Press category: Challenges

SEATTLE–(BUSINESS WIRE)–Today, Prize4Life, Sage Bionetworks and the DREAM community announced the winners of the DREAM ALS Stratification Prize4Life Challenge, a global data analysis competition to computationally identify different subgroups of ALS patients. In ALS, there is currently no way to determine whether someone living with the disease will survive the average of 3-5 years after diagnosis or live with ALS for decades. The goal of the Challenge is to find answers that may inform clinical practice, new trial designs, and ultimately personalized approaches to the discovery and development of new ALS medicines.

“We want to accelerate ALS drug discovery and believe that critical breakthroughs will come from new ways of thinking, collaborating, and sourcing ideas,” said Shay Rishoni, CEO at Prize4Life. “I’m excited by the results of the ALS Stratification Challenge and congratulate the winners who significantly outperformed the bar.”

Participants were free to compete as individuals or on teams and could work on as many as 4 different sub-challenges.

In Sub-challenge 1, the winner, Team UglyDuckling is from the Department of Computer Science and Information Engineering at the National Cheng Kung University, Taiwan. The team comprises Dr. Wen-Chieh Fang, Huan-Jui Chang, Chen Yang, Prof. Hsih-Te Yang, and Prof. Jung-Hsien Chiang. Dr. Wen-Chieh Fang, a post doc at Prof. Jung-Hsien Chiang’s lab, is the leader. This is Team UglyDuckling’s second DREAM Challenge participation and first win.

In Sub-challenge 2 and Sub-challenge 4, the winner, Team Guanlab_Umich, is from the Department for Computational Medicine and Bioinformatics at the University of Michigan, USA. Prof. Yuanfang Guan is a faculty member, and having won seven DREAM challenges (three in 2015 alone), is an emerging leader in machine learning.

In Sub-challenge 3, the winner, Team Jinfeng_Xiaofrom is from the Center for Biophysics and Quantitative Biology at the University of Illinois at Urbana-Champaign, USA. Jinfeng Xiao is a second year PhD student and repeat Challenge winner. This is Xiao’s first individual win.

“We thank the participants of the DREAM ALS Stratification Prize4Life Challenge,” said Stephen Friend, President, Co-Founder, and Director of Sage Bionetworks. “ALS is a variable disease and the speed of progression is different from person to person. Through our community-based approach, our participants were able to mine the largest ALS clinical trials and registry databases and produce promising computational models to find patterns and identify subgroups of ALS patients.”

The winning teams will share a $28,000 cash prize, be invited to present their winning models at the DREAM Conference on Regulatory and Systems Genomics meeting on November 16-18, and have the opportunity to co-author a Challenge overview paper for which the journal partner is Nature Biotechnology.

The ALS Stratification Challenge is a unique competition defined by the diversity of its participants and resourceful sponsorship. The Challenge featured over 70 entrants from 30 teams across 15 countries and was sponsored by leading research-based biopharmaceutical companies Biogen and Eli Lilly and Company. IBM also supported the Challenge with computational resources. The cash prizes were raised by running a crowdfunding campaign called “Fund the Prize” that ran in winter 2014-2015 and succeeded in raising $28,000 for prizes.

“The Challenge winners and participant community will help deepen our understanding of ALS, a devastating and complicated disease,” says Gustavo Stolovitzky, DREAM founder from IBM Research and the Icahn School of Medicine at Mount Sinai. “Crowdsourcing a powerful dataset and having participants submit their source code to predict patient prognosis has advanced the Sage Bionetworks’ and DREAM’s mission of fostering open and collaborative science while addressing the problem of stratification in ALS.”

Prize4Life provided the largest open-access ALS clinical trials database in the world (PRO-ACT: ALSDatabse.org), developed with NEALS and MGH, which served as the basis for the Challenge along with national ALS registries from Ireland and Italy. Sage Bionetworks and DREAM created a cloud-based Challenge platform called Synapse (www.synapse.org) where participants accessed the data and shared ideas.

