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GBrowse: What’s New?

GBrowse: What’s New?. Lincoln Stein GMOD Meeting, Toronto October 2011. Open source web-based genome browser used by model organism Dbs and many other groups. Adaptors for flat files, indexed files and many relational databases. Highly customizable. Large user and support community.

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GBrowse: What’s New?

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  1. GBrowse:What’s New? Lincoln Stein GMOD Meeting, Toronto October 2011

  2. Open source web-based genome browser used by model organism Dbs and many other groups. • Adaptors for flat files, indexed files and many relational databases. • Highly customizable. • Large user and support community. • Part of the GMOD suite of integrated genome database applications

  3. Features Added in 2011 • v2.20 (1/2011) -> v2.41 (10/2011) • User Interface • Horizontal dragging of tracks • Floating ruler • Track favorites • Snapshots & user accounts • iPad support • Internals • Authentication plugin architecture (PAM, LDAP) • Performance improvements • EC2 cloud image (in progress)

  4. Live Demo Time • Horizontal Scrolling • Floating Ruler • Track Filtering and Favorites • User Accounts • Track Sharing • Snapshots

  5. Horizontal Scrolling

  6. Floating Ruler

  7. Track Filtering and Favorites

  8. User Accounts

  9. Track Sharing

  10. Snapshots

  11. Authentication Plugins • Very general • Plugin modules accept credentials. • Return true if user is authenticated. • (Optional) Provide user name and group(s) • Distributed plugins • PAM – support Unix, LDAP, Kerberos, etc. • LDAP – Support LDAP users and groups.

  12. Performance Improvements • Cache parsed configuration files. • Useful for configs with 1000’s of tracks. • Render-slave servers use preforking.

  13. Cloud Image (in progress) Master Render Slaves Yeast Fly Worm Human Amazon Snapshots

  14. Cloud Admin Interface

  15. Faceted Track and Source Management (2.43?)

  16. Source code, installation instructions & tutorials available at www.gmod.org OICR Scott Cain Sheldon McKay Peter Ruzanov University of Waterloo Ian Davies Tony deCatanzaro Ahmed Einalem Sukhwinder Lall Chris Vandevelde

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