WWW Server Operation

Markus KrummenackerFred Gilham

Bioinformatics Research Group

SRI International

kr@ai.sri.com

gilham@ai.sri.com

SRI InternationalBioinformaticsWWW vs. Desktop

http://biocyc.org/desktop-vs-web-mode.shtmlWWW:

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

Ongoing effort to move Desktop features to Web

SRI InternationalBioinformatics

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 Windows—just click on “Web Server” desktop shortcut

SRI InternationalBioinformatics

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 Database Links: Link to/from PGDB and external web site

UG section 8.5.10 Manual and bulk

SRI InternationalBioinformaticsUnsupervised Web Server

Operation Pathway Tools needs some X ServerXvfb is a display-less X Server Use screen for starting pathway-tools Description: http://bioinformatics.ai.sri.com/ptools/web-logout.html

SRI InternationalBioinformaticsLab Exercise

Start up Pathway Tools in web server mode Connect to it with your browser: http://localhost:1555

Oops! Too many organisms! Fix so it shows ONLY the HPY organism

Do it on the command line -www-publish hpy

Edit the ptools-local/ptools-init.dat file WWW-Publish entry