CellCycleDB

From Informatics

CellCycleDB

 

• What labs or how many are using CellCycleDB?

  - Rost lab

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

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

  - Phil Carter

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

  - indexed flat-files formatted by SRS (Sequence Retrieval System)

• Size of database?

  138 MB

  599 proteins

• Anticipated yearly growth? (Megabytes/Gigabytes)

- 300 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 => 156.145.30.81
• Red Hat Linux WS Release 3 (Taroon Update 5)

• 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>

  Cell Cycle DB</li>

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

  • CellCycleDB allows the user to submit a protein sequence to determine estimates for involvement in the cell cycle process or to search CellCycleDB for predicted cell cycle proteins among six eukaryotic proteomes
  • It is currently a first detailed analysis through homology assignment for identifying proteins functioning in the cell cycle process, focusing on cell cycle control
  • It can be searched using an SRS web interface as well

• 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)

• ask Phil

• Would they like help in administering the database?

• ask Phil

• 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