About Sage BionetworksSage BionetworksSB_5df26e71-e325-11e4-9151-0f6dde3d8a72Sage Bionetworks was founded in 2009 as a non-profit research organization but has a lineage dating back to 1994, when Stephen Friend and Lee Hartwell launched the "Seattle Project" at the Fred Hutchinson Cancer Center. The Seattle Project's purpose was to link genetics and drug discovery, based on the assumption that pattern recognition could allow researchers to intuit cellular activity directly from data as opposed to using hypothesis-driven, narrative approaches to biology. By 1997 the Seattle Project evolved into Rosetta Inpharmatics, a for-profit company with the same mission. Rosetta was one of the first, and most successful, bioinformatics startups matching genetic variation and function to drug response, and was sold to Merck in 2001 for over $660 million.MerckMerck integrated the Rosetta approach across the global pharmaceutical enterprise, and Dr. Friend served as Merck's global head of cancer research. By 2008, Drs. Friend and Schadt made a series of proposals to Merck's senior leadership to create an open approach to linking genetics and drug discovery through pattern recognition. One of the original presentations is preserved here for posterity. The estimated cost to Merck would have been approximately $300M, but would only have created a short term competitive advantage. Thus Merck was willing to instead allow the founders to convert the computational approaches pioneered there into a global biomedical research commons. Thanks to Merck's generosity, we were able to negotiate the exit of key patents, software, data, hardware, and staff into the launch of Sage Bionetworks. Cure Huntington’s Disease Initiative FoundationTogether with the support of founding contributors the Cure Huntington’s Disease Initiative Foundation, an anonymous donor, Quintiles, and the Canary Foundation, Sage was launched.Canary FoundationSage Bionetworks BoardStephen H. Friend MD PhDPresident, Co-Founder and Director of Sage Bionetworks -- Dr. Friend is the President of Sage Bionetworks, a non-profit organization that provides the tools and environment to conduct dynamic, large-scale collaborative biomedical research. He is an authority in the field of cancer biology and a pioneer in the field of the genetics of gene expression, integrating system biology approaches to complex diseases. Dr. Friend believes that successful biomedical research requires the active participation from all stakeholders. He is reimagining the role of citizens in the research process and is building tools to empower them to contribute both their data and expertise as they see fit. He also believes in the importance of iteratively generating and testing novel hypotheses transparently and collaboratively. Under his leadership, Sage Bionetworks has developed an open-source technology platform, called Synapse, for data-intensive analysis, sharing and reuse, enabling researchers to perform cutting edge computational biology and research. Dr. Friend is engaging the community to crowd-source solutions to complex biomedical questions through targeted DREAM challenges. Previously Dr. Friend was Senior Vice President and Franchise Head for Oncology Research at Merck & Co., Inc. where he led Merck's Basic Cancer Research efforts. Formerly Dr. Friend along with Dr. Hartwell founded and co-led the Fred Hutchinson Cancer Research Center’s "Seattle Project", an advanced institute for drug discovery and later they co-founded Rosetta Inpharmatics with Dr. Leroy Hood. Dr. Friend also held faculty positions at Harvard Medical School from 1987 to 1995 and at Massachusetts General Hospital from 1990 to 1995. He received his M.D/Ph.D. from Indiana University. Dr. Friend was named an Ashoka Fellow for his work at Sage Bionetworks.Eric E. Schadt PhDCo-Founder, Director and Chair of Sage Bionetworks Scientific Advisory Board -- Dr. Schadt is the Director of the Institute for Genomics and Multiscale Biology, Chair of the Department of Genetics and Genomics Sciences and the Jean C. and James W. Crystal Professor of Genomics at Mount Sinai School of Medicine. He is an industry leader in network biology with a number of high-profile publications over the past 5 years and is the Editor-in-Chief of the new journal Open Network Biology. Dr. Schadt helped start Sage Bionetworks while Executive Scientific Director, Genetics at Rosetta Inpharmatics where he founded its Research Genetics Department after Rosetta was acquired by Merck in 2001. His extensive applications in systems biology have helped define the genetics of gene expression as a new field in statistical genetics. Prior to joining Rosetta Dr. Schadt was a Senior Research Scientist at