20120220 Tri-Con Cloud Computing Symposium

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Andrew Su

Technology Business

2
High-throughput molecular profiling is powerful

m/z

Gene/protein
list

Testable
hypothesis

3

20 million papers
900,000 new papers / year

4
Gene databases are numerous and overlapping

… and hundreds
more …

5
Community extensibility and user customizability

http://biogps.org

6
Crowdsourcing depends on positive feedback

Utility

1 100
2 200

Contributors Users

7
Utility: A simple and universal plugin interface
Utility

Contributors Users

8
Utility: A simple and universal plugin interface
Utility

Contributors Users

9
Utility: A simple and universal plugin interface
Utility

Contributors Users

10
Utility: A simple and universal plugin interface
Utility

Contributors Users

11
Utility: A simple and universal plugin interface
Utility

Contributors Users

12
Utility: A simple and universal plugin interface
Utility

Contributors Users

Total of 389 gene-centric online
databases registered as BioGPS plugins

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
Contributors: Explicit and implicit knowledge
Utility

Contributors Users

389 plugins registered
(65% publicly shared)

by over 75 users

spanning 150+ domains

15
BioGPS architecture

http://mygene.info

16
mygene.info architecture

http://mygene.info

NGINX

17
BioGPS as a cloud computing consumer
EC2 Small

EC2 Micro

NGINX

Total monthly cost: ~$100

EC2 Micro EC2 Micro

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

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
The future of BioGPS

Third party
content providers

23
The future of BioGPS

Semantic
interpretation,
change
detection, etc.

Third party
content providers

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)

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20120220 Tri-Con Cloud Computing Symposium

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)

Editor's Notes

next gen sequencing identifies candidate genesAlso Microarray data, proteomics, GWAS, methylation, post-translational modifications, translocation detection, etc.What do these genes do?
MODs and portals
Genetics resources
Literature resources
Protein resources
Pathway and expression databases
Pathway and expression databases
Nginx -- load balancing and reverse proxyTornado – application server (python)
Nginx -- load balancing and reverse proxyTornado – application server (python)

20120220 Tri-Con Cloud Computing Symposium

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Editor's Notes