The bioinformatics community faces numerous challenges in developing research and clinical software for analyzing genomic data. The DNAnexus Platform enables solutions to these problems. This presentation will cover its features: massively scalable ondemand cloud infrastructure, fully configurable and scriptable genomics API, commandline interface and SDKs, collaboration and community support, visualization and publication tools, enterprise-grade security, compliance with clinical and diagnostic standards.

1. Powering the genomics revolution
Genomics applications in the cloud
with the DNAnexus Platform
Andrey
Kislyuk
SFAF
2013

2. What drives DNAnexus?
Grad
students,
industry
scien9sts,
researchers.
We
kept
hi>ng
bioinforma9cs
roadblocks.
– Don’t
know
how
much
compute
we’ll
need
– Resource
conten9on
– I/O
boKlenecks
– Storage
shortages
– Bad
interfaces
– Byzan9ne
IT
– Overpriced
and
underu-lized
– Blocks
clinical
applica-ons

3. What if there was a way to…
Break IT limitations
Publish your tools
Work together

4. Powering the genomics revolution
It’s here.

5. The DNAnexus Platform
Configurable
cloud
infrastructure
for
genomics

6. The DNAnexus Platform
Open
and
comprehensive
API

7. The DNAnexus Platform
Open
and
comprehensive
SDK
Linux
OS
X
Windows
Upload
agents
(Dropbox-­‐like)

8. Powering the genomics revolution
Batteries are included

9. The DNAnexus Platform
Powerful
visualiza9on
tools
built
in

10. The DNAnexus Platform
Powerful
visualiza9on
tools
built
in

11. The DNAnexus Platform
Powerful
visualiza9on
tools
built
in

12. The DNAnexus Platform
Quality
control
reports

13. Your visualization engine here
(there’s an API for that)

14. Yes, we have Circos

15. Powering the genomics revolution
DNAnexus is ready
for clinical data

16. Secure, compliant, audited

17. Those are not just acronyms…
• All
data
encrypted
with
full-­‐disk
AES-­‐256
at
rest,
SSL
on
the
move
• Produc9on
access
controls
• Third-­‐party
security
audits
• Op9onal
2-­‐Factor
Auth
• LXC
(Linux
Containers)
hypervisor
• Auditable
by
user

18. Your data is yours
We
will
never
hold
your
data
hostage
– Always
exportable
– Always
downloadable
– We’re
not
allowed
to
look
at
it

19. The DNAnexus Platform
Reliability
• Triple
data
redundancy
• Geographically
distributed
• Job-­‐level
hardware
fault
tolerance
• Reproducible
and
auditable
results
for
6+
years
DNAnexus
is
ready
for
clinical
data

20. Powering the genomics revolution
Blazing fast development

21. Open-source stack
App
wizard
walks
you
through
app
crea1on
Learn
by
example
fork
our
repos
Collaborate
deploy
apps
from
GitHub

22. Debug quickly
• SDK
tools
for
debugging
• Jobs
start
in
5
seconds
under
most
circumstances
• Real-­‐9me
job
logs

23. Data standards
• GTable:
Columnar
indexed
data
store
for
genome
data
– Suitable
for
storing
SAM,
GFF/GTF,
BED,
VCF,
etc.
• I/O
specifica9ons
– Contracts
between
apps
enable
composi9on
• Data
type
defini9ons
and
validators
Foundations for
Interoperability

24. Powering the genomics revolution
Massive on-demand compute

26. Instant-on supercomputer
at your fingertips…
…only when you need it
Spin up thousands of instances
Specify instance types
Pay by the second

27. Powering the genomics revolution
Community
Collaboration

28. DNAnexus Answers
A
community
working
together

29. Instant collaboration
• Eliminate
data
transfer
headaches
• Collaborate
on
data,
tools,
workflows
in
one
environment
• Enable
bioinforma9cs
experts
to
deliver
tools
to
biologists

32. So how do I add my app?

33. 1. Run App Wizard

34. So how do I add my app?

35. app spec

37. 2. Add entry point code

40. 3. Build, test, publish

42. done

47. Reproducibility
Ever
try
to
reproduce
results
from
a
bioinforma9cs
paper?
How
about
CLIA
compliance?
All
objects
are
versioned
Analysis
I/O
is
read-­‐only
Jobs
enter
into
project’s
permanent
record

48. Publishing
Authors
who
publish
their
sohware
• Don’t
worry
about
suppor9ng
diverse
installs
– You
installed
my
package
on
WHAT?
• Leverage
all
Plajorm
features
– Accessible
UI
• Compose
with
other
apps
– It’s
an
ecosystem
– Publish
your
workflows
as
apps,
too

49. Recognition
Users
are
encouraged
to
cite
app
authors
One-­‐click
bibliographies
coming
soon

50. Powering the genomics revolution
We care about
developers

51. DNAnexus developer program
• $1000
credit
• App
Boun9es
• Featured
Apps

52. Powering the genomics revolution
Vision

53. DNAnexus roadmap
• App
mone9za9on
(Summer
2013)
• Channels
for
organiza9ons
• AWS
Glacier
–
cheap
data
archival
• Projects
as
publica9ons
Supplementary
materials!
And
of
course…
• More
apps

54. DNAnexus roadmap
Always
improving…
…And
so
are
our
cloud
providers
We
pass
on
the
savings
to
you

55. DNAnexus vision
Unlock the potential for DNA-based
medicine and biotechnology
with a collaborative and scalable
data platform

56. DNAnexus is the platform for
publishing your algorithms

57. DNAnexus is the platform for
delivering genomics results to users

58. Powering the genomics revolution
Acknowledgments
DNAnexus is
Andreas Sundquist
Arend Sidow
Serafim Batzoglou
Evan Worley
George Asimenos
Joseph Dale
Lee Bendekgey
Mike Furness
Michael Kawai

59. Powering the genomics revolution
Thank you
dnanexus.com

60. Pricing: Individuals

62. Institutions
Volume
pricing
for
genome
centers
20-­‐30%
cheaper
than
TCO
of
your
average
neighborhood
cluster