1. BioGPS and mygene.info:
Consuming and Providing Cloud
Computing Resources
Molecular Med Tri-Con
February 20, 2012
Andrew Su, Ph.D.
http://sulab.org
@andrewsu
+Andrew Su
asu@scripps.edu

2. 2
High-throughput molecular profiling is powerful
m/z
Gene/protein
list
Testable
hypothesis

3. 3
20 million papers
900,000 new papers / year

4. 4
Gene databases are numerous and overlapping
… and hundreds
more …

5. 5
Community extensibility and user customizability
http://biogps.org

6. 6
Crowdsourcing depends on positive feedback
Utility
1 100
2 200
Contributors Users

7. 7
Utility: A simple and universal plugin interface
Utility
Contributors Users

8. 8
Utility: A simple and universal plugin interface
Utility
Contributors Users

9. 9
Utility: A simple and universal plugin interface
Utility
Contributors Users

10. 10
Utility: A simple and universal plugin interface
Utility
Contributors Users

11. 11
Utility: A simple and universal plugin interface
Utility
Contributors Users

12. 12
Utility: A simple and universal plugin interface
Utility
Contributors Users
Total of 389 gene-centric online
databases registered as BioGPS plugins

13. 13
Users: BioGPS has critical mass
Utility Daily pageviews
Contributors Users
• > 4100 registered users Top 10 organizations
• 4000 unique visitors per week 1. Harvard 6. Cambridge
2. NIH 7. U Penn
• 40,000 page views per week
3. UCSD 8. Stanford
4. Scripps 9. Wash U
5. MIT 10. UNC

14. 14
Contributors: Explicit and implicit knowledge
Utility
Contributors Users
389 plugins registered
(65% publicly shared)
by over 75 users
spanning 150+ domains

15. 15
BioGPS architecture
http://mygene.info

16. 16
mygene.info architecture
http://mygene.info
NGINX

17. 17
BioGPS as a cloud computing consumer
EC2 Small
EC2 Micro
NGINX
Total monthly cost: ~$100
EC2 Micro EC2 Micro

18. 18
BioGPS as a cloud computing provider
Use case: Create web application to display
custom Affymetrix data
Gene Annotation
as a Service
“CDK2” (GAaaS)
“204252_at”
Users
Users Developers
Developers Users
204252_at
Developers
Expression
Data set samples

19. 19
Gene query web service
http://mygene.info/query?q=204252_at
http://mygene.info/query?q=P24941
http://mygene.info/query?q=GO:0000307
http://mygene.info/query?q=cdk?
http://mygene.info/query?q=cdk2

20. 20
Gene annotation web service
http://mygene.info/query?q=cdk* http://mygene.info/gene/1017

21. 21
Optimized for performance in web apps
10
Time (s)
1
0.1
0.01
10 100 1000 10000 100000
# of query terms
# of hits
More documentation (paging, sorting, filtering, etc.)
plus code snippets at http://mygene.info.

22. 22
The future of BioGPS
Third party
content providers

23. 23
The future of BioGPS
Semantic
interpretation,
change
detection, etc.
Third party
content providers

24. 24
Group members Contact
Erik Clarke Ian Macleod http://sulab.org
Ben Good Chunlei Wu asu@scripps.edu
Salvatore Loguercio @andrewsu
+Andrew Su
Funding and Support
(BioGPS: GM83924,
Gene Wiki: GM089820)