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20170424 - Big Data in Biology - Vancouver - Simon Fraser University

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BigData Opportunities in Biology - personal preso, not in any way affiliated with Google

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20170424 - Big Data in Biology - Vancouver - Simon Fraser University

  1. 1. BigData Opportunities in Biology Allen Day @ Simon Fraser // 2017.04.24
  2. 2. Open Source Software & Open Access Data
  3. 3. Established, Large Market Share, Large Value, Low Growth
  4. 4. Established, Large Market Share, Large Value, Low Growth Newcomers, Small Market Share, Small Value, High Growth Digital => Physical $180 $25 $70 $60 $30 $30 $50 $200
  5. 5. Established, Large Market Share, Large Value, Low Growth Newcomers, Small Market Share, Small Value, High Growth Digital Informational => Physical $180 $70 $60 $30 $30 $50 $200 $25
  6. 6. Established, Large Market Share, Large Value, Low Growth Newcomers, Small Market Share, Small Value, High Growth Digital Informational => Physical $180 $70 $60 $30 $30 $50 $200 ?$25
  7. 7. On-demand transport, owns no cars On-demand real estate, owns no real estate Content licensee & distributor, produces no content It’s All About the Data Flow ?
  8. 8. Company IP Production Distribution Market Access Monsanto Centralized Centralized (Strain Breeding) Partners (Grow Commodities) Decentralized Roche Centralized Centralized (Design, Synthesis) Partners Partners Marriott N/A Centralized Centralized Partners Disney Centralized Centralized Centralized Centralized Hertz N/A Partners Centralized Partners Snap Decentralized Decentralized Centralized Centralized Alibaba Decentralized Decentralized Hybrid Centralized Airbnb N/A Decentralized Decentralized Centralized Uber N/A Decentralized Decentralized Centralized
  9. 9. Company IP Production Distribution Market Access Monsanto Centralized Centralized (Strain Breeding) Partners (Grow Commodities) Decentralized Roche Centralized Centralized (Design, Synthesis) Partners Partners Marriott N/A Centralized Centralized Partners Disney Centralized Centralized Centralized Centralized Hertz N/A Partners Centralized Partners Snap Decentralized Decentralized Centralized Centralized Alibaba Decentralized Decentralized Hybrid Centralized Airbnb N/A Decentralized Decentralized Centralized Uber N/A Decentralized Decentralized Centralized Enabled by Mobile Internet
  10. 10. Company IP Production Distribution Market Access Monsanto Centralized Centralized (Strain Breeding) Partners (Grow Commodities) Decentralized Roche Centralized Centralized (Design, Synthesis) Partners Partners Marriott N/A Centralized Centralized Partners Disney Centralized Centralized Centralized Centralized Hertz N/A Partners Centralized Partners Snap Decentralized Decentralized Centralized Centralized Alibaba Decentralized Decentralized Hybrid Centralized Airbnb N/A Decentralized Decentralized Centralized Uber N/A Decentralized Decentralized Centralized Artificial Bottleneck of Data Flow = $$$$$ Prevented by Self-Replicating Property of Product
  11. 11. Company IP Production Distribution Market Access Monsanto Centralized Centralized (Strain Breeding) Partners (Grow Commodities) Decentralized Roche Centralized Centralized (Design, Synthesis) Partners Partners Marriott N/A Centralized Centralized Partners Disney Centralized Centralized Centralized Centralized Hertz N/A Partners Centralized Partners Snap Decentralized Decentralized Centralized Centralized Alibaba Decentralized Decentralized Hybrid Centralized Airbnb N/A Decentralized Decentralized Centralized Uber N/A Decentralized Decentralized Centralized Next Disruptions Occur Here...
  12. 12. Company IP Production Distribution Market Access Monsanto Centralized Centralized (Strain Breeding) Partners (Grow Commodities) Decentralized Roche Centralized Centralized (Design, Synthesis) Partners Partners Marriott N/A Centralized Centralized Partners Disney Centralized Centralized Centralized Centralized Hertz N/A Partners Centralized Partners Snap Decentralized Decentralized Centralized Centralized Alibaba Decentralized Decentralized Hybrid Centralized Airbnb N/A Decentralized Decentralized Centralized Uber N/A Decentralized Decentralized Centralized Next Disruptions Occur Here... ...but self-replicating products will require a new business model
  13. 13. Environments Genotypes Phenotypes Products are High-precision
  14. 14. Products are High-precision Reductionism Requires Understanding Components Environments Genotypes Phenotypes
  15. 15. Environments Phenotypes Quantifying Genotypes
  16. 16. t log($-1 ) reads writes edits
  17. 17. t log($-1 ) reads writes edits
  18. 18. Google Cloud Platform Marker-Assisted Breeding Rapidly Increases Frequency of Favorable Genes https://www.slideshare.net/finance28/monsanto-082305a
