apidays LIVE Australia 2021 - Accelerating Digital September 15 & 16, 2021 Locknote: APIs enable global collaborations and accelerate health and medical research Dr. Denis Bauer, Head Cloud Computing Bioinformatics at CSIRO

1. Australia’s National Science Agency
Cloud-based bioinformatics
APIs enable global collaborations and
accelerate health and medical research
A/Prof. Denis C. Bauer, Sept 2021, Virtual

2. Australia’s National Science Agency
Digital Health needs
strong APIs for
solutions that are
larger than the sum of
their parts.

3. APIs accelerate health | @allPowerde @Tbioinf
Australia’s largest digital health program
• Powers Australia’s and England’s
clinical terminology service.
• First clinically validated mobile
APP for heart rehabilitation.
• Developed the Total Wellbeing &
Low-Carb Diets.
3 |

4. Manipulating
the genome
… for new therapeutic
applications
Modernizing
collaborations
… to empower
innovation
Cloud-based Bioinformatics
APIs accelerate health | @allPowerde @Tbioinf
Understanding
the Genome
… to advance clinical
genomics
4 |

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6. Everyone has
mutations that
should inform their
clinical care.
Chanfreau-Coffinier et al. JAMA Netw Open. 2019
APIs accelerate health | @allPowerde @Tbioinf
5 |

7. The era of
Mega-biobanks
requires analytics to
go to the data.
credit kotoffei/shutterstock
APIs accelerate health | @allPowerde @Tbioinf
6 |

8. APIs broker access to data
7 | APIs accelerate health | @allPowerde @Tbioinf
API
Data Analytics

9. VariantSpark ElasticMapReduce cluster
APIs accelerate health | @allPowerde @Tbioinf
8 |

10. Population-scale genomic data analysis requires
BigData solutions
High-performance compute
cluster
Apache Spark cluster
Focus Compute-intensive Data-intensive
Node-bound Yes No
Parallelization 100+ CPU 1000+ CPU
Parallelization procedure bespoke standardized
APIs accelerate health | @allPowerde @Tbioinf
9 |

11. World-first analysis of 1 trillion genomic datapoints
APIs accelerate health | @allPowerde @Tbioinf
Bayat et al. GigaScience 2020
• 3.6 times faster than BigData
competitors on today’s data
• Tomorrow’s data: 15h vs
100,000 years
McCann, Journal of Medical Genetics, 2020
Nicolas, Cell Neuron, 2018
10 |

12. Australia’s National Science Agency
Disease Genes:
cardiovascular disease
Cloud-native machine learning | A/Prof Denis Bauer | @Tbioinf @allPowerde
VariantSpark
By jesse orrico
By Catherine Please
50,000 case/control

13. Which strain to build a vaccine for?
Cloud-basd Bioinformatics | @Tbioinf @allPowerde
most
infectious

14. Australia’s National Science Agency
Cloud-native bioinformatics accelarates health research | @Tbioinf @allPowerde
VariantSpark
Case
(2162 samples)
Control
(2166 samples)
Variants of Interest:
Covid-19 virus

15. Capturing ‘Patient status’
Cloud-native bioinformatics fighting COVID-19 | @Tbioinf @allPowerde
GISAID May 2020 GISAID Oct 2020
GISAID May 2021

16. APIs translate meaning
15 | APIs accelerate health | @allPowerde @Tbioinf
API
Data
Data

17. Future analysis: better data
Cloud-native bioinformatics fighting COVID-19 | @Tbioinf @allPowerde
GISAID May 2020

18. •FHIR®-based for enabling
and syndication of clinical
terminologies.
•Supports the advanced use of
SNOMED CT & underpins UK’s
NHS.
Ontoserver: One-stop-shop for advanced terminology
Medical science at scale | @allPowerde @Tbioinf
17 |

19. By 2030 it is estimated that 50% of the world
population will have been sequenced.
20 EB Storage / year
Stephens et al. BigData: Astronomical or Genomical (2015)
Data acquisition of BigData disciplines in 2025
Genomics
YouTube
Astronomy
Twitter
Frost&Sullivan
Cloud-native machine learning | A/Prof Denis Bauer | @Tbioinf @allPowerde

20. Desktop
computers
Cloud server
(Autos-scale)
Serverless
Focus Full control Flexible Agility
Flexibility
No Overhead
Scalability
Cost-effective
Analogy
own car
by madd.org
ride share
by blacklane.com
chauffeur
Exchanging genomic data with cloud-native solutions
Bringing the compute to the data | @Tbioinf @allPowerde

21. Cloud-native data exchange
Bringing the compute to the data | @Tbioinf @allPowerde
• Scales to 30 quadrillion
datapoints.
• Handle dynamic
patient consent
because data is not
replicated in a
database.
• Modular for real-time
analytics.

