Sage Bionetworks

Programs: Research: the synapse platform is an open access environment for collaborative research on biological network models and their application to problems of human disease and biology. Sage related research communities using synapse include: the amp ad (alzheimer's disease) knowledge portal, an nia funded repository and workspace for multi-omic data; the cancer genome atlas (tcga) pan-cancer consortium, engaging 30 organizations to perform integrative analysis on data from 12 different tumor types; the colorectal cancer consortium of researchers from15 academic, pharmaceutical, and non-profit partners; the commonmind consortium bringing together large scale brain sample collections to generate and analyze genomic data related to neuropsychiatric disease; and the nhlbi funded progenitor cell biology consortium. Research also includes open computational challenges conducted with ibm dream and hosted on synapse. Designed and run by researchers, these challenges invite participants to propose solutions to questions about systems biology and translation medicine -fostering collaboration and open research communities. In 2014, the 8. 5 and 9. 0 challenge seasons included the somatic mutation calling challenge, the gene essentiality prediction challenge, and challenges on rheumatoid arthritis, alzheimer's disease and acute myeloid leukemia.

center for cancer systems biology (ccsb) and the washington state life sciences discovery fund (lsdf): 2014 was the fifth year of the nci funded sage bionetworks center for cancer systems biology. As a member of the ccsb consortium, the sage bionetworks ccsb has leveraged its expertise in systems biology and genomic analyses, software and platform development, and community building, resulting in several high profile publications and impactful cancer discoveries. The sage ccsb's 5th year was focused on executing and completing the aims of the ccsb program, including the supplemental programs on colorectal molecular subtyping, the dream cancer challenges, and expanded functionality of the synapse platform. The sage bionetworks ccsb, together with funds from the washington state life sciences discovery fund, supported the continued development of the synapse platform (http://synapse. Org), hosted online and free for public use with the source code available under an open source license on git-hub. Synapse currently hosts a growing base of over 1700 active users, predominately in large-scale collaborative projects like the sage-dream challenges and the research collaborations described in 4a.

bridge platform and patient engagement: in 2014, sage bionetworks expanded efforts in citizen engagement with the continued development of bridge, a cloud-based collaborative science platform designed to incorporate open data, patient wisdom and public involvement into biomedical research. Bridge, like synapse, is a key piece of it infrastructure essential for empowering citizens to share and track their data, to partner on research and to fund the projects that matter most to them. On bridge, citizens, patients and researchers are able to use online tools that connect people, their data and their stories to build online communities focused on defining a specific disease or area of health research. In 2014, sage bionetworks developed the first two mobile app-based research studies on bridge. Enrollment in the parkinson's mpower study and the share the journey breast cancer survivor study opened in march 2015. The sage bionetworks governance team works with legal, ethical, and regulatory experts to develop, implement and enforce the policies and procedures for the responsible collection and use of digital research assets for the benefit of researchers and data subjects, and for appropriate data sharing on synapse and bridge. In 2014 this team developed the participant-centered consent (pcc) toolkit for researchers who are designing clinical studies, including the mobile app based studies on bridge.