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Cancer Genomics
Data Pipelines
Lynn & Samantha Langit
CSIRO Bioinformatics / Australia
June 2017 - Oslo
3 Billion data points per patient DNA sample
Up to 25% of the population could be sequenced by 2025
Two Perspectives
Bioinformatics
Research
• Insight
• Reproducibility
Cloud
Architecture
• Speed
• Low Cost
• Simplicity
Cloud Data Pipeline Pattern
Problem
• Define business
problem
Data
• Quality
• Quantity
Candidate
Technologies
• Ingest
• ETL
• Biz Analytics
• ML
• Visualization
Build MVPs
• Iterate
• Learn
Assemble
Pipeline
• Validate each
section
• Test at scale
Genomic Sequencing Results
CRISPR-Cas9 for molecular engineering technology
enables the accurate editing of genomes for researchers.
It…
 Pattern-matching unique sequences of DNA
 Huge demand for large-scale computation
 Time-critical dimension to compute
 NIH-approved for human health
 Could revolutionize cancer treatments
Serverless Lambda
Architecture Pattern
Lambda
function
1
Lambda
function
2
Lambda
function
3
buckets with
objects DynamoDB
API Gateway Users
CSIRO: Commonwealth Scientific & Industrial Research Organization
GT-Scan2
Demo
GT-Scan2
Scale Genomic Analysis
GWAS = genome-wide sequencing data association
studies
 Analysis on large cohort data or imputed SNP array data
 Clustering on genomic profiles to stratify large-cohort
genomic data
 Viewing datasets with millions of features
Cloud Data Pipeline Pattern
Problem
• Define business
problem
Data
• Quality
• Quantity
Candidate
Technologies
• Ingest
• ETL
• Biz Analytics
• ML
• Visualization
Build MVPs
• Iterate
• Learn
Assemble
Pipeline
• Validate each
section
• Test at scale
Genomics (ML) Pipeline Pattern
What is CSIRO’s solution?
For Scale at
reasonable cost Use Apache Hadoop
For Scale at
speed Use Apache Spark for Hadoop
For Usability
in
bioinformatics
Create a domain-specific API (OSS library)
For global use
Leverage Cloud Pipeline Patterns
GWAS Analysis with Variant-Spark
On premise Hadoop Cluster
with Apache Spark
Genomics Analysts
corporate data center
What is Apache Spark?
What is variant-spark?
Demo
80% faster than ADAM
90% faster than R
90% faster than Python
VariantSpark
Uses Apache Spark to massively parallelize the generation of
random forests to identify disease genes efficiently
 Analyzes 3,000 samples with 80 million features in < 30 minutes
 Enables real-time diagnosis by finding similar patients
 Contributes to motor neuron disease (ALS) research in Australia
Data
Prep
Statistics
Probabilistic
Algorithms
Data Viz
Machine
Learning…
Spark ML Classification Algorithms
Wide Random Forest Ensemble
of Decision Trees
Logistic Regression
variant-spark other libraries
OSS Library variant-spark for all
 usable? performant?
 extendable? (clean code)
 using the best language
(Scala)?
 using the ‘best version’ of
Spark?
 using a version of wide
random forests that is
understandable?
Is it…
How best to Deploy Cloud Hadoop?
• IaaS
 EC2 instances with Apache Hadoop, Apache Spark, more…
• PaaS
 Elastic Map Reduce (EMR) Hadoop cluster
• SaaS
 Vendor-managed, i.e. DataBricks w/Jupyter Notebooks
What is Databricks?
DEMO: Jupyter Notebooks
Variant-Spark and
Databricks
Demo
Solving
Important
Questions…
Cancer Genomics?
DEMO: Who is a Hipster?
 AWS EC2 Spot Instances
GWAS Analysis with Variant-Spark
EC2 Hadoop Cluster with Apache Spark
Genomics Analysts
Availability Zone
1000 Genomes
GWAS input
Spot EC2 Hadoop
worker instances
EC2 Hadoop
instances
Cloud Data Pipeline Pattern
Problem Data
Candidate
Technologies
Build MVPs
Assemble
Pipeline
Analyze GWAS -> S3/Hadoop Ingest
ETL
Analyze
Viz
S3 -> Databricks DBFS
Apache Spark
Variant-Spark ML
Notebook SQL, R or Python
SaaS
Cloud Data Pipeline Pattern
Problem Data
Candidate
Technologies
Build MVPs
Assemble
Pipeline
1. Scan vcf -> S3/DynamoDB Ingest
ETL
Analyze
Viz
S3
Lambda
Lambda
Lambda/API Gateway
Serverless
2. Analyze GWAS -> S3/Hadoop Ingest
ETL
Analyze
Viz
S3 -> Databricks DBFS
Apache Spark
Variant-Spark ML
Notebook SQL, R or Python
SaaS
Modern Big Data Pipelines
• Problem #1 - Scan
• Solution: Serverless Cloud Pipeline
• Problem # 2 - Analyze
• Solution: SaaS Cloud ML Pipeline
Cancer Genomics
Data Pipelines
Lynn & Samantha Langit
CSIRO Bioinformatics & variant-spark
June 2017 - Oslo

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Editor's Notes

  1. http://www.nature.com/news/first-crispr-clinical-trial-gets-green-light-from-us-panel-1.20137
  2. http://bioinformatics.csiro.au/ and https://www.csiro.au/en/Locations/NSW/North-Ryde
  3. https://www.gt-scan.net/ --AND- AMA with Dr, Bauer -- https://www.reddit.com/r/science/comments/5fiicm/science_ama_series_im_denis_bauer_a_team_leader/
  4. https://aws.amazon.com/blogs/aws/genome-engineering-applications-early-adopters-of-the-cloud/
  5. https://github.com/csirobigdata/variant-spark
  6. https://en.wikipedia.org/wiki/Random_forest --and-- https://spark.apache.org/docs/1.6.2/ml-classification-regression.html
  7. https://databricks.com/
  8. https://aws.amazon.com/blogs/aws/genome-engineering-applications-early-adopters-of-the-cloud/
  9. https://github.com/csirobigdata/variant-spark