Welcome to the ISCB Community News Blog

This blog collects news, announcements or other information which could be of interest to our ISCB members. We are a group ISCB members who volunteer to populate this blog on a regular basis. In case you want to become an "ISCB-News Reporter" yourself, let us know: contact ISCB
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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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Copyright © 2014 Sage Bionetworks, All rights reserved.
Your participation in Sage Bionetworks/DREAM competitions has placed you on this email list.
Our mailing address is:
Sage Bionetworks
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Seattle, WA 98109

URL: http://www.synapse.org/#!Challenges:DREAM8.5

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

Wednesday, January 15, 2014

DEADLINE APPROACHING FAST!!! APPLY TODAY! 2014 MBI Undergraduate Summer Research Program

DEADLINE APPROACHING FAST!!! APPLY TODAY!
2014 MBI Undergraduate Summer Research Program
(June 2 - August 15, 2014)
This program introduces students to exciting new areas of mathematical biology and involves them in collaborative research with their peers and faculty mentors. For full consideration, completed applications must be received by Monday, January 27, 2014. The program consists of three parts:

Two-week Introduction (June 2-13, 2014): Tutorials, computer labs, and team efforts designed to introduce students to a variety of topics in mathematical biology. Applications for the TWO-WEEK INTRODUCTION ONLY will be due in April.

Eight week REU Program (June 16 - August 8, 2014): An individualized research experience as part of a research team at a participating institution. There are 14 projects to choose from.

Capstone Conference (August 11-15, 2014): A student centered conference featuring talks and posters by student researchers in math biology, keynotes by prominent math biologists, and a graduate studies recruitment fair. Applications for CAPSTONE CONFERENCE ONLY will be due in June.


To apply visit http://www.mbi.osu.edu/eduprograms/undergrad2014.html


Mathematical Biosciences Institute
The Ohio State University, Jennings Hall 3rd Floor, 1735 Neil Ave., Columbus, OH 43210 • 614-292-3648
URL: http://www.mbi.osu.edu/eduprograms/undergrad2014.html

Contact Person: Dennis Pearl (pearl.1@osu.edu)

Friday, January 3, 2014

VIZBI 2014 registration closes on 31st January

A quick reminder that registration for VIZBI 2014 closes 31 January 2014. ISCB Members receive a 15% discount.

VIZBI 2014 is the 2nd EMBO Conference on 'Visualizing Biological Data', and the 5th international meeting on this topic, which will be held March 5-7 at the EMBL, Heidelberg (Germany).

VIZBI 2014 features 21 invited talks from high-profile speakers that review the state-of-the-art and challenges in visualizing a diverse range of biological data. As with previous years, participants can present a poster and lightning talk describing their work, and have the option of remote participation via streaming video and chat.

Prior to the meeting (March 4), there will also be 13 half-day tutorials covering a broad range of visualization tools & methods.

If you are interested in promoting your organization or professional society during VIZBI 2014, a range of sponsorship options are also available.

We hope you can join us for what promising to be another exciting VIZBI event!

URL: http://vizbi.org/2014/

Contact Person: Adela Valceanu (valceanu@embl.de)