The Translational Genomics Research Institute (TGen) is a non-profit organization dedicated to using genomic and other -omic generated information to provide a greater understanding of the underlying biological defects that cause diseases and disorders. The human genome has over 3 billion nucleotide base pairs residing in our 23 pairs of chromosomes, each of which has up to thousands of genes. Talk about looking into The Matrix! The bioinformatics industry is undergoing a sea change, driven by advances in biological research and gains in computational power that accelerates the ability to find treatments and cures. While inexpensive compute infrastructure made this work possible, managing those enormous workloads was a massive headache, until science found a cure: Docker! This talk will describe how TGen uses Docker and the Docker storage plugins API to run a large-scale, big data compute cluster to push the limits of biological science. You will learn: - How TGen uses bioinformatics to predict disease behavior and hypothesize a cure - How to package bioinformatics workloads into Docker containers How to orchestrate elastic compute clusters at scale - How to manage big data workloads using the Docker plugins API v2

1. Cool Genes The
Search for a Cure
Using Genomics, Big
Data, and Docker

2. A non-profit 501 (c)(3) research
institute focused on
• Discovering genetic changes &
mechanisms that underlie a
variety of human diseases
• translating discoveries into new
diagnostic tests and
therapeutics.
Translational Genomics
Research Institute (TGen)
Basic Research
Understanding
of disease
Translational Research – Tgen
Development of diagnostics
and therapeutics
Clinical Application
Application to patient

3. By the Way

5. Timeline of Precision
Medicine Innovation
exomes & genomes
2,965
transcriptomes to
date in prospective
studies
1307
2006 2008 2010 2012 2014 2016 2018
2020
CLINICALTRIALS
Bipolar disorder
General Oncology
Triple Negative Breast Cancer
Various cancers
Pancreatic Cancer
Melanoma
Multiple Myeloma
Pediatric Cancer -NMTRC
Small Cell Lung Cancer
Glioblastoma
Breast Cancer
Rare Childhood Disorders
Concussion
Childhood Cancer

6. Why We Do This…
http://goo.gl/zinVVS
Computational time cut
from weeks to hours
Optimized, purpose-built
hardware for analyzing NGS
Get treatments to
patients faster!

8. IoT Ecosystem
Analytics Data StorageRemote Devices
Internet Network Gateway
IoT Devices
Analysis
Command/RFI

9. Downstream
Analytics
Sboner et. all. "The Cost of Sequencing: Higher Than You Think!" Genome Biology 2011, 12:125,
and thanks to Intel for the drawing
Sample collection &
experimental design
Sequencing
Data Reduction
Data Management
Downstream Analysis
Future
(Approximately 2020)
Pre-NGS
(Approximately 2000)
Now
(Approximately 2010)
0%
100%
Sequencing
Sample
Collection
Experimental
Design
Data Management
Data Reduction
Raw reads
(FASTA, FASTQ)
High-level summaries
(VCP, Peaks, RPKM)
Mapped reads
(BAM, CRAM, MRF)
Downstream Analysis
(differential expression, novel
TARs, regulatory networks,…)

10. Existing HPC Storage
Architecture
Sequencer Compute Archive
RAW
BCL
IRF
Lustre
Scratch
Lustre
Isilon
FASTQ
VCF
BAM Workstation S3

11. TGen HPC Workflows
Orchestration ApplicationCompute
Storage
Torque
Maui
Moab
Slurm
LSF
Bright
Computing
Lustre CIFS/SMB NFS DASD Isilon NASHSM/Tape
Pipeline
Ad-hoc
Reference data, STAR_GTF, GTF Mask,
DNA aligner, RNA aligner, Fusion Detector,
Indel realignment, Recalibrate, Copy
number, Allele count, Circos, Mutect,
Strelka, Snpsniff, Cuffquant, Sailfish,
IGLBEDCOV, Digar, BWA, Tophat
Java, R, STAR, bcl2fastq, blast, boost,
bowtie2, bwa, perl, python, picard-tools,
sailfish, salmon, samtools, cufflinks, bwa,
and many many others.

12. TGen HPC Hybrid
WorkflowsHybrid Orchestration Application
PipelineAd-hoc
Reference data, STAR_GTF, GTF Mask, DNA aligner, RNA
aligner, Fusion Detector, Indel realignment, Recalibrate,
Copy number, Allele count, Circos, Mutect, Strelka, Snpsniff,
Cuffquant, Sailfish, IGLBEDCOV, Digar, BWA, Tophat
Java, R, STAR, bcl2fastq, blast, boost, bowtie2, bwa, perl,
python, picard-tools, sailfish, salmon, samtools, cufflinks,
bwa, and many many others.
Hybrid Compute
Storage
Docker
Single and multi layer
containers
Kubernetes
Deployment with
services & pods
Flexibility on-prem
and cloud
SVCS

13. Basic Pipeline
Persistence
Compute
Persistent Volumes in
Sequencing Orchestrator
BCL
Containers
FASTQ
Containers
IRF Volumes
(Prepared Input)
VCF Volumes
(Working Set)
BAM Volumes
(Shared Format)
Archive
(File, Object)
Downstream
Containers

14. Containermania
Collaborative
Data
Warehouse
PHI Data
Laboratory
Quality
Control
Data
Processing
Reporting
LabUI
Interface
Access Portal
Agile CLIA
Lab
Rapid Test
Development
Healthcare Partner
Clinical
Reports
Specimens
Consent
DataIntegration
Pharma Research
Infrastructure at
Regulatory Compliant
Data Center
Data Analytics
Minimal Infrastructure
Required

15. Docker Workflow RNA
Expression
Counts
Merge
fastqs
Mark
Duplicates
RNA Align
HT Seq
Merge
fastqs
Fusion
Detection
Differential
Expression
Stats/
Metrics
Expression
Counts

16. Future Visions….
To the cloud we go…..
Long term storage
Sustainability
Research vs clinical application
Sequencing platform(s)
Downstream is where the “good stuff” is
Disparate data types
Politics
Legal
Patient owned information

17. Thank you!
Acknowledgements
Portworx
DellEMC
Dr. David Craig
Dr. Matt Huentelman
Dr. Jonathan Keats
Nelson Kick
TGen HPC Team