Challenge participants performed work on cloud-based computational resources donated by IBM. An exciting technical feature of this Challenge was that participants submitted their open source algorithms in a portable framework to the IBM cloud for scoring. At the end of the Challenge all of the submitted analysis methods will be available on Sage’s Synapse platform as a Challenge library and community resource that can serve as the basis of ongoing research.

“We are committed to finding answers to ALS and dedicated to supporting new approaches like crowdsourcing and big data analysis that have the potential to provide powerful insights into the disease,” said Donald R. Johns, M.D., Vice President, ALS Development at Biogen. “We are grateful to the participants of the DREAM ALS Stratification Prize4Life Challenge who have created new knowledge and an important repository for research that may bring improved trials, new treatments, and hope to ALS patients.

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CARY, N.C.–(BUSINESS WIRE)–Winners of the Prostate Cancer DREAM Challenge were formally recognized at the Prostate Cancer Foundation’s 22nd Annual Scientific Retreat, October 8-10, in Washington, D.C. The Prostate Cancer DREAM Challenge is the first research challenge in prostate cancer to marry crowdsourcing with data sharing, paving a new way to tackle key research questions about metastatic castration-resistant prostate cancer (mCRPC), an advanced form of the disease with poor outcomes.

“Prostate Cancer DREAM Challenge participants produced first-class work in an incredibly competitive landscape,” said Dr. Howard Soule, Chief Science Officer, Prostate Cancer Foundation. “The findings of the best performers could impact trial design by addressing the historical challenge of clinical trials to define their inclusion/exclusion criteria.”

The Challenge called upon the cancer research and computational biology community to find solutions to key open clinical research questions about mCRPC and explore innovative research and modeling approaches. The two specific questions posed were to:

• Predict overall survival for prostate cancer patients using clinical data
• Predict treatment discontinuation for prostate cancer patients treated with docetaxel

This challenge produced unprecedented levels of participation, with more than 550 registrants, comprising more than 60 teams. Three rounds of leaderboard scoring allowed teams to submit up to five predictions per round; in total, nearly 1,200 model predictions and almost 160 final submissions were received across two sub-challenges.

A total of 11 teams were selected as winners between the two sub-challenges. Team FIMM-UTU from the University of Turku, Finland, and the University of Helsinki, Finland, was the best performing team for the first sub-challenge regarding prediction of overall survival; the best performing teams for the second sub-challenge regarding prediction of treatment discontinuation came from a variety of departments at universities across Japan, Canada, the United States and Europe.

“The Prostate Cancer DREAM Challenge attracted a substantial number of participants to address specialized questions in prostate cancer research,” said Dr. Oliver Sartor, Laborde Professor of Cancer Research, Medicine and Urology Departments, Tulane University School of Medicine. “The best performing teams developed very credible methodologies that could have implications for moving beyond overall survival as an endpoint for prostate cancer studies.”

Complete results can be found on the Prostate Cancer DREAM Challenge homepage. The winners will be invited to co-author a Challenge overview paper that will be submitted for peer review to Nature Biotechnology. Winners will also each receive a share of an educational award from Project Data Sphere, LLC, sponsored by AstraZeneca. Also, top performers will be invited to present their team’s winning method at the RECOMB/ISCB Regulatory and Systems Genomics/DREAM Conference in Philadelphia, Pa., in November. Finally, solvers will be able to submit write-ups on their models toF1000Research, an open science publishing platform, where the models can be reviewed.

Data for the Challenge was standardized and integrated from four different, de-identified clinical trials with more than 2,000 mCRPC patients treated with first-line docetaxel. The data sets were provided to Project Data Sphere, LLC by AstraZeneca, Celgene, Memorial Sloan Kettering Cancer Center and Sanofi US.

Project Data Sphere, LLC, and Sage Bionetworks with the support and experience of the DREAM Challenges Initiative, came together to make the Challenge possible. Utilizing multiple clinical trial data sets from the Project Data Sphereplatform (www.ProjectDataSphere.org), the Challenge was hosted on Synapse (https://www.synapse.org), Sage Bionetworks’ open compute platform that allowed data to be worked on interactively by Challenge participants, as individuals or as teams.

