LOChom

From Informatics

• What labs or how many are using LOChom?

  - Rost lab

  - a few labs at Oklahoma University, Baylor University

• Who is the main database authority for LOChom?

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

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

  - flat-files

• Size of database?

  - 4.6 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 (LOChom)

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

  • LOChom is a database of subcellular localization predictions based on sequence hommology to experimentally annotated proteins.
  • Subcellular localization is predicted using the explicit "Accuracy versus Scaled HSSP distance" curves for the five major localizations.
  • For the minor (under-represented) localization classes, the average (over all classes) "Accuracy versus Scaled HSSP distance curve" was used. The assigned localization is inferred from the homologue that most accurately predicts localization for the protein.

• 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