smc-rna biovis data visualization dream challenge preview

http://www.biovis.net/2016/dream

SMC-RNA BioVis Data Visualization DREAM Challenge





What is a DREAM Challenge?



• http://dreamchallenges.org

• DREAM Challenges pose fundamental questions about systems biology and translational medicine.

• Vision: Allowing individuals and groups to collaborate openly so that the “wisdom of the crowd” provides the greatest impact on science and human health.

• DREAM was launched in 2006 by Gustavo Stolovitzky (IBM) in collaboration with Andrea Califano (Columbia University). Sage Bionetworks has been providing institutional support since 2013.


http://dreamchallenges.org


What is the SMC-RNA DREAM Challenge?



• https://www.synapse.org/#!Synapse:syn2813589/wiki/401435

• The challenge is to computationally predict gene/transcript fusions and transcript isoforms based on RNA-seq data.

• This will yield many new tools and predictions for fusions and transcript isoforms.


https://www.synapse.org/#!Synapse:syn2813589/wiki/401435


What are isoforms and fusions? Why are they important?



Alternative Splicing

Liu S, Cheng C. Alternative RNA splicing and cancer. Wiley interdisciplinary reviews RNA. 2013,4(5),547-566.



Isoforms in Cancer

Liu S, Cheng C. Alternative RNA splicing and cancer. Wiley interdisciplinary reviews RNA. 2013,4(5),547-566.



Gene + Transcript

Fusions

Mertens, F., et al. (2015). The emerging complexity of gene fusions in cancer. Nature Reviews Cancer, 15(6), 371-381.



Fusions in Cancer




Why a visualization challenge?



Fusions in Cancer




What are we looking for?



• What exactly we are looking for will be announced later this summer.

• We won’t have any preconceived notion about what we will accept as solutions.

• It will be important that the solution can be used to enhance our understanding of biology.

• It needs to be usable by a wide range of investigators.



What is the time line?



• Anticipated launch in Summer 2016.

• Submissions in Fall/Winter 2016.

• The visualization challenge will be synchronized with the SMC-RNA challenge (https://www.synapse.org/#!Synapse:syn2813589/wiki/401435)

• Unlike past data contests, this challenge is decoupled from the BioVis meetings.


https://www.synapse.org/#!Synapse:syn2813589/wiki/401435


What are the incentives?



What we aim for (but no promises):

• All participants will be invited as consortium co-authors on Challenge marker papers

• Winners will receive speaking invitations at the next DREAM conference or a future BioVis meeting

• New methods will be considered for co-publication with the Challenge marker papers by our publishing partner

• Other rewards will be announced as they are determined.



Where to get more information and how to

receive updates?



1. Go to www.biovis.net/2016/dream.2. Follow link to Synapse Wiki.



3. Scroll down.4. Click link to “Join” to pre-register.



Who is organizing this?



BioVis Team

• Raghu Machiraju, The Ohio State University, USA

• Cagatay Turkay, City University London, UK

• Angela Brooks, University of California Santa Cruz, USA

• Nils Gehlenborg, Harvard Medical School, USA

Advisors and Support

• Paul Boutros, OICR, Canada (SMC-RNA Challenge Leader)

• Thea Norman, Sage Bionetworks, USA (DREAM Challenge Director)



Do you have questions?


smc-rna biovis data visualization dream challenge preview

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