First of all you will need to be familiar with Illumina data sets and this appears to be a project that will help answer questions about false positives and negatives. This is not a huge prize from what we normally see from the X-Prize Foundation but it all stems around software genomics research. I do have to say one thing, it’s an interesting concept and will even be more interesting to see how the challenge works. BD From the Website:
Challenge Guidelines
Date: September 10, 2012
I) PRIZE: $2,500
II) CHALLENGE PERIOD:
A) Phase I:
i) BEGINS: 9:00 AM (0900) PST, Wednesday, September 12, 2012
ii) ENDS: 5:00 PM (1700) PST, Monday, November 27, 2012
B) Phase II:
i) BEGINS: 9:00 AM (0900) PST, Tuesday, November 28, 2012
ii) ENDS: 5:00 PM (1700) PST, Monday, December 7, 2012
III) PURPOSE: To incentivize global submission of comments for the refinement of the Competition Validation Protocol, which is the mechanism by which we will declare a winner(s) of the $10 million Archon Genomics X PRIZE presented by Express Scripts (Competition).
IV) GUIDELINES FOR ONLINE SUBMISSIONS:
A) CHALLENGE: Submit comments that provide insight into 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.
B) CHALLENGE: Improve 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.
C) CHALLENGE: Refine approaches to 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.
D) CHALLENGE: Test and propose specific refinements to the software, web platform, or report functionality of the software.
V) INSTRUCTIONS:
A) Each Contributor shall register on the Competition Scientific Community according to the Rules stated below
B) Each Contributor must visit the Competition Public Phase wiki to obtain the technical details required for participation by visiting (http://bit.ly/NGVbIs)
C) Following the conclusion of analysis prior to the conclusion of Phase I, each contributor shall provide written comments directly on the Competition Scientific Community (this site) under the Caption “Please Enter Our Bioinformatics Challenge” to be considered a valid written submission. Registered users are allowed to provide written submissions on multiple, (up to four) Challenges.
D) Each Contributor may also submit clarifying questions directly in the appropriate section of the Competition Scientific Community
E) For specific technical questions, please contact Justin Johnson at EdgeBio via email at mail to: JJohnson@edgebio.com. Please include “BIOINFORMATICS CHALLENGE QUESTION” in subject line
F) For questions relating to the Rules and Guidelines of the Bioinformatics Challenge, please contact Grant Campany at grant.campany@xprize.org and include “BIOINFORMATICS CHALLENGE QUESTION” in subject line
VI) RULES:
A) Only one cash prize of $2,500 USD (Prize) will be awarded at the sole discretion of the X PRIZE Foundation based upon written submissions via "Reply to This Topic" section below (this site)
B) To qualify, each person is required to provide his/her given/legal name as a user name and may not have more than one user name registered on the Competition Scientific Community site (Contributor)
C) Each Contributor acknowledges that only submitted comments received via the "Reply to This Topic" section below during Phase I of the Challenge Period will be considered for the Prize
D) Each Contributor may submit multiple comments during Phase I of the Challenge Period
E) Phase I will be considered the “comment submission” phase of the Challenge Period. During Phase I each Contributor shall submit written comments on the online Scientific Community (this site). The X PRIZE Foundation shall identify a list of finalists to enter into Phase II. The X PRIZE Foundation shall select the finalists of the Bioinformatics Challenge based on material contribution per section IV above.
F) Phase II shall be considered the “voting and selection” phase of the Bioinformatics Challenge. The X PRIZE Foundation shall present submissions by the finalists to the Scientific Community (this site) for final voting. The submission receiving the most unique positive votes shall determine the winner of the Prize.
G) All Contributors hereby acknowledge and agree to:
i) The Guidelines of the Bioinformatics Challenge stated herein,
ii) The declaration of the winner is at the sole discretion of the X PRIZE Foundation, and
iii) The winner of the Bioinformatics Challenge shall agree to participate in commercially reasonable public relations efforts deemed appropriate between the X PRIZE Foundation and the winner
iv) The RULES are subject to change, so please check this site for most up-to-date version of Guidelines as indicated by the Date above.
http://agxpprotocol.xprize.org/agxp/topics/_2_500_bioinformatics_challenge
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