WWW Server Operation Markus Krummenacker Fred Gilham Bioinformatics Research Group SRI International kr@ai. sri. com gilham@ai. sri. com
lanscttamrofnioi. S oi ianretn. I IRB WWW vs. Desktop http: //biocyc. org/desktop-vs-web-mode. shtml WWW: Comparative Genomics Tools (HTML Tables) Advanced Query Tool, using Bio. Velo 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
lanscttamrofnioi. S oi ianretn. I IRB 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
lanscttamrofnioi. S oi ianretn. I IRB 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
lanscttamrofnioi. S oi ianretn. I IRB Unsupervised Web 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/ptools/web-logout. html
lanscttamrofnioi. S oi ianretn. I IRB Lab 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
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