Geneways
From Informatics
GeneWays
- What labs or how many are using GeneWays?
- Rzhetsky lab, Califano lab, a few external users
- Who is the main “database authority” for GeneWays?
- Marc Hadfield
- What kind of database is it? (flat-file, relational, XML, etc)
- relational & indexed flat-files
- Size of database?
- Flat-file/Lucene indices: 500 GB
- Oracle part: 5-10 GB
- Anticipated yearly growth? (Megabytes/Gigabytes)
- Backup procedures? How often?
- Database backups (Hot, Cold, Both) [and/or]
- Operating system backup
- ask Hans-Erik
- What servers/operating systems are hosting them (IP addresses)
- will probably make the Terabyte range in a year or so
- http://geneways.cu-genome.org
- IP => 156.111.188.210
- Red Hat Linux
- Approximately how many *active* users?
- How often is the database used? (Daily, Weekly, Monthly)
- approximately 200 users signed up, but difficult to find out the amount per user
- What platforms are being used? (Oracle, MySQL, PostgreSQL, etc)
- Oracle 9i Release 2
- What applications are using these databases?
- Web interface?
- Application (GUI)?
- Command line interface (CUI)?
- Web interface
- CUI - used infrequently
- daily
- Is it accessible from outside the firewall to public users?
- YES (<a href="http://genetraffic.cpmc.columbia.edu/">http://geneways.cu-genome.org</a>)
- What is the primary purpose of the database & types of data stored?
- Geneways is built to help integrate research results by providing automatic tools to gather knowledge from scientific literature
- It scans thousands of research articles in order to automatically extract relevant molecular knowledge
- It seeks to provide the collective knowledge of the whole research community in an integrated form
- The core of the system is a knowledge base of molecular actions which can be queried, analyzed, critiqued, and visualized
- 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)
- it is slow due to an old server which they are looking to replace
- Would they like help in administering the database?
- not at the moment
- 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)
- the user interface needs improvement