Prostate cancer is the most common cancer among men, with approximately 233,000 new diagnoses in 2014 in the U.S.¹For patients whose disease has spread (metastasized), survival rates are often poor due to the loss of efficacy of hormonal therapy, which has been the standard of care treatment of prostate cancer for more than 70 years².

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CARY, N.C.–(BUSINESS WIRE)– Project Data Sphere (PDS) is an independent not-for-profit initiative of the CEO Roundtable on Cancer’s Life Sciences Consortium (LSC). The CEO Roundtable on Cancer has expanded the executive leadership of PDS to continue building on PDS’s first-year data collection successes and broaden the academic, government and industry collaborations that continue to drive the progress of this innovative research library-laboratory.

Currently, nearly 1,000 authorized users of the Project Data Sphere^®platform can access 51 comparator arm data sets representing more than 27,000 patient lives across a broad array of cancer tumor areas. In order to ensure that researchers can realize the full potential of this data, PDS teamed with CEO Roundtable on Cancer Member SAS Institute Inc. (SAS), a leader in data and health analytics, which developed and hosts the platform and provides free state-of-the-art analytic tools to the platform’s authorized users.

Christopher A. Viehbacher, Chairman of Board of the CEO Roundtable on Cancer, has announced the appointment of Dr. Martin J. Murphy as PDS’s Chief Executive Officer, Kenneth B. Lee, Jr. as Treasurer and John N. Dornan, Jr. as Chief Operating Officer. Dr. Kald Abdallah, who most recently served as Chief Project Data Sphere Officer, has left the organization to pursue a new career opportunity.

“Already within its first year, the broad-access approach of the Project Data Sphere® platform has proven its innovation potential by aggregating and permitting analysis of a massive volume of data otherwise hidden in historical clinical trials,” said Robert A. Ingram, founding Chairman, and current Vice Chairman of the Board of the CEO Roundtable on Cancer. “We must now expand the number of clinical trials from both industry and academia, because these new data will hasten our ability to improve clinical trial design, enhance our understanding of cancer cell biology, and catalyze practice-changing discoveries.”

Through The Prostate Cancer DREAM Challenge, an effort launched in collaboration with Sage BioNetworks with the support of the Prostate Cancer Foundation, more than 50 teams comprised of more than 500 solvers in the cancer research and computational biology community worked to find solutions to key unanswered clinical research questions and explore innovative research and modeling approaches. In addition to working with Sage BioNetworks on an innovative crowdsourcing challenge, PDS has provided access, through the Project Data Sphere platform, to previously untapped data as well as powerful analytic software tools with which to interrogate it. The result has been an increasing number of research outcomes including several peer-reviewed papers published recently in The Oncologist and research abstracts published in conjunction with the annual meeting of the American Society of Clinical Oncology earlier this year.

The achievement of these research milestones was made possible by organizations that provided data and catalyzed the use of the platform for research innovation. Charter data providers include AstraZeneca, Bayer, Celgene, Johnson & Johnson, Memorial Sloan Kettering Cancer Center, Pfizer and Sanofi. Most of these organizations also increased their level of data provision throughout the year. Additionally, the ranks of data providers grew to include other leading oncology research organizations such as Amgen, EMD Serono, Lilly, Synta and The Alliance for Clinical Trials in Oncology, one of the five U.S. network groups of the National Cancer Institute’s (NCI) National Clinical Trials Network (NCTN) Program.

PDS Chief Executive Officer, Martin J. Murphy, DMedSc, PhD, FASCO, is a member of PDS’s Executive Committee which also includes Victor Dzau, MD, President, National Academy of Medicine; Stephen Friend, MD, PhD, President, Co-Founder and Director, Sage Bionetworks; Dennis Gillings, PhD, Executive Chairman, Quintiles; Richard Goldberg, MD, Physician-in-Chief, James Cancer Hospital and Solove Research Institute; Charles A. Sanders, MD, Executive Chairman, Foundation for the National Institute of Health; and Elias Zerhouni, MD, President, Global R&D, Sanofi.

