PEP
From Informatics
PEP (Database of Predictions for Entire Proteomes)
- What labs or how many are using PEP?
- Rost lab, NESG groups
- Who is the main “database authority” for PEP?
- Phil Carter
- What kind of database is it? (flat-file, relational, XML, etc)
- indexed flat-files formatted by SRS
- Size of database?
- 40 GB
- Anticipated yearly growth? (Megabytes/Gigabytes)
- 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)
- 15 GB
- http://rostlab.org/db/PEP/index.html
- IP => 156.145.30.81
- Red Hat Linux WS Release 3 (Taroon Update 5)
- Approximately how many *active* users?
- How often is the database used? (Daily, Weekly, Monthly)
- difficult to predict
- 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
- Command line (SRS commands can be issued)
- weekly
- Is it accessible from outside the firewall to public users?
- YES (<a href="http://cubic.bioc.columbia.edu/PEP" title="PEPlink">http://cubic.bioc.columbia.edu/PEP</a>)
- What is the primary purpose of the database & types of data stored?
- PEP is a database of Predictions for Entire Proteomes. PEP sequences are ORFs (open reading frames). PEP is created from all proteins available for each respective genome, aligned against SWISS-PROT, TrEMBL, the PDB, and by individual analysis of each PEP sequence using COILS, MaxHom, NSR, PHD, SEG, and SignalP.
- 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