apidays Australia 2023 - The Power of APIs in Genomic Research, Dr. Adrien Oliva, Ph.D, CSIRO

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October 11 & 12, 2023
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The Power of APIs in Genomic Research
Dr. Adrien Oliva, Ph.D, Post-Doc in Multi-Cloud Genomic Research at CSIRO

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Transcript

1. Australia’s National Science Agency Cloud-based bioinformatics The Power of APIs in Genomic Research Dr. Adrien Oliva, Oct 2023
3. Australia’s largest digital health program • Powers Australia’s and England’s clinical terminology service. • First clinically validated mobile APP for heart rehabilitation. 3 | The power of APIs in Genomic Research| @Tbioinf
4. 4 | The power of APIs in Genomic Research| @Tbioinf LIFE
5. APIs accelerate health | @allPowerde @Tbioinf 5 | The power of APIs in Genomic Research| @Tbioinf 5 |
6. Genomics helped track COVID-19 outbreak 6 | but requires • secure, federated data management • real-time analytics. The power of APIs in Genomic Research| @Tbioinf
7. 20 EB Storage / year Stephens et al. BigData: Astronomical or Genomical (2015) Genomics YouTube Astronomy Twitter The power of APIs in Genomic Research| @Tbioinf 7 | 1 EB = 1,024 PB or 1,048,576 TB YouTube estimated all time storage = 2 EB
8. Creating Trust with appropriate evolving consents Secure data exchange to empower innovation via collaboration APIs in Genomic Research Analyse data to advance clinical genomics 8 | The power of APIs in Genomic Research| @Tbioinf
9. Creating Trust with appropriate evolving consents Secure data exchange to empower innovation via collaboration APIs in Genomic Research Analyse data to advance clinical genomics 9 | The power of APIs in Genomic Research| @Tbioinf
10. VariantSpark 10 | • Machine Learning Framework for genomic data • Associate mutations with a traits The power of APIs in Genomic Research| @Tbioinf
11. cases controls Gene1 Gene2 A B C Detect up to 4 SNP interactions Smarter 11 | The power of APIs in Genomic Research| @Tbioinf Bayat, Scientific Report, 2021 Bayat, GigaScience, 2020
12. 12 | Distributions The power of APIs in Genomic Research| @Tbioinf
13. Analyzes 1 trillion datapoints in 15h (other tech 100,000 years) Faster Used by Chromosome On all major cloud providers Available The power of APIs in Genomic Research| @Tbioinf 13 |
14. Creating Trust with appropriate evolving consents Secure data exchange to empower innovation via collaboration APIs in Genomic Research Analyse data to advance clinical genomics 14 | The power of APIs in Genomic Research| @Tbioinf
15. 15 | Data copies everywhere, Losing Data ownership Individual owners Centralised Organisation owned Too much power, security concerns, Blanket consents The power of APIs in Genomic Research| @Tbioinf
16. Secure Newborn screening 16 | The power of APIs in Genomic Research| @Tbioinf Consent Transparent Auditable Data Sovereignty PATIENT
17. Dynamic Consent Protocol 17 | The power of APIs in Genomic Research| @Tbioinf
18. Dynamic Consent Protocol 18 | The power of APIs in Genomic Research| @Tbioinf
19. Dynamic Consent Protocol 19 | The power of APIs in Genomic Research| @Tbioinf
20. 20 | The power of APIs in Genomic Research| @Tbioinf
21. Dynamic Consent Protocol 21 | The power of APIs in Genomic Research| @Tbioinf
22. Dynamic Consent Protocol 22 | The power of APIs in Genomic Research| @Tbioinf
23. 23 | The power of APIs in Genomic Research| @Tbioinf
24. Dynamic Consent Protocol 24 | The power of APIs in Genomic Research| @Tbioinf
25. Dynamic Consent Protocol 25 | The power of APIs in Genomic Research| @Tbioinf
26. Dynamic Consent Protocol 26 | Power to the patient The power of APIs in Genomic Research| @Tbioinf
27. Creating Trust with appropriate evolving consents Secure data exchange to empower innovation via collaboration APIs in Genomic Research Analyse data to advance clinical genomics 27 | The power of APIs in Genomic Research| @Tbioinf
28. 28 | The power of APIs in Genomic Research| @Tbioinf Source: https://beacon-project.io
29. Exchanging genomic data cloud-natively 29 | Partners Serve a query in 1s and update data in 20s (1800 times faster) Faster Zero idle costs Cheaper Scalable Scale up to 3 billion genomic locations and 40 million individuals The power of APIs in Genomic Research| @Tbioinf
30. 30 | Beacon V2 compliant The power of APIs in Genomic Research| @Tbioinf
31. 31 | The power of APIs in Genomic Research| @Tbioinf
32. 1. Connect the data to the analytics: VariantSpark and BitEpi – finding disease genes, to treat and even prevent disease. 2. Give data sovereignty and power back to the patient Dynamic Consent Protocol – Creating trust with evolving consent management. 3. Secure data exchange to empower innovation via collaboration: sBeacon – Enable safe global data sharing for federated genomic discoveries. Three things to remember 32 | The power of APIs in Genomic Research| @Tbioinf
33. Australia’s National Science Agency CSIRO Health and Biosecurity Adrien.Oliva@csiro.au Let’s work together Visit our site: https://bioinformatics.csiro.au @Tbioinf