BioGPS and mygene.info:Consuming and Providing Cloud    Computing Resources        Molecular Med Tri-Con         February ...
2High-throughput molecular profiling is powerful         m/z                                   Gene/protein               ...
320 million papers900,000 new papers / year
4Gene databases are numerous and overlapping                            … and hundreds                               more …
5Community extensibility and user customizability                   http://biogps.org
6Crowdsourcing depends on positive feedback                       Utility                         1   100                 ...
7Utility: A simple and universal plugin interface         UtilityContributors       Users
8Utility: A simple and universal plugin interface         UtilityContributors       Users
9Utility: A simple and universal plugin interface         UtilityContributors       Users
10Utility: A simple and universal plugin interface         UtilityContributors       Users
11Utility: A simple and universal plugin interface         UtilityContributors       Users
12Utility: A simple and universal plugin interface         UtilityContributors         Users                       Total o...
13Users: BioGPS has critical mass         Utility           Daily pageviewsContributors       Users   • > 4100 registered ...
14Contributors: Explicit and implicit knowledge         UtilityContributors       Users     389 plugins registered      (6...
15BioGPS architecture      http://mygene.info
16mygene.info architecturehttp://mygene.info                     NGINX
17BioGPS as a cloud computing consumer                   EC2 Small                                       EC2 Micro        ...
18BioGPS as a cloud computing provider       Use case: Create web application to display           custom Affymetrix data ...
19Gene query web servicehttp://mygene.info/query?q=204252_athttp://mygene.info/query?q=P24941http://mygene.info/query?q=GO...
20Gene annotation web servicehttp://mygene.info/query?q=cdk*   http://mygene.info/gene/1017
21Optimized for performance in web apps                        10             Time (s)                         1          ...
22The future of BioGPS                    Third party                 content providers
23The future of BioGPS                                        Semantic                                     interpretation,...
24       Group members                                    ContactErik Clarke         Ian Macleod                      http...
Upcoming SlideShare
Loading in …5
×

20120220 Tri-Con Cloud Computing Symposium

437 views

Published on

Published in: Technology, Business
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
437
On SlideShare
0
From Embeds
0
Number of Embeds
5
Actions
Shares
0
Downloads
3
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide
  • 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

    1. 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. 2High-throughput molecular profiling is powerful m/z Gene/protein list Testable hypothesis
    3. 3. 320 million papers900,000 new papers / year
    4. 4. 4Gene databases are numerous and overlapping … and hundreds more …
    5. 5. 5Community extensibility and user customizability http://biogps.org
    6. 6. 6Crowdsourcing depends on positive feedback Utility 1 100 2 200 Contributors Users
    7. 7. 7Utility: A simple and universal plugin interface UtilityContributors Users
    8. 8. 8Utility: A simple and universal plugin interface UtilityContributors Users
    9. 9. 9Utility: A simple and universal plugin interface UtilityContributors Users
    10. 10. 10Utility: A simple and universal plugin interface UtilityContributors Users
    11. 11. 11Utility: A simple and universal plugin interface UtilityContributors Users
    12. 12. 12Utility: A simple and universal plugin interface UtilityContributors Users Total of 389 gene-centric online databases registered as BioGPS plugins
    13. 13. 13Users: BioGPS has critical mass Utility Daily pageviewsContributors 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. 14Contributors: Explicit and implicit knowledge UtilityContributors Users 389 plugins registered (65% publicly shared) by over 75 users spanning 150+ domains
    15. 15. 15BioGPS architecture http://mygene.info
    16. 16. 16mygene.info architecturehttp://mygene.info NGINX
    17. 17. 17BioGPS as a cloud computing consumer EC2 Small EC2 Micro NGINX Total monthly cost: ~$100 EC2 Micro EC2 Micro
    18. 18. 18BioGPS 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. 19Gene query web servicehttp://mygene.info/query?q=204252_athttp://mygene.info/query?q=P24941http://mygene.info/query?q=GO:0000307http://mygene.info/query?q=cdk?http://mygene.info/query?q=cdk2
    20. 20. 20Gene annotation web servicehttp://mygene.info/query?q=cdk* http://mygene.info/gene/1017
    21. 21. 21Optimized 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. 22The future of BioGPS Third party content providers
    23. 23. 23The future of BioGPS Semantic interpretation, change detection, etc. Third party content providers
    24. 24. 24 Group members ContactErik Clarke Ian Macleod http://sulab.orgBen Good Chunlei Wu asu@scripps.eduSalvatore Loguercio @andrewsu +Andrew Su Funding and Support (BioGPS: GM83924, Gene Wiki: GM089820)

    ×