Roche Bioscience. He received his B.S. in applied mathematics/computer science from California Polytechnic State University, and his M.A. in pure mathematics and his Ph.D. in bio-mathematics from UCLA.Anthony W. Ford-Hutchinson PhDDirector of Sage Bionetworks -- Dr. Ford-Hutchinson is Senior Vice President, Vaccines Research and Development Merck Research Laboratories. He has a 30 year record of success at Merck & Co., Inc. and was Senior Vice President and Site Head of Merck Frosst Canada during the development of Singulair® for the treatment of adult and pediatric asthma and allergic rhinitis and the discovery of selective COX-2 inhibitors for the treatment of osteoarthritis and pain. Before joining Merck he was a lecturer in the Chemical Pathology Department at Kings College Hospital Medical School in London doing leukotriene and prostaglandin research. Dr. Ford-Hutchinson obtained his Bachelor’s Degree in Biochemistry from the University of Birmingham, a Masters Degree in Molecular Enzymology from the University of Warwick, and a Ph.D. in Biochemistry from the University of London.Jeff HammerbacherDirector of Sage Bionetworks -- Jeff Hammerbacher is a founder and the Chief Scientist of Cloudera. Jeff was an Entrepreneur in Residence at Accel Partners immediately prior to founding Cloudera. Before Accel, he conceived, built, and led the Data team at Facebook. The Data team was responsible for driving many of the applications of statistics and machine learning at Facebook, as well as building out the infrastructure to support these tasks for massive data sets. The Data team produced open source projects such as Hive and Cassandra and their work was recognized at conferences such as CHI, ICWSM, SIGMOD, and VLDB. Before joining Facebook, Jeff was a quantitative analyst on Wall Street. Jeff earned his Bachelor’s Degree in Mathematics from Harvard University and recently served as a Contributing Editor for O’Reilly's "Beautiful Data".Jun Wang PhDDirector of Sage Bionetworks -- Dr. Wang is the Executive Director of the BGI (previously known as the Beijing Genomics Institute). He was instrumental in the 1999 founding and the growth of the BGI Bioinformatics Department, which is now widely recognized as one of world’s premier research facilities committed to excellence in genome sciences. Dr. Wang also holds a position as an Ole Rømer professor at the University of Copenhagen. He has been recognized with an award from His Royal Highness Prince Foundation in Denmark, an Outstanding Science and Technology Achievement from the Chinese Academy of Sciences, Top 10 Scientific Achievements in China, and the prize for Important Innovation and Contribution from the Chinese Academy of Sciences. His research focuses on genomics and related bioinformatics analysis of common diseases and agricultural crops, with the goal of developing applications using this genomic information.Gustavo A Stolovitzky, PhDDirector of Sage Bionetworks -- Dr. Gustavo Stolovitzky is the Director of the Translational Systems Biology and Nano-biotechnology Program at IBM Research, and an adjunct Professor at Columbia University and at the Icahn School of Medicine at Mount Sinai. He has led many industry projects at IBM Research while also being heavily involved in academic pursuits through University collaborations. In 2006 Dr. Stolovitzky founded and since 2013 co-leads (along with Stephen Friend) the DREAM Challenges, a joint effort by DREAM and Sage Bionetworks that nucleates a community of researchers to assess the performance of systems biology methods, to foster collaborative models of research and to accelerate the solution of important translational problems. Dr. Stolovitzky is also a co-organizer of the “RECOMB/ISCB Systems and Regulatory Genomics with DREAM challenges” conference series, which has nucleated thousands of attendees over the past 7 years. Besides the organization of scientific challenges, Dr Stolovitzky has published over 120 papers and patented over 20 inventions on high-throughput biological-data analysis, reverse engineering biological circuits, the mathematical modeling of biological processes and nano-biotechnology. Dr. Stolovitzky joined IBM Research in 1998. Previously he was a postdoctoral researcher at the Center for Studies in Physics and Biology at The Rockefeller University. He received his PhD in Mechanical Engineering from Yale University (1994) and his M.Sc. in Physics, from the University of Buenos Aires (1987). Dr Stolovitzky has received Yale University’s Henry Prentiss Becton Prize award (1994), the HENAAC’s Pioneer Award for Great Minds in STEM (2013), the World Technology Awards (2013), and was distinguished as a Master Inventor in IBM Research (2013). Dr. Stolovitzky has been elected Fellow of the NY Academy of Sciences, Fellow of the World Technology Network, Fellow of the American Physical Society and Fellow of the American Association for the Advancement of Sciences.Sage Bionetworks LeadersStephen H. Friend MD PhDPresident, Co-Founder and Director of Sage BionetworksDiane GaryDirector, Business Operations -- Diane Gary has responsibility for the organization's finance, human resources, grant management and general business activities. Ms. Gary has held similar roles in other early-stage companies, including Rosetta Inpharmatics through the initial funding, IPO and acquisition by Merck & Co. Inc., and KidStar Interactive Media. Most recently, she was HR Director for Merck’s Seattle and San Francisco research sites. Prior experience also includes work with a hospital foundation, with a nonprofit healthcare association, and on the board of the Country Doctor Community Health Centers. Ms. Gary holds an MBA degree from the University of Washington.Justin GuinneyDirector, Computational Oncology -- Justin Guinney is the Director of the Computational Oncology group at Sage Bionetworks. His group contains specialists from multiple domains, including molecular biology, computer science, and oncology, and focuses on the development of computational models for optimizing patient diagnosis, prognosis, and treatment in cancer. Justin is an expert at large-scale analysis of genomic data, and works regularly with clinicians to link these models to complex cancer phenotypes. Prior to joining Sage Bionetworks, Justin co-founded and managed a software company called FiveSight Technologies, now part of Intalio Corp. Dr Guinney received a BA from the University of Pennsylvania in History, a BS from the University of Illinois, Urbana-Champaign in Electrical Engineering, and a PhD from Duke University in Computational Biology and Bioinformatics.Mike KellenDirector, Technology and Software Development -- Michael Kellen leads the technology platforms and services team at Sage Bionetworks. Since 2009, the team has supported open projects and challenges in the collaborative analysis of human health data through the development of the Synapse platform, and by providing support with data hosting, curation, and analysis. The team is now expanding scope into the collection of rich human phenotypic data though the development of the Bridge platform. Michael has over 10 years experience developing software for academic and corporate users in the life sciences, and has brought several award-winning products to market in this space covering simulation, data capture and analysis workflow, data integration, and team collaboration. Prior to Sage, Michael held a variety of positions with Teranode corporation since joining as the company's first employee in 2002, covering product development, field consulting, product management, and development management. Michael completed a doctorate in bioengineering at the University of Washington in 2002 with a focus in computational biology where he also helped develop scientific modeling and simulation technology subsequently licensed by Teranode.Arno KleinDirector of Neuroimaging and Director of SIMPL(E) -- Arno is the Director of two new groups at Sage: Neuroimaging, which analyzes biomedical image data, and SIMPL(E), which seeks and interprets meaningful patterns and latent explanations in data. Arno is particularly excited about imaging and visualization of complex information as well as by open science initiatives, and is coordinating open science challenges. He is the lead developer of open source software packages such as Mindboggle (for automated brain labeling and shape analysis), and is actively involved in a range of projects, including visual taxonomies and Indian cave temple documentation. He received his PhD in Neuroscience from Cornell Medical School, an M.S. from MIT’s Media Laboratory, and a B.S. in Biopsychology at the University of Michigan, and was an assistant professor at Columbia and Stony Brook Universities for six years prior to joining Sage.Lara Mangravite, PhDDirector, Systems Biology -- Lara Mangravite, PhD is Director of the Systems Biology research group. This team focuses on application of systems biology approaches to advance understanding of disease biology and treatment outcomes with the overriding goal of improving clinical care. As part of these efforts, the team is working in parallel to pilot new approaches to scientific process that use open systems to enable community-based collaborative research efforts to solve complex problems in a collective manner that is more efficient and effective than standard research approaches. Lara’s previous research