GeneTraffic

From Informatics

GeneTraffic Inventory

 

• What labs or how many are using GeneTraffic?

  - Approximately 10 labs

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

  - Yonghui Zhang

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

  - relational

• Name/Size of database?

  - GeneTraffic 3.2

  - approximately 205 GB

• Anticipated yearly growth? (Megabytes/Gigabytes)

- approximately 70 GB

• 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)

• genetraffic.cpmc.columbia.edu
• IP => 156.111.129.113
• Red Hat Linux release 7.1 (Seawolf)

• Approximately how many *active* users?

  It is difficult to tell because one username in GeneTraffic might be shared by several people in one lab. However, Yonghui states that he doesn’t think that there are many users because he notices the number of people logged on from time to time. There are 10 licenses (meaning a maximum of 10 people can access it at the same time), but it is uncommon to see more than two people using it at one time.

• How often is the database used? (Daily, Weekly, Monthly)

  - monthly

• What platforms are being used? (Oracle, MySQL, PostgreSQL, etc)

  - PostgreSQL (version 7.1)

• What applications are using these databases?
• Web interface?
• Application (GUI)?
• Command line interface (CUI)?

• Web interface consisting of PHP and ActiveX components
• Interface is available only through Internet Explorer running on Windows

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

  - YES (<a href="http://genetraffic.cpmc.columbia.edu/">http://genetraffic.cpmc.columbia.edu</a>)

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

  • to store and analyze microarray data
  • behaves like a FTP server as well to store CEL, CHP, DAT & TXT files

• 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)

• ActiveX errors pop up
• GeneTraffic often freezes
• Sometimes the user is disconnected from the session

• Would they like help in administering the database?

• perhaps create a pg_dump backup along with Kristen’s OS backups
• confirm with developers (Harry Liu) before you attempt this

• 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 is not intuitive and NOT user-friendly
• unfortunately, it is a commercial product and it is not clear how active development has been since Stratagene absorbed Iobion

• May I access the database and if so, what is the login info?

  - YES, I was given an admin account to the web interface and read-only privileges to connect via SSH to view the underlying database/tables