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Tuesday, January 28, 2014

The ICGC-TCGA-DREAM Somatic Mutation Calling Challenge


Sign up now for the DREAM8.5 Challenges: https://www.synapse.org/#!Challenges:DREAM8.5
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Important Updates For The ICGC-TCGA-DREAM Somatic Mutation Calling Challenge

Dear DREAM Colleague,

We write to share a few exciting reminders and updates on the ICGC-TCGA-DREAM Somatic Mutation Calling (SMC) Challenge:

Challenge overview: In the SMC Challenge, registered participants will identify the best pipelines for detecting mutations in the high-throughput sequencing reads of cancer genomes (https://www.synapse.org/#!Synapse:syn312572). The Challenge opened for participation on November 7, 2013: contestants will have until July 2014 to optimize their predictive models. Both experimental and in silico data sets are currently available for downloading by registered participants.

At the time of this writing, 120 teams have already signed up to participate! You can join the Challenge here: https://www.synapse.org/#!Synapse:syn312572

To get all your questions about the Challenge answered, please register for the January 29 SMC Challenge Webinar:

Clink the link below to reserve a seat for the webinar ("Mostly Everything You Need To Know About the ICGC-TCGA-DREAM Somatic Mutation Calling Challenge") taking place on Jan 29, 2014 9:00 AM PST at:

https://attendee.gotowebinar.com/register/5813241477194794498

The following details of the SMC Challenge will be covered at this webinar:

1. Background and motivation for the Challenge
2. Demo of Challenge web services
3. Demo of available compute resources for the Challenge
4. Answering your questions in real-time.

After registering, you will receive a confirmation email containing information about joining the webinar.

February 1 is the model submission deadline for Synthetic.Challenge.set1.v2: To see the real-time leaderboard for this Challenge follow the link: (https://www.synapse.org/#!Synapse:syn312572/wiki/61509). The leaderboard includes the scores for both Structural Variant (SV) and Single Nucleotide Variant (SNV) calls. Make sure your model is submitted and scored in time for the February 1st deadline!

In addition, we are excited to share an important development that we believe will open the door for a whole new set of participants who do not have access to large compute clusters at their own institutions:
Google is offering Google Cloud Platform credits of $2,000 to approved DREAM contest participants, including free access to contest data in Google Cloud Storage. These credits can be used for Compute Engine VMs and other Cloud Platform services.

Access to Challenge data is provided via a Google Cloud Storage bucket, so all computation and submissions can be performed on the Google Cloud Platform. A detailed Getting Started Guide and a custom image are provided for participants who wish to use this option.

To get the credits, sign up for an account at https://cloud.google.com/, create a cloud project, set up billing for that project by providing a credit card, and then send an email to dream-smc-credits@googlegroups.com with the following information:the Cloud project number of:

1. the project to which you'd like the credits applied
2. the Gmail addresses of each contestant on the team
3. the institution(s) of the team members

After using the initial credits to successfully analyze data on Google Cloud Platform, contest participants may apply for additional credits.
The contest organizers thank Google for their generous contribution.

Sincerely,
The SMC Challenge Organizers
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Your participation in Sage Bionetworks/DREAM competitions has placed you on this email list.
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URL: http://www.synapse.org/#!Challenges:DREAM8.5

Contact Person: Josh Stuart (Jstuart@ucsc.edu)

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