Murphy is the founding and current Chief Executive Officer of the non-profit CEO Roundtable on Cancer, Inc., founded at the request of forty-first President, George H.W. Bush. Murphy is also founding Chairman and Chief Executive Officer of AlphaMed Consulting, Inc. and founding Executive Editor of the peer-reviewed journal, The Oncologist. The founder and former Chief Executive Officer of the Hipple Cancer Research Center, Murphy is also a member of the National Cancer Policy Forum of the Institute of Medicine and a director of the Foundation for the National Institutes of Health. Murphy is Chairman Emeritus of the Conquer Cancer Foundation of the American Society of Clinical Oncology (ASCO), convener of ACT-China (Advanced Clinical Trials-China) and a steering committee member and senior consultant of the Chinese Society of Clinical Oncology. Murphy is a charter member and Vice Chairman of C-Change, also founded at the request of former President George H. W. Bush and former First Lady Barbara Bush. In 2014, Murphy accepted the 2014 Project HOPE Global Health Impact Award on behalf of the CEO Roundtable on Cancer recognizing its ongoing, global, workplace health and wellness efforts as well as the organization’s leadership in the much–needed area of sharing critical clinical trial data in oncology.

Lee is a general partner of Hatteras Venture Partners and plays a key role in deal sourcing, investment decisions, management recruitment and evaluation and implementing exit strategies. Lee is the former co-head of International Life Sciences for Ernst & Young, where he established a career over 29 years advising biotechnology and pharmaceutical companies throughout the world. He got his start in biotech as part of the first audit team of Genentech in 1976. As co-founder and manager of Ernst & Young’s national life sciences practice from his location in the San Francisco Bay Area, he advised numerous high profile life science companies with their initial public offerings, mergers and acquisitions, and strategic financings. Among others, these included Affymax, Affymetrix, Applied ImmuneSciences, Chiron, Circadian, Genentech, Heartport, Systemix, ALZA and Collagen.

Dornan is the Executive Director of the CEO Roundtable on Cancer, Inc., overseeing the group’s initiatives including the CEO Cancer Gold Standard workplace accreditation program that recognizes employers who provide state-of-the-art preventive care, wellness support and cancer treatment; and the Life Sciences Consortium, whose efforts to encourage researchers to work collaboratively to accelerate the discovery and development of new therapies for cancer patients resulted in the formation of Project Data Sphere, LLC. He is a former Vice President of Trone, a mid-Atlantic regional advertising and public relations agency. He previously headed corporate public relations for SAS and held marketing and communications positions with Healthsource North Carolina prior to its acquisition by CIGNA. He began his career in North Carolina’s Department of Health and Human Services where he provided outreach and communications services for the state’s welfare reform efforts and programs for children and families including the nationally renowned Smart Start early childhood initiative created by Gov. James B. Hunt.

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BETHESDA, Md.–(BUSINESS WIRE)–Sage Bionetworks, in partnership with the National Cancer Institute’s (NCI) Division of Cancer Control and Population Sciences (DCCPS), launched a new prize competition this week, “Up For A Challenge (U4C) – Stimulating Innovation in Breast Cancer Genetic Epidemiology.” U4C encourages innovative approaches to more fully decipher the genomic basis of breast cancer.

Breast cancer is the second most common cause of cancer death in women in the United States. Genome-wide association studies (GWAS) helped to identify more than 90 common genetic variations that are associated with breast cancer risk. Although GWAS have greatly enhanced our understanding of the genetic component of breast cancer susceptibility, the results to date explain only a small portion of the estimated genetic contribution to breast cancer risk.

