leveraging the web to make science more collaborative
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Sage Bionetworks is a non-profit organization that aims to make biomedical research more open and collaborative. It develops the Synapse platform to enable sharing of data, code, results and communication among researchers. Sage supports various research communities and projects through Synapse, including the CRC Subtyping Consortium, TCGA Pan-Cancer Consortium and Accelerating Medicines Partnership. These projects involve collaborative analysis of complex datasets toward goals like cancer subtyping and target identification for diseases.
leveraging the web to make science more collaborative
- 1. Synapse leveraging the web to make science more collaborative brian m. bot | sage bionetworks | @BrianMBot
- 2. sage bionetworks 35 FTEs - hiring 5 additional 1/2 research - 1/3 platform - 1/6 leadership & support
- 3. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons focused on a world where biomedical research will fundamentally change to be more open and collaborative supports communities of researchers working collaboratively across disciplines
- 4. sage bionetworks focused on a world where biomedical research will fundamentally change to be more open and collaborative
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- 6. open sage bionetworks access focused on a world where biomedical research will fundamentally change to be more open and collaborative
- 7. sage bionetworks accessibility focused on a world where biomedical research will fundamentally change to be more open and collaborative
- 8. open sage bionetworks access focused on a world where biomedical research will fundamentally change to be more open and collaborative
- 9. open sage bionetworks focused on a world where biomedical research will fundamentally change to be more open and collaborative
- 10. open sage bionetworks data focused on a world where biomedical research will fundamentally change to be more open and collaborative
- 11. open sage bionetworks science focused on a world where biomedical research will fundamentally change to be more open and collaborative
- 12. sage bionetworks science focused on a world where biomedical research will fundamentally change to be more open and collaborative
- 13. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons focused on a world where biomedical research will fundamentally change to be more open and collaborative supports communities of researchers working collaboratively across disciplines
- 14. sage bionetworks tool for collaborative science re-imagined informed consent patients as partners a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons
- 15. sage bionetworks enables sharing of all resources (data, code, results) and their relationships to one another multi-channel communication instead of uni-directional broadcasting aides in reproducibility by enabling communication throughout the research process not only at time of publication a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons
- 16. sage bionetworks distributed & versioned file system rich annotations (metadata) customizable schemas for structured data agnostic to storage solution (cloud, local server, etc.) wiki authoring access controls (share whatever with whomever) a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons
- 17. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons open RESTful APIs www.synapse.org programmatic clients
- 18. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons User registra*on/cer*fica*on User agreement to Terms and Condi*ons of Use Data Use Procedure Data privacy Policy Removal of direct iden*fiers Tier access Login requirement, encryp*on in and out, firewalls IT policy Training-‐ Audi*ng-‐ Monitoring Consequences for viola*on (inten*onal or not) Synapse Governance a complete process
- 19. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons focused on a world where biomedical research will fundamentally change to be more open and collaborative supports communities of researchers working collaboratively across disciplines
- 20. sage bionetworks supports communities of researchers working collaboratively across disciplines
- 21. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder Oncology Molecular Classifiers Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
- 22. DREAM Challenges
- 23. DREAM Challenges Columbia Professor Dimitris Anastassiou MPEG-2 compression of digital audio and video signals Modules of co-expressed genes shared across cancers Belief that these ‘attractors’ represent underlying biological mechanisms (bioinformatic ‘hallmarks of cancer’1) 1D. Hanahan, R. A. Weinberg. Hallmarks of cancer: The next generation. Cell 144, 646–674 (2011)
- 24. DREAM Challenges 17 April 2013
- 25. DREAM Challenges
- 26. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder Oncology Molecular Classifiers Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
- 27. Accelerating Medicines Partnership public / private partnership between NIH, 10 biopharmaceutical companies and several non-profit organizations
- 28. Accelerating Medicines Partnership biopharma AbbVie Biogen Idec Bristol-Myers Squibb GlaxoSmithKline Johnson & Johnson Lilly Merck Pfizer Sanofi Takeda non-profit Alzheimer’s Association Alzheimer’s Drug Discovery Foundation American Diabetes Association Arthritis Foundation Foundation for the NIH Geoffrey Beene Foundation Juvenile Diabetes Research Foundation Lupus Foundation of America Lupus Research Institute/Alliance for Lupus Research PhRMA Rheumatology Research Foundation USAgainstAlzheimer’s
- 29. Accelerating Medicines Partnership ($ Millions) Total Project Total NIH Total Industry Alzheimer’s Disease 129.5 67.6 61.9 Type 2 Diabetes 58.4 30.4 28 Rheumatoid Arthritis 41.6 20.9 20.7 TOTAL 229.5 118.9 110.6
- 30. Accelerating Medicines Partnership cross-project data generation shRNA compounds RNAi human mouse drosophila iPSC RNA-seq Whole exome WGS methylation miRNA proteomics phenotypic measurements modificationssystems data generation X X
- 31. Accelerating Medicines Partnership Target Discovery Target Discovery Target Discovery Target Discovery Target Validation Target Validation Target Validation Target Validation Shared Information for Target Identification coordinate sharing of early-phase target identification insights
- 34. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder Oncology Molecular Classifiers Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
- 35. TCGA Pan-Cancer Consortium 18NPG papers 68core projects 248researchers 28institutions 1070datasets 1723results
- 37. TCGA Pan-Cancer Consortium Cyriac Kandoth
- 39. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder Oncology Molecular Classifiers Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
- 41. CRC Subtyping Consortium A B C D E F 1 2 3 4 5 6 groups datasets subtypes
- 42. CRC Subtyping Consortium A B C D E F 1 2 3 4 5 6 groups datasets subtypes …
- 43. collaborative analyses cloud-based file storage CRC Subtyping Consortium
- 44. code associated with results CRC Subtyping Consortium
- 46. Synapse leveraging the web to make science more collaborative brian m. bot m1-a111 brian.bot@sagebase.org @BrianMBot Synapse engineering team Michael Kellen, Director Christopher Bare Marcel Blonk John Hill Jay Hodgson Bruce Hoff Xavier Schildwachter