can incentivise adoption and adherence of the DAS protocol.

This project would likely comprise three phases:

  1. Rationalise the underlying codebase, including the removal of redundant code
  2. Build a new lightweight user-focussed interface based on the underlying DAS web services
  3. Expand functionality, for example ontological-based searching

The project would suit individuals with knowledge of:

  • Java development
  • RESTful web services
  • User-experience and interface design

Mentors: Jonathan Warren and Andy Jenkinson

DAS Server for large files on local filesystems

DAS servers allow organisations and individuals to visualise the results of their experiments alongside other public data in web-based DAS clients such as the Ensembl Genome Browser. However, running a DAS server on a publicly-accessible dedicated web server is often beyond the skill or resources available to a typical researcher. New developments such as easyDAS go some way to addressing this problem by allowing a user to upload files to a DAS server, but are not ideal when dealing with large data files such as large scale sequencing experiments.

We would like to develop a DAS server that may be run on a researcher's own machine in order to inject large-scale data into DAS clients for visualisation. This has a major technical challenge: web addressing. Such an application would need to somehow make a machine on a firewalled local network visible to the outside world. This problem affects many application areas other than DAS, but we believe a viable solution exists in the form of a "client pull" proxy system, inspired by Opera Unite.

The project would suit individuals with knowledge of:

  • The HTTP protocol
  • Java development

Mentor: Andy Jenkinson