The goal of the Challenge is for participants to use innovative approaches to identify novel pathways—including new genes or combinations of genes, genetic variants, or sets of genomic features—involved in breast cancer susceptibility in order to generate new biological hypotheses. The Challenge also provides an opportunity to examine the genetic heritable contribution to health disparities, by facilitating greater access to GWAS data sets from African American, Asian, European, and Latino women.

Says Gustavo Stolovitzky, from IBM Research and the Icahn School of Medicine at Mount Sinai and founder of the crowdsourced DREAM Challenges that examine questions in biology and medicine: “Crowdsourcing the elucidation of the epidemiology of breast cancer susceptibility is a great way to maximize our chances of finding the genetic causes of one of the more serious health problems for women. We hope the DREAM community, and the computational biology community at large, will see NCI and Sage’s “Up For A Challenge” as a great new opportunity to make the wisdom of the crowds useful one more time in translational research.”

These data sets, some of which will be released for the first time via the National Institutes of Health (NIH) database of Genotypes and Phenotypes (dbGaP), will be made available through controlled access to researchers. Scientists will also be able to use other publicly available data sets for the purposes of developing and applying methods for identification of the novel pathways.

NCI will award up to $50,000 in funds based on the identification of novel findings, replication of findings, innovation of approach, evidence of novel biological hypotheses, and collaboration. Selected winners will be invited to prepare a manuscript for publication describing their approach and results, with the goal of a special journal issue (PLoS Genetics) highlighting the Challenge. All Challenge participants will be acknowledged in this issue.

For more information about the Challenge application, due dates, rules, and other FAQs, visit the Challenge website athttps://www.synapse.org/upforachallenge. U4C submissions are due by 8 P.M. ET on January 15, 2016.

The Challenge is being launched under the America Creating Opportunities to Meaningfully Promote Excellence in Technology, Education, and Science (COMPETES) Reauthorization Act of 2010.

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SEATTLE–(BUSINESS WIRE)–Today Prize4Life (http://www.prize4life.org.il/) in partnership with Sage Bionetworks (www.sagebio2018.wpengine.com) and the DREAM Challenges (www.dreamchallenges.org) announced the opening of the DREAM ALS Stratification Prize4Life Challenge (https://www.synapse.org/#!Synapse:syn2873386/wiki/), a global open science data analysis competition geared to develop more personalized approaches for the research, prognosis and treatment of ALS.

Computational DREAM Challenges engage diverse communities of data-focused scientists to competitively solve a specific problem in a given time period by placing scientific data, tools, leaderboards and the resulting predictive models into an open, cloud-based computational workspace — in effect, “crowdsourcing” data analysis.

ALS (amyotrophic lateral sclerosis), also known as Lou Gehrig’s disease, or Motor Neuron Disease, is a fatal, rapidly progressing neurodegenerative disease that leads to paralysis and eventually death. One in 1,000 individuals will live with, and die of, ALS. There is no cure and the average lifespan is 3-5 years.

“How long do I have to live?” “What will the quality of my life be while I live?” For patients with ALS, these are immediate questions because there is currently no way to determine whether someone with ALS will die in 2 years, like baseball great Lou Gehrig (about 90% of those patients diagnosed with ALS), or will live with the disease for up to 50 years, like physicist Stephen Hawking (who has survived longer than almost any other ALS patient). Without an ability to distinguish between patients with very different disease progressions, clinical trial efforts to evaluate potential new ALS treatments end up being expensive and fraught with failure.

The key goal of the DREAM ALS Stratification Prize4Life Challenge (or ALS Stratification Challenge) is to identify the attributes that differentiate ALS patients. Such information will help patients and families plan accordingly to increase their quality of life and will also help guide the development of so-called stratified ALS clinical trials that could enroll specific ALS subgroups for the testing of new treatments.

The ALS Stratification Challenge will run from June to mid-September, 2015, and spur the development of quantitative solutions to stratify ALS patients based on their disease progression or survival.

