LOC3d

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  • What labs or how many are using LOC3d?

    - Rost lab

    - a few labs at Oklahoma University, Baylor University

  • Who is the main database authority for LOC3d?

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

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

    - flat-files

  • Size of database?

    - 24 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 (LOC3d)

  • What is the primary purpose of the database & types of data stored?
    • LOC3d is used to predict subcellular localization for eukaryotic proteins of known 3-D structure
    • Subcellular localization is currently predicted using four different methods:
      • predictNLS (nuclear localization signal)
      • LOChom (using homology)
      • LOCkey (using keywords)
      • LOC3d (neural network based prediction)
    • The reported localization is based on the method which predicts localization of a given protein 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)
  • 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
         
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