1. WWW Server Operation Markus Krummenacker Fred Gilham Bioinformatics Research Group SRI International kr@ai.sri.com gilham@ai.sri.com

2. SRI International Bioinformatics 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 Ongoing effort to move Desktop features to Web

3. SRI International Bioinformatics 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

4. SRI International Bioinformatics WWW Server: Advanced Several more ptools-init.dat parameters Some exotic parameters supplied as command-line args Command-line 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

5. SRI International Bioinformatics 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

6. SRI International Bioinformatics Lab Exercise Start up Pathway Tools in web server mode Connect to it with your browser: http://localhost:1555http://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

7. SRI International Bioinformatics Setup MySQL PGDBs Configure mysql server http://bioinformatics.ai.sri.com/ptools/installation- guide/released/mysql.html http://bioinformatics.ai.sri.com/ptools/installation- guide/released/mysql.html User account that will update curation DB Set in ptools-init.dat

8. SRI International Bioinformatics Configure Ptools Configure ptools-init.dat Convert FileKB to MySQL via Pathologic

9. SRI International Bioinformatics PGDB Snapshot Pathologic Backup DB to File Upgrade DB version