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Monday, September 19, 2011

Announcing Critical Assessment of Genome Interpretation & Prediction season open

The Critical Assessment of Genome Interpretation (CAGI) is a community experiment to assess computational methods for predicting the phenotypic impacts of genomic variation. The CAGI 2011 experiment is now well underway with 11 datasets available at the CAGI website: http://genomeinterpretation.org/. Remaining deadlines to submit predictions start September 30, 2011 and continue until 31 October.

In the CAGI experiment, modeled on the Critical Assessment of Structure Prediction (CASP), participants are provided genetic variants and make predictions of resulting molecular, cellular, or organismal phenotype. These predictions are evaluated against experimental characterizations, and independent assessors perform evaluations. The CAGI Conference 2011 will be held 9 - 10 December at UCSF Mission Bay campus to disseminate results, assess our collective ability to make accurate and meaningful phenotypic predictions, and better understand progress in the field. From this experiment, we expect to identify bottlenecks in genome interpretation, inform critical areas of future research, and connect researchers from diverse disciplines whose expertise is essential to methods for genome interpretation.

The CAGI 2011 challenges include:
• Disease-associated variants of a human metabolic enzyme.
• Variants from the resequencing of breast cancer patients and control subjects.
• Disease-associated variants of a human sodium channel.
• Genome and RNA-seq data from identical twins with discordant disease.
• Multiple genomics data for cancer cell lines, with differential response to drugs.
• Exomes of Crohn's disease patients and healthy individuals.
• Double mutants of p53 to identify mutations that restore the activity of inactive p53.
• Predicting the medical phenotypes of individuals with genome data.
• Microbial dataset measuring the effect of gene disruptions under stress conditions.
• The riskSNPs dataset to identify potential causative SNPs from lists of candidates in the disease-associated loci for seven complex trait diseases.
The CAGI submission deadline for the mouse exomes challenge already passed, but we are accepting submissions for archival purposes.

The first CAGI experiment, called pre-pro-CAGI, was organized in 2010. Assessors are preparing a manuscript to discuss these results. While the identities of the prediction methods have been embargoed for this "training" CAGI, we will de-anonymize methods from predictors who give us the permission to do so and future CAGI experiments will be more open. The next CAGI experiment is anticipated for 2013.

In order to access the challenges, download datasets, and submit predictions to CAGI 2011, please go to the website http://genomeinterpretation.org and register. For more information, contact the organizers at cagi@genomeinterpretation.org.

We are grateful to the following:

Data providers:
Adam Arkin, George Church, Andre Franke, Joe W. Gray, Rick Lathrop, Jasper Rine, Jeremy Sanford, Nicole Schmitt, Jay Shendure, Michael Snyder, and Sean Tavtigian.

Confirmed Assessors:
Rui Chen, Iddo Friedberg, Gad Getz, Sean Mooney, Pauline Ng, and Sean Tavtigian.

Confirmed CAGI Advisory Board:
Russ Altman, George Church, Tim Hubbard, Scott Kahn, and Sean Mooney.

Confirmed CAGI Scientific Council:
Patricia Babbitt, Atul Butte, Garry Cutting, Rachel Karchin, Robert Nussbaum, Michael Snyder, and Liping Wei.

URL: http://genomeinterpretation.org

Contact Person: Susanna Repo (srepo@compbio.berkeley.edu)

Sunday, September 11, 2011

BeNeLux Bioinformatics Conference (BBC) - Enabling Translational Biomedical Research - ISCB affiliated conference

BeNeLux Bioinformatics Conference (BBC) 
Luxembourg - Luxembourg 
Hosted by:CRP-Santé
Venue:Alvisse Parc Hotel
Dates:Dec 12, 2011 through Dec 13, 2011
Call for Papers or Oral Presentations:2011-09-01 through 2011-10-28
Event Registration:2011-08-15 through 2011-11-27
Putting the Lux on BeNeLux

The BeNeLux Bioinformatics Conference (BBC) will be hosted in Luxembourg for the first time, and CRP-Santé will lead its organization in partnership with other local institutions. BBC will be held on 12 and 13 December 2011, and will showcase research advances from the region and beyond.

A key theme of BBC2011 will be "Bioinformatics: Enabling Translational Biomedical Research".

Invited speakers

Thomas Lengauer, Max-Planck-Institut für Informatik, Germany

Burkhard Rost, Technical University Munich, Germany

Peter van der Spek, Erasmus Medical Center, The Netherlands

Ioannis Xenarios, Swiss Institute of Bioinformatics and Vital-IT
Additional Information
Event URL:http://www.bbc11.lu
ISCB Member Discount:15 percent
Contact Person:Francisco Azuaje ( francisco.azuaje@crp-sante.lu)

Wednesday, September 7, 2011

BioVis 2011 registration open

Registration for the 1st IEEE Symposium on Biological Data Visualization (BioVis 2011) is now open. BioVis is an affiliated conference of the ISCB and will take place in Providence, RI (USA), co-located with IEEE VisWeek, the premier forum for visualization advances for academia, government, and industry.

Early registration (reduced rate) for this meeting ends on Friday, 16 September. Single day and two day registrations are available in addition to full week registration. Discounts are available for ISCB, IEEE and ACM members, details are can be found on the registration page.
The goal of BioVis is to create the premier international and interdisciplinary event for all aspects of visualization in biology. This symposium will bring together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in biological data visualization, as well as bioinformatics and biology researchers in state-of-the-art visualization research. As the first annual BioVis Symposium, this event seeks to emphasize inclusion and interaction between these communities as its primary impact.
The program of the meeting includes:

  • a keynote by Lynda Chin (MD Anderson Cancer Center / Broad Institute of MIT and Harvard)
  • a primer by Lawrence Hunter (UC Denver) and Kun Huang (Ohio State)
  • a special session on BioVis challenges with invited speakers Arthur Olson (The Scripps Research Institute), Cydney Nielsen (BC Cancer Agency Genome Sciences Centre) and Willy Supatto (California Institute of Technology)
  • four paper sessions with 24 presentations from all areas of biology
  • 27 posters and demos
  • presentation of the results from the BioVis Contest
The full list of accepted papers, posters, demos, and videos is available on the BioVis website.