VPIN: Project Resources

1
VPIN Project Resources

• Scientific Advisory Board Meeting
• June 2006
• Mary Montoya

2
Project Resources as of 06/06

• Human
• Hardware/Systems
• Software
• Environments
• Web
• Processes

3
Human Resources VPIN teams

• NCGR Damian Gessler (PI)
• Gary Schiltz (SW)
• Lonny Montoya (SW)
• Mary Montoya (SW)
• Linda Julien (Web)
• Forrest Black (Systems)
• TIGR Chris Town (co-PI)
• Foo Cheung
• Hank Wu
• CSHL Lincoln Stein (co-PI)
• Shuly Avraham
• LIS Bill Beavis (co-PI)
• Kamal Gajendran
• Andrew Farmer
• All VPIN personnel are part-time

4
Hardware/Systems computers, etc

• Two computer servers and several laptops loaded
  with
• Apache
• Handles http requests
• Tomcat
• http requests to java
• Postgres
• Relational db
• Jena
• RDF/OWL graphs to java
• Java
• Programming language
• Security
• http access based on server role
• Backup software and procedures

5
Software/Tools code bases, etc

• Moby protocol ( message )
• Pre-defined RDF/OWL graph
• Api package
• Java programming interface to protocol
• Discovery server
• Graph persistence
• Graph searching
• Discovery client
• Developer tools
• Keyword search
• Registration
• Admin tools ( db querying )
• URL rewriting proxy
• PDK provider developer kit
• CDK client developer kit

6
Discovery Server Runtime Environments

• Production - open
• Discovers providers production resources
• Sandbox - open
• Discovers providers test resources
• Test NCGR only
• Tests discovery code prior to release
• Integration - NCGR only
• Tests new features on production-like hardware
• Development developer only
• Tests new features locally

7
VPIN Public Web Domains

• Hosted sites
• semanticmoby.org
• semanticmoby.org/stats
• Website usage
• sandbox.semanticmoby.org
• vpin.ncgr.org
• Documentation
• Discussion forums
• lin.ncgr.org (legume client)
• ontologies.ncgr.org
• Source repository
• open-bio.org hosted by Open Bioinformatics
  Foundation

8
Processes

• Software development
• Agile and iterative
• Daily standup meetings
• Bugzilla for bug tracking
• XPlanner for feature development
• Release process
• Bi-weekly releases
• Tag build test
• document and deploy
• Ontology generation
• Protégé tool validate
• Splitter tool
• Commit to open-bio.org for hosting at
  ontologies.ncgr.org

9
Ready to Rock-n-Roll

• Network population status
• LIS 10 in production
• TIGR 2 in test
• Gramene coming soon
• TAIR 1 in test
• CCGB 6 needing upgrade
• IRRI coming soon