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X Prize Launches Open Bioinformatics Challenge


By Allison Proffitt 

September 11, 2012 | The Archon Genomics X Prize is launching a Bioinformatics Challenge tomorrow morning at 9:00 PST. The challenge is offering a $2,500 prize for the “most impactful, most material” improvements to the validation protocol and software for the X Prize said Grant Campany, senior director & prize lead, Archon Genomics X PRIZE presented by Express Scripts.  

The validation protocol and software for the X Prize are available on a public wiki. Members of the community can download the software and the biological data to test the platform.  

“The purpose is that people will run this on their own or collaborate with a colleague and find ways to improve upon the software,” says Campany. The challenge is open to the global scientific community, he says. “We certainly want people to feel like this is an opportunity to compete in who can come up with the best idea or best contribution for refinement.”  

The challenge will take place in two phases. In the first phase—open until November 27—members of the community are invited to comment on various aspects of X Prize Competition Validation Protocol. There are several challenge areas that are specifically of interest:  

  • Potential false positives and negatives. By combining comparison information between the unified call set and external resources, we can identify 17,654 fosmid variants (10%) not found in both the Complete Genomics and Illumina datasets. Additionally, Illumina and Complete Genomics combine to call 1,228 variants (0.7%) that are not in the fosmid call set. Perform additional in-depth analysis to classify either uniquely identified fosmid calls or potential false positives, or false negative calls in the individual technologies.  
  • Variant representation and assessment. The variation software framework works hard to make variant representations as uniform as possible. Indels are especially challenging and we welcome practical examples of regions that need additional standardization.  
  • Unifying variant calls: What we learn from the additional inspection of discordant variants can help inform improved approaches to filtering. This is a great opportunity to develop generalized, reusable methods for combining variants from multiple approaches.  
  • Test and propose specific refinements to the software, web platform, or report functionality of the software. 

All suggestions will be made via the community thread on the Bioinformatics Challenge website.  

After the open comment period has ended, the best suggestions will be put forward for community voting. 

“We’re trying to keep this somewhat simple and let the community determine what they feel is the most material contribution,” says Campany.  

 

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