Prize4Life is providing the largest open ALS clinical trials database in the world (PRO-ACT:https://nctu.partners.org/ProACT), which will serve as the basis for the Challenge. Sage Bionetworks and DREAM have created an engaging set of incentives and a cloud-based Challenge environment — called Synapse (www.synapse.org) — where Challenge participants can access and analyze the data, work alone or on teams, submit their quantitative solutions to a leaderboard for scoring against a hidden validation data set and share their ideas, code, and analysis results with others in the Challenge. IBM is donating computational resources for the Challenge and working with Sage Bionetworks to provide a cloud-based environment to empower participants with limited computational power. An exciting technical feature of this Challenge is that participants will submit their open source algorithms in a portable framework to the IBM cloud for scoring. At the end of the Challenge all of the submitted analysis methods will be available on Sage’s Synapse platform as a Challenge library and community resource that can serve as the basis of ongoing research.

The top-performing teams will each receive a $7,000 cash prize, be invited to present the winning model at DREAM’s conference this fall, and have the opportunity to co-author a Challenge overview paper that Nature Biotechnology has expressed interest in considering.

“We believe the ALS Stratification challenge holds great promise to unlock the mysteries of how ALS develops and accelerates the development of ALS treatments and a cure,” says Shay Rishoni, Prize4Life CEO. “We established the PRO-ACT database in 2012 — with the support and partnership of the Northeast ALS Consortium, the ALS Therapy Alliance and, of course, drug companies — exactly for these goals — to bring hundreds of fresh new minds into the world of ALS research. A breakthrough for ALS research will come; we invite the brilliant minds of the computational research community to participate in that victory.”

Prize4Life and DREAM have already demonstrated the power of open Challenges to advance ALS disease research. The ALS Prediction Prize (http://www.innocentive.com/prize4life-announces-50000-als-prediction-prize-winners), conducted in 2012, had over 1,000 registrants from 63 countries, and the winning approaches — described in an article in the November 2014 issue of Nature Biotechnology — outperformed the predictions of more than 12 expert clinicians of ALS, and should make it possible to reduce the costs of future clinical trials by roughly $6 million per trial in part by reducing patient enrollment by up to 20%.

Says Gustavo Stolovitzky, from IBM Research and the Icahn School of Medicine at Mount Sinai: “We are delighted to work again with Prize4Life to organize a follow-up to our previous ALS Prediction DREAM Challenge (https://www.synapse.org/#!Synapse:syn2826267). In this Challenge, and with a data set that is around 5 times larger than in the first Challenge, we expect to deepen the findings of the first Challenge. Crowdsourcing this powerful dataset and requiring participants to submit their source code to predict patient prognosis advances the Sage and DREAM mission of fostering open and collaborative science while addressing the problem of stratification in this devastating disease.”

A unique component of the ALS Stratification Challenge is the diversity of groups involved. Leading research-based biopharmaceutical companies Biogen and Eli Lilly and Company are helping fund the Challenge effort and providing key advice, and IBM is providing cloud computing. The cash prizes for the Challenge were raised by running a crowdfunding campaign called “Fund the Prize” that ran in Fall, 2014, and succeeded in raising $28,000 for prizes (https://www.indiegogo.com/projects/fund-the-prize-solve-als-together#/story). In addition to the PRO-ACT Challenge dataset, registry data from the Irish National ALS Register and the Italian Piemonte and Valle d’Aosta Register for ALS will be released mid-Challenge. Finally, the Challenge organizing team includes winners from the earlier ALS Prediction Prize Challenge and the Rheumatoid Arthritis Responder Challenge.

Remarked Liuxia Wang (Principal Scientist of Sentrana, Inc.), who was a top performer in the first ALS Challenge and is now a member of the Challenge organizing team for the ALS Stratification Challenge, “It’s been an honor to be a part of both challenges, first as a participant, and now as a part of the organizing team. When we participated in the first ALS Challenge, we had no idea about ALS, but we did know how to dig into sales data and to sort out meaningful business insights using various statistical/machine learning algorithms. I am glad to help to organize the second Challenge to further understand why some patients progress faster than others. I would encourage all data scientists, no matter if you are in the field of life science or not, to join the mysterious, but rewarding, journey to help to accelerate the cure for ALS.” Wang’s innovative work in the first DREAM ALS Challenge provided the foundation for the launch of a new startup company, Origent Data Sciences. Origent now helps ALS researchers and biopharma companies to accelerate their ALS research and to better analyze and design their ALS clinical trials.

