Pfam

From Informatics

• What labs and/or how many are using Pfam?

  20 C2B2/MAGNet labs
  
  50 Cancer-center and non-cancercenter labs

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

  Richard Friedman (friedman<at>cancercenter.columbia.edu),
  Pavel Morozov (pm259@columbia.edu)

  Michael Honig (mhonig@c2b2.columbia.edu) - relational version

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

  Flat-file and relational (2 versions)

• Size of database?

  Statistical models of 9,000 protein families

• 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)

• http://cancercenter.columbia.edu
• bonsai.bioc.columbia.edu

• Approximately how many *active* users?

200

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

Monthly

• 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 (GCG package) and x-Windows (seqlab)

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

  YES

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

  • Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families.
  • For each family in Pfam you can:

  • Look at multiple alignments
  • View protein domain architectures
  • Examine species distribution
  • View known protein structures
  • Follow links to other databases

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

  • http://cancercenter.columbia.edu; for account => Contact: Janie Weiss (janie<at>cancercenter.columbia.edu)
  • adgate.cu-genome.org; for account => Contact: Hans-Erik Aronson (hga1<at>columbia.edu)