LOC3d
From Informatics
- 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)
- 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)
- don't know
- IP => 156.111.6.99 (Ginkgo)
- Red Hat Linux WS Release 3 (Taroon Update 6)
- 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 (Perl CGI)
- 5 to 10 users daily
- 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