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NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge Opens Today

NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge Opens Today

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Published by: Crowdsourcing.org on Jun 11, 2013
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The collaboration withSage/DREAM is animportant extension of our ongoing partnershipwith NIEHS and UNC”
 June 11, 2013 02:59 AM Eastern Daylight Time
NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge Opens Today
Finding better ways to predict the toxicity of chemicals
DREAM Conference 2013SEATTLE--(BUSINESS WIRE)--An innovative crowdsourced computational Challenge, called the NIEHS-NCATS-UNCDREAM Toxicogenetics Challenge, launches today. The objective of this Challenge is to obtain a greater understandingabout how a person’s individual genetics can influence cytotoxic response to exposure to widely used chemicals. It isbeing led and organized by scientists from Sage Bionetworks, DREAM, the University of North Carolina, the NationalInstitute of Environmental Health Sciences (NIEHS) and the National Center for Advancing Translational Sciences(NCATS).Challenges such as the NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge engagediverse communities of scientists to competitively solve a specific problem in a given timeperiod by placing scientific data, tools, and the resulting predictive models into an openCommons or workspace – in effect, “crowdsourcing” data analysis. Those interested to participate in this Challenge can sign up here:https://www.synapse.org/ - !Challenges:DREAM8. The Challenge will close onSeptember 15, 2013, and the top-scoring team(s) will be announced at the November, 2013 DREAM Conference(www.iscb.org/recomb-regsysgen2013) taking place in Toronto, Canada.
The NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge
 The NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge represents the type of Challenge that Sage Bionetworks andDREAM are most interested to run: namely those with the potential to provide powerful scientific insights and meaningfulpublic impact. Toxicity testing that monitors health risks posed to humans through chemical exposure is a crucialcomponent of public health. Yet currently, for every chemical that has been tested for toxicity, there are thousands thatremain as yet untested. To address this, toxicologists are highly interested to leverage the dramatic technologicaladvances in molecular biology and computer science that now make it possible to use high throughput in vitrobiochemical- and cell-based assays and genomic data for toxicological testing. Towards this goal, theNIEHS/NCATS/UNC team recently conducted the largest ever population-based in vitro cytotoxicity study by treating 1086human lymphoblastoid cell lines representing 9 distinct geographic subpopulations (made available via the 1000 GenomesProject:www.1000genomes.org), with 179 pharmaceutical and environmental chemicals. The resulting cytotoxicity datawhen paired with the publicly available genetic and genomic data on each of the respective cell lines provides a unique
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dataset that researchers can use to predict toxic responses to chemical compounds across a genetically diverse humanpopulation.Predicting how different people or groups of people will respond to certain chemicals is difficult to determine, butimportant for protecting the public’s health,” said Raymond Tice, Ph.D., who heads the Biomolecular Screening Programat NIEHS. By positioning this data for a DREAM Challenge, a community of Challenge participants will be asked to solveone or both of two related sub-Challenges: (1) Use the data to develop a model that accurately predicts individualresponses to compound exposure based on genomic information and (2) Use the data to develop a model that accuratelypredicts how a particular population will respond to certain types of chemicals.“We are delighted to partner with Sage/DREAM to release this unique dataset obtained through a broad partnership withNIEHS and NCATS,” said Ivan Rusyn, M.D., Ph.D., professor of environmental sciences and engineering at UNC’s GillingsSchool of Global Public Health. “The long-term strategic value of accurate predictive models will be invaluable for bothprotection of human health and the environment, and support of innovations in the chemical industry.”“The collaboration with Sage/DREAM is an important extension of our ongoing partnership with NIEHS and UNC,” addedAnton Simeonov, Ph.D., NCATS acting scientific director of discovery innovation. “We have capitalized on NIEHS’expertise in toxicology, UNC’s expertise in genomics and NCATS’ quantitative high throughput screening technologyplatform to evaluate thousands of chemicals at multiple concentrations.”
Three-month Challenge period with continuous participation
Sage and DREAM’s organizers plan to deploy tools and incentives throughout the three-month Challenge period tostimulate a high level of continuous participation. For example, within a month of opening this Challenge, organizers will golive with a real-time leaderboard for one of the sub-Challenges: this leaderboard will post the “scores” of submittedpredictions as evaluated against a held back portion of the data. And to foster collaboration in the Challenge community,organizers are planning to roll out a few rewards during the Challenge. These will encourage participants to, for example,submit code for their models so that it can be used by others to build new and improved hybrid models (for which boththe creator and borrower of code will be rewarded) and to write-up the so-called “provenance” description for theirfavorite model, describing the analytical steps taken to build that model, so that others can have a better understandingof how different models are constructed. Finally, funds from the DREAM conference sponsors, including the NCI’s MagnetCenter (at Columbia University) and IBM Research, will be used to provide small travel grants to top performing teams topresent their results at the annual DREAM conference.“We anticipate that this Challenge will attract a lot of enthusiasm from the modeling community due to the size, scale, anduniqueness of this fantastic dataset,” said Gustavo Stolovitzky, co-founder of the DREAM project and a key leader on theplanning of this Challenge. “With the special features in this Challenge, such as the real time leaderboard and incentivesto share and borrow model code, which in the 2012 Sage-DREAM Breast Cancer Prognosis Challenge attracted over1500 models, we expect that the Toxicogenetics Challenge will also elicit submission of thousands of model predictions.”
Three Challenges open today
 The NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge is one of three Challenges that Sage Bionetworks andDREAM opened to the public today. The two other Challenges are:
The Heritage Provider Network-DREAM Breast Cancer Network Inference Challenge
: Infer the signaling networks inbreast cancer cell lines
The Whole Cell Parameter Estimation Challenge
: Infer the kinetic parameters underlying biological processes in wholecell models
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More information on these DREAM8 Challenges including how to participate is available here:https://www.synapse.org/ -!Challenges:DREAM8
Chartered in 1789 as the nation’s first public university, The University of North Carolina at Chapel Hill has earned areputation as one of the best universities in the world. UNC’s Gillings School of Global Public Health is the top-rankedpublic school of public health in the nation. The work that has led to this collaboration was conducted by the students andstaff of the Carolina Center for Computational Toxicology under direction of Ivan Rusyn, M.D., Ph.D., and Fred Wright,Ph.D., who are faculty members in UNC-Gillings’ Department of Environmental Science and Engineering and Departmentof Biostatistics.
 The NIEHS supports research to understand the effects of the environment on human health and is part of NIH. For moreinformation on environmental health topics, visithttp://www.niehs.nih.gov. Subscribe to one or more of the NIEHS newslists to stay current on NIEHS news, press releases, grant opportunities, training, events, and publications.
Sage BionetworksStephen Friend, 206-667-2101friend@sagebase.orgorGustavo Stolovitzky, 914-945-1292gustavo@us.ibm.com
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