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enabling communities of researchers working together across institutional boundaries

  1. 1. brian m. bot | sage bionetworks | @BrianMBot mayo clinic - 2015 jan 28 enabling communities of researchers working together across institutional boundaries
  2. 2. sage bionetworks ~40 FTEs 1/2 research - 1/3 platform - 1/6 leadership/support
  3. 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. 4. focused on a world where biomedical research will fundamentally change to be more open and collaborative open sage bionetworks
  5. 5. open access focused on a world where biomedical research will fundamentally change to be more open and collaborative sage bionetworks
  6. 6. accessibility focused on a world where biomedical research will fundamentally change to be more open and collaborative sage bionetworks
  7. 7. open access focused on a world where biomedical research will fundamentally change to be more open and collaborative sage bionetworks
  8. 8. open science focused on a world where biomedical research will fundamentally change to be more open and collaborative sage bionetworks
  9. 9. science focused on a world where biomedical research will fundamentally change to be more open and collaborative sage bionetworks
  10. 10. 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 sage bionetworks
  11. 11. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons tool for collaborative science re-imagined informed consent patients as partners sage bionetworks
  12. 12. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons enables sharing of all resources (data, code, results) and their relationships to one another provides mechanism to communicate in real time instead of only at time of publication supports open scientific collaborations for clear, reproducible science sage bionetworks
  13. 13. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons enables sharing of all resources (data, code, results) and their relationships to one another sage bionetworks
  14. 14. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons sage bionetworks open RESTful APIs www.synapse.org programmatic clients
  15. 15. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons 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)
  16. 16. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons sage bionetworks User registration/certification User agreement to Terms and Conditions of Use Data Use Procedure Data privacy Policy User certification Removal of direct identifiers Tier access Login requirement, encryption in and out, firewalls IT policy Training- Auditing- Monitoring Consequences for violation (intentional or not) Synapse Governance a complete process
  17. 17. 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 sage bionetworks
  18. 18. “biomedical research needs to empower patients with the voice and the tools they need to manage their health, understand their disease and partner in research” a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons sage bionetworks patients as partners
  19. 19. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons sage bionetworks “participants will be provided real-time graphical representations of their data, access to their own data at will (to provide to healthcare professionals, donate to other studies, etc.), and also research notifications when new insights are available” sharing two ways
  20. 20. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons sage bionetworks
  21. 21. 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 sage bionetworks
  22. 22. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons written by a doctor reviewed by a lawyer edited by a committee sage bionetworks
  23. 23. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons interaction design prioritizes the user and the experience patient-centered consent (pcc) toolkit sage bionetworks
  24. 24. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons deploy consent as a process via mobile, web patient-centered consent (pcc) toolkit sage bionetworks
  25. 25. a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons assist informedness for complex documents patient-centered consent (pcc) toolkit sage bionetworks
  26. 26. icons representing concepts a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons patient-centered consent (pcc) toolkit sage bionetworks
  27. 27. sage bionetworks metadata& survey& sensor&tasks& wearables& Consent& Toolkit& Bridge& Server& Synapse& Stores&study&data& Assigns&study&code& De<iden=fies&& Syndicates& Consent& Data&capture& No=fica=ons& Study<specific&folder& Auto<deposit&aAer&embargo&period& Authorized&users&
  28. 28. 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 sage bionetworks
  29. 29. supports communities of researchers working collaboratively across disciplines end game is not collaboration
  30. 30. supports communities of researchers working collaboratively across disciplines do good research
  31. 31. supports communities of researchers working collaboratively across disciplines impact on health
  32. 32. collaboration around common data collaboration around common question
  33. 33. “systematic exploration of the entire spectrum of genomic changes involved in more than 20 types of human cancer”
  34. 34. TCGA Pan-Cancer Consortium analysis of: 12 tumor types 6 molecular profiling platforms
  35. 35. 18NPG papers 68core projects 248researchers 28institutions 1070datasets 1723results TCGA Pan-Cancer Consortium
  36. 36. TCGA Pan-Cancer Consortium
  37. 37. TCGA Pan-Cancer Consortium
  38. 38. doi:10.7303/syn1710680.4 TCGA Pan-Cancer Consortium
  39. 39. CommonMind Consortium large public / private partnership phase I: prefrontal cortex ~300 SCZ, 300 control, 60 BD processing pipelines developed in collaboration between sage and mssm public release: February 2015
  40. 40. CommonMind Consortium public release: February 2015
  41. 41. CommonMind Consortium public release: February 2015
  42. 42. CommonMind Consortium public release: February 2015
  43. 43. collaboration around common data collaboration around common question
  44. 44. CRC Subtyping Consortium
  45. 45. A B C D E F 1 2 3 4 5 6 CRC Subtyping Consortium expert team data subtype
  46. 46. A B C D E F 1 2 3 4 5 6 ... CRC Subtyping Consortium expert team data subtype
  47. 47. CRC Subtyping Consortium
  48. 48. collaborative analyses cloud-based file storage CRC Subtyping Consortium
  49. 49. code associated with results CRC Subtyping Consortium
  50. 50. CRC Subtyping Consortium
  51. 51. collaboration around common data and question
  52. 52. public / private partnership between NIH, 10 biopharmaceutical companies and several non-profit organizations Accelerating Medicines Partnership
  53. 53. 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
  54. 54. Accelerating Medicines Partnership mt sinai mayo / ufl / isb broad / rush emory integrated network analysis target discovery 300 case-control rnaseq, genotype, clinical 1000 case-control rnaseq, methylation, genotype, clinical 300 ad, tauopathy, control rnaseq, clinical 200 AD, MCI, control Proteomic, clinical data
  55. 55. Accelerating Medicines Partnership iPS neurons and astrocytes Mouse hippocamal slices Drosophila model Genetic analysis aB and Tau mouse models rAAV delivered models Proteomics Cultured neurons & astrocytes iPS compound screens Proteomics Cell Culture, Mouse Models Drosophila model mt sinai mayo / ufl / isb broad / rush emory target validation 2 3 5 12
  56. 56. 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
  57. 57. Accelerating Medicines Partnership AMP-AD Collaborative Workspace Quarterly Depositions Broad/ RUSH Mt. Sinai U Fl/ ISB/ Mayo Emory Sage Other Partners Individual Partner Workspaces AMP-AD Data Portal Consortium Space Public space AMP-AD Synapse Project Structure
  58. 58. increasingly decentralized research ecosystem
  59. 59. democratization of research cloud infrastructure gov’t agencies and public pushing for > sharing increasingly decentralized research ecosystem
  60. 60. mayo clinic - 2015 jan 28 brian m. bot —————— brian.bot@sagebase.org @BrianMBot sage bionetworks enabling communities of researchers working together across institutional boundaries

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