NLSdb

From Informatics

• What labs or how many are using NLSdb?

  - Rost lab

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

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

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

  - flat-files

• Size of database?

  - ? MB

• Anticipated yearly growth? (Megabytes/Gigabytes)

- static

• 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 => 156.145.30.81 (Walnut)
• Red Hat Linux ES 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)?

• SRS web interface

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

  - YES (NLSdb)

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

  • NLSdb is a database of nuclear localization signals (NLSs) and of nuclear proteins. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus
  • NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases
  • NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins
  • The data are stored and managed using the portal of the Sequence Retrieval System (SRS)
  • NLSdb has been formated in an EMBL-like flat-file format, thus allowing indexing of the database in SRS
  • Proteins in NLSdb can be identified through their SWISS-PROT/TrEMBL, PDB or PEP identifiers

• 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)

• links to proteomes do not always work

• 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