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WWW Server Operation

WWW Server Operation. Markus Krummenacker Fred Gilham Bioinformatics Research Group SRI International kr@ai.sri.com gilham@ai.sri.com. WWW vs. Desktop. http://biocyc.org/desktop-vs-web-mode.shtml WWW: Comparative Genomics Tools (HTML Tables)‏ Advanced Query Tool, using BioVelo

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WWW Server Operation

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  1. WWW Server Operation Markus Krummenacker Fred Gilham Bioinformatics Research Group SRI International kr@ai.sri.com gilham@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 Ongoing effort to move Desktop features to Web

  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 Windows—just click on “Web Server” desktop shortcut

  4. 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. 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. 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

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

  8. Configure Ptools • Configure ptools-init.dat • Convert FileKB to MySQL via Pathologic

  9. PGDB Snapshot • Pathologic Backup DB to File • Upgrade DB version

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