Said Donald R. Johns, M.D., Vice President, Head, ALS Innovation Hub at Biogen. “This is part of our ongoing effort to participate in projects that have the potential to improve our understanding of ALS, and we are hopeful that this effort will provide insights that make future clinical trials more effective and efficient. We are excited to collaborate with Prize4Life, DREAM, and Sage Bionetworks to advance the use of crowdsourcing and big data analysis to help bring understanding and hope to people with ALS.”

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SEATTLE–(BUSINESS WIRE)–Working with partners at the Broad Institute, MD Anderson Cancer Center, Rice University and the Global CEO Initiative for Alzheimer’s Disease, DREAM and Sage Bionetworks today opened three computational Challenges (https://www.synapse.org/#!Challenges:DREAM), leveraging big data in cancer and Alzheimer’s Disease. These Challenges will run until mid-September and are expected to attract the participation of hundreds of scientific teams.

Started in 2006 by IBM Research’s Dr. Gustavo Stolovitzky, the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project consists of a distributed community of computational biologists who have been collaborating to run open DREAM Challenges every year; these Challenges engage diverse communities of scientists to competitively solve a specific problem in biomedicine in a given time period. In the past 7 years, DREAM has run 27 successful Challenges in systems biology, published over 60 DREAM Challenge-related papers, and aggregated a “crowd” of thousands of “DREAMERs.”

In 2013, Sage Bionetworks joined with the DREAM community to co-lead a new generation of Challenges that leverage collaborative data hosting and analysis tools available on Synapse (www.synapse.org), Sage Bionetworks’ open bioinformatics compute space. Running on Synapse, the last 6 DREAM Challenges made use of engaging features such as real-time Challenge leaderboards that score participants’ predictions and immediately report the result. In the first three month season of running Challenges together, DREAM and Sage Bionetworks were delighted to see the level of participation nearly double: Synapse’s Challenge leaderboards allowed participants to submit more than 2,000 predictions for scoring and to evolve their models throughout the competition period.

States DREAM Founder Dr. Gustavo Stolovitzky, “It is really gratifying to be opening the 9^th season of DREAM Challenges where we will focus on important questions in cancer and Alzheimer’s Disease. Each year I grow more convinced that with DREAM Challenges, we’ve really hit upon a powerful approach for accelerating research. The combination of hosting exciting data sets and posing impactful Challenge questions that can be objectively evaluated makes DREAM Challenges a powerful catalyst for building new communities of experts that keep working together even after a Challenge closes.”

Anyone can sign up for the three DREAM Challenges that opened today (signup is open athttps://www.synapse.org/#!Challenges:DREAM) and will close in the fall. Challenge winners will be announced in early October. Key information about each of the Challenges is provided below:

