LOCtarget

From Informatics

• What labs or how many are using LOCtarget?

  - Rost lab

  - a few labs at Oklahoma University, Baylor University

• Who is the main “database authority” for LOCtarget?

  - Raj Nair (nair@cubic.bioc.columbia.edu)

• What kind of database is it? (flat-file, relational, XML, etc)

  - flat-files

• Size of database?

  - 76 MB

• Anticipated yearly growth? (Megabytes/Gigabytes)

- don't know

• Backup procedures? How often?
• Database backups (Hot, Cold, Both) [and/or]
• Operating system backup

  - OS backup whenever the database is updated (around twice a year)

• What servers/operating systems are hosting them (IP addresses)

• IP => 156.111.6.99 (Ginkgo)
• Red Hat Linux WS Release 3 (Taroon Update 6)

• Approximately how many *active* users?

- difficult to predict

• How often is the database used? (Daily, Weekly, Monthly)

- 5 to 10 users daily

• What platforms are being used? (Oracle, MySQL, PostgreSQL, etc)

  - N/A

• What applications are using these databases?
• Web interface?
• Application (GUI)?
• Command line interface (CUI)?

• Web interface (Perl CGI)

• Is it accessible from outside the firewall to public users?

  - YES (LOCtarget)

• What is the primary purpose of the database & types of data stored?

  • LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets
  • Targets are taken from the central registration database for structural genomics, namely, TargetDB
  • LOCtarget predicts localization through a combination of four different methods:
  • known nuclear localization signals (PredictNLS)
  • homology-based transfer of experimental annotations (LOChom)
  • inference through automatic text analysis of SWISS-PROT keywords (LOCkey)
  • de novo prediction through a system of neural networks (LOCnet)
  • The final prediction is based on the method with the highest confidence

• Are there any issues or problems with the database?
• Specific error messages popping up?
• Problems connecting from the application or web interface?
• Performance issues (queries are slow, freezes at times, etc)

• no

• Would they like help in administering the database?

• no

• What additional features or changes would users like to see?
• new tables or queries
• additional screens on application or web interface
• migrate to different database platform (i.e. MySQL to Oracle)

• no feedback has been provided by users