  19. 19. Yield needs to increase by 3% per year to match GDP growth
  20. 20. Marker-assisted selection for quantitative traits https://www.sec.gov/Archives/edgar/data/1110783/0000950134 02011773/c71992exv99w2.htm
  21. 21. Select & Recombine Identify desirable individuals Grow
  22. 22. Select & Recombine Grow Generate Marker Fingerprint Sample tissue Extract DNAModel Data & Identify desirable carriers Marker-Assisted Breeding Rapidly Increases Frequency of Favorable Genes
  23. 23. Select & Recombine Grow Generate Marker Fingerprint Sample tissue Extract DNAModel Data & Identify desirable carriers Marker-Assisted Breeding Rapidly Increases Frequency of Favorable Genes DNA sequencing is no longer the bottleneck...
  24. 24. Select & Recombine Grow Generate Marker Fingerprint Sample tissue Extract DNAModel Data & Identify desirable carriers Marker-Assisted Breeding Rapidly Increases Frequency of Favorable Genes Leading to increased investment in machine learning DNA sequencing is no longer the bottleneck...
  25. 25. Select & Recombine Grow Generate Marker Fingerprint Sample tissue Extract DNAModel Data & Identify desirable carriers Marker-Assisted Breeding Rapidly Increases Frequency of Favorable Genes Increased investment in machine learning… ...requires more data and other data types
  26. 26. Genotypes Phenotypes Quantifying Environments
  27. 27. anezconsulting.com/precision-agronomy/ Agronometric Integration ● Satellite & UAV Images ● Geological Data ● Meteorological & Sensor Data ● Cultivar Data ● Other GIS Data ● Yield Data
  28. 28. TensorFlow https://cloudplatform.googleblog.com/2015/11/startup-spotlight-Descartes-Labs-monitors-planet-Earths-resources-with-Google-Compute-Engine.html
  29. 29. Open Source Software & Open Access Data
  30. 30. Bootstrapping a Virtuous Cycle ● Increased profit (from risk modeling) leads to increased investment and risk reduction in the form of: ● More accurate forecasting / engineering of climate ○ Collect & model more meteorological data ● Development of crop varieties to complement future terrestrial / climate conditions ● High-precision placement and monitoring of individual plants ○ Autonomous planting ○ remote sensing
  31. 31. Environments Genotypes Optimizing Phenotypes
  32. 32. + =
  33. 33. + Tractors are Geospatial Printers
  34. 34. + Tractors are Geospatial Printers Micro-environment optimized cultivars
  35. 35. Mapping the Diversity of Maize Races in Mexico http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114657
  36. 36. Company IP Production Distribution Market Access Monsanto Centralized Centralized (Strain Breeding) Partners (Grow Commodities) Decentralized Roche Centralized Centralized (Design, Synthesis) Partners Partners Marriott N/A Centralized Centralized Partners Disney Centralized Centralized Centralized Centralized Hertz N/A Partners Centralized Partners Snap Decentralized Decentralized Centralized Centralized Alibaba Decentralized Decentralized Hybrid Centralized Airbnb N/A Decentralized Decentralized Centralized Uber N/A Decentralized Decentralized Centralized Next Disruptions Occur Here... ...but self-replicating products will require a new business model
  37. 37. Open Source Software & Open Access Data
  38. 38. Trudeau Unveils Bill Legalizing Recreational Marijuana in Canada https://www.nytimes.com/2017/04/13/world/canada/trudeau-marijuana.html
  39. 39. Why Cannabis? ● Intellectual Property - No patented genes or strains… yet ● Update Mar 18, 2017: US PTO issues trademark for Gorilla Glue #4
  40. 40. Why Cannabis? ● Intellectual Property - No patented genes or strains… yet ● Update Mar 18, 2017: US PTO issues trademark for Gorilla Glue #4 ● Production - Breeding is highly fragmented… for now ● However, unclear that breeding will centralize due to cheap DNA sequencing and digital phenotyping ● Distribution (Growing) - Most likely to centralize due to economies of scale (e.g. multi-tenant greenhouses), and already crowded, wtf? ● Market Access - Unclear that this is a viable segment of supply chain (see GG#4 above). Also self-replication property of plants...
  41. 41. Why Cannabis? ● Intellectual Property - No patented genes or strains… yet ● Update Mar 18, 2017: US PTO issues trademark for Gorilla Glue #4 ● Production - Breeding is highly fragmented… for now ● However, unclear that breeding will centralize due to cheap DNA sequencing and digital phenotyping ● Distribution (Growing) - Most likely to centralize due to economies of scale (e.g. multi-tenant greenhouses), and already crowded, wtf? ● Market Access - Unclear that this is a viable segment of supply chain (see GG#4 above). Also self-replication property of plants... ● Threat: does Cannabis become like Yogurt starter kits?
  42. 42. Cannabis Genomics @ Google Cloud https://cloud.google.com/bigquery/public-data/1000-cannabis
  43. 43. Build What’s Next! Thank You ~ @allenday

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