AACR 2016: NCI's Cancer Genomics Cloud Pilots Sunday, Apr 17, 2016, 3:45 PM - 5:15 PM

1. SCALABLE, COLLABORATIVE,
REPRODUCIBLE,AND EXTENSIBLE
ANALYSIS OFTCGA DATA INTHE
CLOUD
Brandi Davis-Dusenbery, PhD
AACR
April 18, 2016

2. DISCLOSURE & FUNDING
This project has been funded in whole or in
part with Federal funds from the National
Cancer Institute, National Institutes of Health,
Department of Health and Human Services,
under Contract No. HHSN261201400008C.
I am an employee of Seven Bridges

3. GUIDING PRINCIPLES
Making data
available isn’t
enough to make
it usable
The best science
happens in
teams
Reproducibility
shouldn’t be
hard
The impact of
TCGA is
extended by
new data & tools

4. MAKING DATA
AVAILABLE
ISN’T
ENOUGHTO
MAKE IT
USABLE

5. THE CGC ALLOWSYOUTO ACCESS MORETHAN
1PB OF MULTIDIMENSIONAL -OMICS DATA.
multiple Samples per Case
Primary Tumor
SolidTissue Normal
Blood Derived Normal
Metastatic
… …
multiple Analyses per Sample
Genomic Transcriptomic
Proteomic Epigenomic
… …
Open Data Controlled Data

6. EXPLORETHE DATASET…

7. … ANDTHEN IMMEDIATELY RUN AN ANALYSIS.

8. THE BEST
SCIENCE
HAPPENS IN
TEAMS

9. SECURE AND COMPLIANT PROJECT
MEMBERSHIP
• Projects serve as isolated workspaces
for your data and tools.
• Fine-grained permissions give you
control over who can see and use your
assets.
• TCGA Controlled data projects access
limited to only Authorized users.

10. RICH COMMUNICATION & EFFECTIVE
COLLABORATION
Project descriptions, conversations, and realtime notifications
keep everyone on the same page.

11. REPRODUCIBILITY
SHOULDN’T BE
HARD

12. The inputs, outputs, and
parameters as well of the
precise tool versions
(including dependencies!)
are always linked and
available for reference days
or months later.
EACHTASK IS REPRODUCIBLE & REMEMBERABLE

13. • Even the most
complex workflows
are captured as small
run-able text files.
• Easy to share and
save.
… AND SELF CONTAINED

14. THE IMPACT
OFTCGA IS
EXTENDED BY
NEW DATA &
TOOLS

15. • Graphical uploader
• Command Line uploader
• FTP / HTTP
• API
FOUR WAYSTO ADDYOUR OWN DATA

16. ~40 properties in visual
interface, unlimited
custom properties via
API.
EASILY ANNOTATE UPLOADED DATATO MAKE IT
EASIERTO FIND LATER

17. ASTHE AMOUNT OF DATA HAS
GROWN, SOTOO HASTHE NUMBER OF
TOOLS AVAILABLETO ANALYZE IT
-omics data analysis tools*
(each with many versions)
50+ used in a single
TCGA marker paper
11,160
*omictools.com

18. DOCKER + CWL MAKES IT EASYTO
PUTTHESETOOLS ONTHE CGC …
AND OTHER PLACES
+

19. DEFINETHETOOL, INPUTS, OUTPUTS AND
PARAMETERS

20. ADDYOURTOOLTO 100’S OF EXISTINGTOOLS
TO CREATE A WORKFLOW

21. WWW.CANCERGENOMICSCLOUD.ORG
MORETHAN $1M IN COMPUTE AND
STORAGE CREDITS AVAILABLE FOR
YOUTO USE
Tiered model allows everyone to access up to $1,600
(~ enough to do whole exome analysis of all
pancreatic carcinoma samples)
Request up to $10,000 credits for large collaborative projects
(Graduate students and Post-docs are particularly
encouraged to submit a request)

22. NEARLY 500 RESEARCHERS ARE
USINGTHE CGCTODAY …
Early Adopter
Open Release
WWW.CANCERGENOMICSCLOUD.ORG

23. … JOINTHEM
Booth 452 Networking event
WWW.CANCERGENOMICSCLOUD.ORG

24. THANKYOU
This project has been funded in whole or in part with Federal funds from the National Cancer Institute,
National Institutes of Health, Department of Health and Human Services, under Contract No.
HHSN261201400008C.