ER-GolgiDB

From Informatics

ER-GolgiDB

 

• What labs or how many are using the ER-GolgiDB?

  - Rost lab

• Who is the main “database authority” for ER-GolgiDB?

  - Kazimierz Wrzeszczynski (kaz@cubic.bioc.columbia.edu)

  - Phil Carter

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

  - flat-files

• Size of database?

  - 5.2 MB

• Anticipated yearly growth? (Megabytes/Gigabytes)

- 10 MB

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

  - OS backup

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

• IP => 156.111.70.150
• 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)

- weekly

• 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

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

  - YES</li>

  ER-GolgiDB</li> </li>

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

    • ER and Golgi localization is predicted using the explicit "Accuracy versus Scaled HSSP distance" curves for each localization. The assigned localization is inferred from the homologue that most accurately predicts localization for the protein and the accuracy based on HSSP distance threshold is provided.
    • Subsets of membrane and lumenal predictions are also provided.

  • 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?

  • not at the moment

  • 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