experience has focused on the identification of prognostic biomarkers through the analysis of genomic and molecular profiles derived from both clinical trials and experimental model systems. Dr. Mangravite obtained a BS in Physics from the Pennsylvania State University and a PhD in Pharmaceutical Chemistry from the University of California, San Francisco. She completed a postdoctoral fellowship in cardiovascular pharmacogenomics at the Children’s Hospital Oakland Research Institute.Thea Norman, PhDDirector, Strategic Development -- Dr. Norman is the Director of Strategic Development at Sage Bionetworks. She works closely in partnership with Dr. Gustavo Stolovitzky of IBM to oversee the running of the Sage-DREAM Challenges. DREAM Challenges foster a collaborative framework for researchers to rapidly evolve predictive disease models for tough problems in biology and medicine that would otherwise take years to produce. Dr. Norman also oversees the design and development of Sage Bionetworks BRIDGE platform. Prior to joining Sage Bionetworks, Dr. Norman spent 12 years as a science, alliance and business leader at two start-up biotechnology companies (Ironwood and Ambrx). Dr. Norman is a co-inventor on seven issued patents including that for the composition of Linzess (which Dr. Norman developed), a First in Class treatment for Irritable Bowel Syndrome. Dr. Norman holds a PhD in Chemistry from the University of California, Berkeley.John WilbanksChief Commons Officer -- John Wilbanks is the Chief Commons Officer at Sage Bionetworks. He has spent his career working to advance open content, open data and open innovation systems. Wilbanks also serves as a senior fellow at FasterCures, and as a senior advisor for big data to the National Coordination Office. Previously, Wilbanks worked as a legislative aide to Congressman Fortney “Pete” Stark, served as the first assistant director at Harvard’s Berkman Center for Internet & Society, founded and led to acquisition the bioinformatics company Incellico, Inc., and was executive director of the Science Commons project at Creative Commons. In February 2013, in response to a We the People petition that was spearheaded by Wilbanks and signed by 65,000 people, the U.S. government announced a plan to open up taxpayer-funded research data and make it available for free. Wilbanks holds a B.A. in philosophy from Tulane University and also studied modern letters at the Sorbonne.Sage Bionetworks PartnersCommon Mind ConsortiumThe CommonMind Consortium is a Public-Private Pre-Competitive partnership that brings together disease area expertise, large scale and well curated brain sample collections, and data management and analysis expertise with a goal to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. The consortium consists of five academic groups, two pharmaceutical companies, and Sage Bionetworks.Center for Cancer Systems BiologySage Bionetworks is establishing a new Center for Cancer Systems Biology (CCSB) under the NCI Integrative Cancer Biology Program (ICBP) featuring an innovative two year postdoctoral training and ambassador program as an integral part of the systems biology and computational modeling research activities.Washington Partners ProgramSage Bionetworks has created the Washington Partners Program (WPP) to provide biomedical researchers with strategic and cost-effective advanced genomics analysis capabilities. Funded by the Washington Life Sciences Discovery Fund, the program is designed to accelerate academic and commercial research and improve healthcare outcomes in the state of Washington.AshokaAshoka envisions an Everyone A Changemaker™ world. A world that responds quickly and effectively to social challenges, and where each individual has the freedom, confidence and societal support to address any social problem and drive change. Ashoka strives to shape a global, entrepreneurial, competitive citizen sector: one that allows social entrepreneurs to thrive and enables the world's citizens to think and act as changemakers.CHDI FoundationCHDI Foundation works with academic and industrial scientists throughout the world to rapidly discover and develop treatments that slow the progression of Huntington's disease.Fred Hutchinson Cancer Research CenterThe Fred Hutchinson Cancer Research Center’s mission is the elimination of cancer and related diseases as causes of human suffering and death. The Center conducts research of the highest standards to improve prevention and treatment of cancer and related diseases.Ingenuity SystemsIngenuity Systems is taking on the challenge of next-generation knowledge management for the life sciences community. Our long-term focus on innovation in semantic search, ontology, and