22. Bringing the compute to the data | @Tbioinf @allPowerde
sBeacon: Lambda
ingestion engine
Laboratory
API
Gateway
Lambda Function:
submitDataset
Dynamic
Datasets
SNS:
summariseDataset
DynamoDB
VerSummaries
Lambda Function:
summariseVCF
Lambda Function:
summariseSlice
SNS: summariseSlice
S3 Buckets containing
VCF files
SNS: summariseVCF
LAMBDA Function:
summariseDataset
2 3 19
24
4 6.22
5.21
7.23
20
17
18
15
16
12
9
13
8
10 11
14

23. Cost-effective: 300-fold monthly cost saving
Bringing the compute to the data | @Tbioinf @allPowerde
$
$
Traditional

24. APIs exchange information between
analytics
23 | APIs accelerate health | @allPowerde @Tbioinf
API
Analytics
Analytics

25. World first: Handling population scale data
350 Million Samples
3
Billion
variants
1 quintillion
datapoints
Real-time
processing
Cloud-basd Bioinformatics | @Tbioinf @allPowerde

26. Manipulating
the genome
… for new therapeutic
applications
Modernizing
collaborations
… to empower
innovation
Cloud-based Bioinformatics
APIs accelerate health | @allPowerde @Tbioinf
Understanding
the Genome
… to advance clinical
genomics
25 |

27. Australia’s National Science Agency
The world around us is being revolutionized by CRISPR,
whether we’re ready for it or not.
Jennifer A. Doudna
Design of model organisms Large scale screens Gene Therapy
Biosecurity

28. CRISPR: programmable genomic addressing system
APIs accelerate health | @allPowerde @Tbioinf
27 |

29. Australia’s National Science Agency
Genome Editing:
Revolutionize medicine
Cloud-basd Bioinformatics | @Tbioinf @allPowerde

30. Gene therapy’s journey to the clinic
Optimizing
editing site

31. Making gene therapy better
Specificity:
better vectors
Efficiency:
better guides
Safety:
better outcomes
Host Vector Host

32. APIs make solutions more modular
31 | APIs accelerate health | @allPowerde @Tbioinf
API
Analytics
Data

33. Transformational Bioinformatics | Denis C. Bauer | @allPowerde
Cloud-basd Bioinformatics | @Tbioinf @allPowerde

34. One of the first Serverless Applications in Research
Cloud-basd Bioinformatics | @Tbioinf @allPowerde

35. Best target for heart
Automated workflows with GT-Scan API
APIs accelerate health | @allPowerde @Tbioinf
34 |

36. Manipulating
the genome
… for new therapeutic
applications
Modernizing
collaborations
… to empower
innovation
Cloud-based Bioinformatics
APIs accelerate health | @allPowerde @Tbioinf
Understanding
the Genome
… to advance clinical
genomics
35 |

37. Australia’s National Science Agency
Time to bridge the gap between
research and industry.
Cloud makes talent &
solutions more
accessible.
Credit: Upklyak & starline/freepik

38. Deployment at the speed of cloud
Medical science at scale | @allPowerde @Tbioinf
CSIRO takes genome product to
the world on Amazon
1 AWS review
“Powerful bioinformatics”
37 |

39. Infrastructure as code makes academic
brilliance accessible to industry
Medical science at scale | @allPowerde @Tbioinf
38 |

40. APIs enable collaborations
39 | APIs accelerate health | @allPowerde @Tbioinf
API
Applicator
Innovator

41. 1. Bringing genomics into clinical practice:
VariantSpark – finding disease genes.
sBeacon – enable global data exchange.
2. Exploring new Treatment avenues:
GT-Scan – making gene editing safer.
3. Enabling collaboration between academia and clinic:
using cloud solutions to bridge the gap.
Three things to remember
Medical science at scale | @allPowerde @Tbioinf
40 |

42. Australia’s National Science Agency
CSIRO Health and Biosecurity
Denis Bauer
Denis.Bauer@csiro.au
Let’s work
together
Visit our site:
https://bioinformatics.csiro.au
@allPowerde
@Tbioinf

43. New York
JULY
Australia
SEPTEMBER
Singapore
APRIL
Helsinki & North
MARCH
Paris
DECEMBER
London
OCTOBER
Jakarta
FEBRUARY
Hong Kong
AUGUST
JUNE
India
MAY
Check out our API Conferences here
50+ events since 2012, 14 countries, 2,000+ speakers, 50,000+ attendees,
300k+ online community
Want to talk at one of our conferences?
Apply to speak here