WWW Server Operation

1
WWW Server Operation

• Markus Krummenacker
• Bioinformatics Research Group
• SRI International
• kr_at_ai.sri.com

2
WWW vs. Desktop

• http//biocyc.org/desktop-vs-web-mode.shtml
• WWW
• Comparative Genomics Tools (HTML Tables)
• Advanced Query Tool, using BioVelo
• BLAST Searching
• Desktop
• Pathologic Prediction of new PGDBs
• Pathway Hole Filler
• All Editing Tools for Curation
• Many Overview Highlighting Options

3
Starting WWW Server Basics

• Configured by ptools-init.dat parameters
• Required (the values are used for generating
  URLs)
• WWW-Server-Hostname
• WWW-Server-Port
• Description UG Section 2.1.1
• Organism Selection
• Start WWW Server pathway-tools -www

4
WWW Server Advanced

• Several more ptools-init.dat parameters
• Some exotic parameters supplied as commandline
  args
• Commandline args override ptools-init.dat
• Description UG Section 2.3.1
• Displaying target of DBLINK for a gene page
• -gene-link-db DBFRAMEID

5
Bulk Loading of DB-Links

• Database Definition File
• Link Definition File
• Format Description UG section 7.5.8.5
• Load with commandline args -dbdef and -linkdef

6
Unsupervised WWW Server Operation

• Pathway Tools needs some X Server
• Xvfb is a display-less X Server
• Use screen for starting pathway-tools
• Description http//bioinformatics.ai.sri.com/ptoo
  ls/web-logout.html