software development has allowed us to create groundbreaking technologies that help life science researchers more effectively search, explore, visualize, and analyze biological and chemical findings related to genes, proteins, and small molecules.Inspire2LiveInspire2Live is the international movement behind charity events like Alpe d'HuZes, currently Holland’s biggest charity action (20M Euros) and many others, such as the Belgian Ven2-4Cancer. All these charities are targeted towards a single goal: Getting Cancer in control within 10 years.The Listwin Family FoundationThe Listwin Family Foundation supports the Canary Foundation and its work on tests that identify and isolate cancer at its earliest most curable stage.Life Science Discovery FundThe Life Sciences Discovery Fund supports innovative research in Washington state to promote life sciences competitiveness, enhance economic vitality, and improve health and health care.NCI Integrative Cancer Biology ProgramThe National Cancer Institute's Integrative Cancer Biology Program (ICBP) focuses on the analysis of cancer as a complex biological system. A cornerstone of the program is the development and implementation of computational models of processes relevant to cancer prevention, diagnostics and therapeutics. The integration of experimental biology with mathematical modeling provides new insights in the biology and new approaches to the management of cancer.Rock HealthUse your powers for good. Each stakeholder's perspective is essential to catalyzing meaningful change in a system that touches every life in this country -- and across the world. Rock Health has brought together partners and entrepreneurs spanning medicine, venture capital, the corporate world, and technology. Diverse minds have the power to transform, and to create surprising, delightful, and innovative new companies and products with the potential to change billions of lives.Quintiles TransnationalQuintiles Transnational helps to improve healthcare worldwide by providing a broad range of professional services, information and partnering solutions to the pharmaceutical, biotechnology and healthcare industries.TraitwiseTraitwise's mission is to develop interconnected communities of people answering questions that will advance human healthcare.Traitwise has developed revolutionary technology to investigate the unexpected correlations between our health, our unique distinguishing traits, and our lifestyles.University of Miami Center for Computational ScienceThe University of Miami Center for Computational Science group operates a HPC system which is a resource for our computational biologists.Wilson Sonsini Goodrich & RosatiWilson Sonsini Goodrich & Rosati is the premier legal advisor to technology and growth enterprises worldwide, as well as the investment banks and venture capital firms that finance them.... transformation of biomedical research approaches and healthcare discoveries through the use of computational models ..._5df27050-e325-11e4-9151-0f6dde3d8a72To improve the understanding and treatment of human disease through data-driven predictive modeling._5df27118-e325-11e4-9151-0f6dde3d8a72Open NetworksOur Projects are unified by a common emphasis on leveraging the power of open networks of contributors to solve complex scientific problems.CollaborationOver the next decade, ever-expanding data will transform biomedical research approaches and feed healthcare discoveries through the use of computational models to predict outcome, and responses to treatment. At Sage Bionetworks we believe that this advance will be best harnessed when individuals and groups can collaborate openly on discoveries, with a fundamental shift in the traditional roles and rewards for individuals and organizations involved.Open SourceOur work revolves around bringing this mission and vision to reality, underpinned by the belief that being open is critical. As part of living our philosophy, all of our tools, platforms, and products are open source. Our software is available in Github, and our non-software creative works are licensed under the Creative Commons Attribution 3.0 Unported license except for legacy publications in closed journals.Open AccessWe now dedicate funds to pay author processing charges for full Open Access on research publications and are actively working to free up our backfile of closed publications.Biological DataRedefine how complex biological data is gathered, shared and used, redefining it through open systems, incentives, and norms._5df271ae-e325-11e4-9151-0f6dde3d8a72We work to redefine how complex biological data is gathered, shared and used, redefining it through open systems, incentives, and norms. We challenge the