• The Alzheimer’s Disease Big Data DREAM Challenge #1 (https://www.synapse.org/#!Synapse:syn2290704):
  • Originally announced at the White House on June 20, 2013 (http://www.whitehouse.gov/blog/2013/06/20/big-data-and-personalized-medicine). Running as a delayed DREAM8.5 Challenge.
  • Data provided by Alzheimer’s Disease Neuroimaging Initiative (ADNI), Rush University Medical Center, and The AddNeuroMed Study.
  • Funders: Alzheimer’s Research UK, Bright Focus Foundation, Pfizer Inc, the Ray and Dagmar Dolby Family Fund, the Rosenberg Alzheimer’s Project, Sanofi, Takeda.
  • Sponsor: European Medicines Agency.
  • Computational resources donated by IBM.
  • Publishing partner: Nature Neuroscience.
  • Challenge Focus: Predict the best biomarkers for early AD-related cognitive decline and for the mismatch between high amyloid levels and cognitive decline.
  • Best performers will be invited to present their results at the International Biomedical Commons Congress, to be held in Paris in April 2015.
• The Broad-DREAM Gene Essentiality Prediction Challenge(https://www.synapse.org/Portal.html#!Synapse:syn2384331/wiki/):
  • Data provided by the Broad Institute.
  • Data Funding: NCI Cancer Target Discovery and Development (CTD2), Instituto Carlos Slim de la Salud (ICSS), EMD Serono, NCI Integrative Cancer Biology Program (ICBP), Eli Lilly and Company, Novartis and Pfizer.
  • Challenge Funding: NCI CTD2, ICBP and Washington State Life Sciences Discovery Fund (LSDF).
  • Computational resources donated by IBM.
  • Challenge Focus: Develop predictive models that can infer levels of gene dependencies (i.e. how essential each gene is to a cancer cell’s survival when suppressed), using features of the cell lines. (see Broad Institute blog about the Challenge: www.broadinstitute.org/node/5775)
  • Best performers will be invited to present their results at the DREAM track of the RECOMB/ISCB Systems and Regulatory Genomics/DREAM Conference, to be held in San Diego, California, November 10-14, 2014.
• The DREAM9 Acute Myeloid Leukemia (AML) Outcome Prediction Challenge(https://www.synapse.org/#!Synapse:syn2455683):
  • Data provided by the MD Anderson Cancer Center.
  • Funders: NCI Integrated Cancer Biology Program (ICBP), Washington State Life Sciences Discovery Fund (LSDF) and Rice University.
  • Challenge Focus: Predict the outcome of treatment of AML patients (resistant or remission), their remission duration and overall survival based on clinical cytogenetics, known genetics markers and phosphoproteomic data.
  • Publishing partner: PLoS Computational Biology.
  • Best performers will be invited to present their results at the DREAM track of the RECOMB/ISCB Systems and Regulatory Genomics/DREAM Conference, to be held in San Diego, California, November 10-14, 2014.

The AD#1 Challenge is the first in what DREAM and Sage Bionetworks envision as a series of Grand Challenges that disrupt the “business as usual” approach to research with innovative Big Data techniques. Remarks George Vradenburg, Convener of The Global CEO Initiative on Alzheimer’s Disease, “There is high expectation internationally for the prospects of using Big Data to accelerate discovery and drug development in the Alzheimer’s space. This is an exciting, first-of-its-kind global Challenge using open science techniques and big data processes to advance Alzheimer’s discovery. The CEOi is pressing the edge of innovative science to accelerate Alzheimer’s discovery and to achieve our national goal of preventing this disease by 2025.”

The Broad-DREAM Gene Essentiality Prediction Challenge seeks to broaden the impact of targeted cancer therapy by identifying drug targets as well as new biomarkers that can be used to identify patient populations likely to respond to a particular therapy. William Hahn, a senior associate member at the Broad Institute and an associate professor of medicine at the Dana-Farber Cancer Institute and Harvard Medical School, says, “We are excited to be a part of the DREAM competition. The next frontier of understanding cancer vulnerabilities will be shaped by predictive modeling and we look forward to the potential impact winning models will have.”

With only 25% of people diagnosed with AML surviving beyond 5 years, there is a high level of urgency to find better treatments. The DREAM9 Acute Myeloid Leukemia (AML) Outcome Prediction Challenge is designed to identify potential new drug targets as well as predictive clinical models that surpass current standards. Remarks Professor Steven Kornblau, from the Department of Leukemia at the MD Anderson Cancer Center, “It’s very exciting to have my dataset selected for use in the DREAM competition. My goal has been to use proteomic information to improve patient outcomes by enabling us to match the right therapy to the right patient. I hope that the collective minds that work on this project help us to achieve this goal.”

To sign up for a Challenge and access the data sets and descriptions of the DREAM8.5 and DREAM9 Challenges, please go to: https://www.synapse.org/#!Challenges:DREAM

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