traditional roles of individuals and groups, patients and researchers. Our work includes the building of platforms and services and undertaking research developing predictors relating to health. We collaborate with a network of partners and individuals, to redefine the way biomedical research results in better health... The five areas we believe now are present and will enable significant advance in this field are: 1. It is now possible to readily generate massive amount of human “omic’s” data as a commodity purchase 2. Network modelling approaches for diseases are emerging 3. IT Infrastructure and Cloud compute capacity allows a generative open approach to biomedical problem solving 4. Nascent movement for patients to control sensitive information allowing sharing 5. Open social media allows citizens and experts to use collaborative tactics to solve problems Combining these factors would suggest that it is only a matter of time, before significant system breakthroughs are made in biomedical research, in a number of fields, particularly oncology. In our dreams, you may be able to predict your risk of developing a certain cancer through genetic and other information, identify the genetic and lifestyles changes responsible and target those specifically to prevent or treat that condition. The reality is that we are a long way from this dream -- and we believe we all need to start thinking about things differently to be able to use the opportunity.ComplexityView complex problems as complex problems._5df2724e-e325-11e4-9151-0f6dde3d8a721We need to start looking at these complex problems as complex problems. Although advances are made at a theoretical or laboratory level, they often fail when replicated in an animal or person. At the heart of this is the undisputable fact that the complexity of biological systems mean that solving one small part of the problem may work alone but not in the wider context of the system.IncentivesReassess incentives for researchers and institutions to encourage truly collaborative research._5df27384-e325-11e4-9151-0f6dde3d8a722ResearchersInstitutionsWe need to reassess incentives for researchers and institutions to encourage truly collaborative research. There are also challenges inherent in the research system. Researchers are recognized for being the first to make significant discoveries, and obtaining future funding by the individual or the organization is inherently linked to this status. This inhibits the sharing of data or discoveries between research centers. Although collaborations exist they are generally limited to a small number of like institutions.PublicationsAddress the ability of publications to truly report results of research in a meaningful and interrogable way._5df27424-e325-11e4-9151-0f6dde3d8a723PublishersMedical JournalsWe need to address the ability of publications to truly report results of research in a meaningful and interrogable way. Publications often report results without the ability of readers to access the models behind the research, which in this field is critical to understanding and assessing the advance.DataReassess the mechanisms of data sharing and collection to allow compatibility and collaboration between institutions, and actively encourage this to happen._5df274ce-e325-11e4-9151-0f6dde3d8a724InstitutionsWe need to reassess the mechanisms of data sharing and collection to allow compatibility and collaboration between institutions, and actively encourage this to happen. Where data is the currency of this new system, it is frequently not able to be accessed by the broadest range of researchers either due to access practicalities or often due to a lack of consent by the patient for broader use.RewardsFocus funding to rewarding for results rather than work._5df2756e-e325-11e4-9151-0f6dde3d8a725InstitutionsResearchersResearch CommunityWe need to focus funding to rewarding for results rather than work. Funding is often given to just one institution or group of researchers, based on reputation. This both misses the vast array of talent available and payment is given for work rather than a concrete result. We need to maximize the input of patients in research. Patients are the group that research can ultimately affect most significantly. Yet, they often are asked purely for defined information or participation in a research project. Research is often initiated from top down, defined by the research community, rather from bottom up. In this way, we can miss input from these disease or patient communities in defining the truly relevant questions to them, as well as missing out on a wealth of information that they could prospectively provide.2015-04-15http://sagebase.org/OwenAmburOwen.Ambur@verizon.net