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WWW Server Operation Markus Krummenacker Fred Gilham Bioinformatics Research Group SRI International

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Presentation on theme: "WWW Server Operation Markus Krummenacker Fred Gilham Bioinformatics Research Group SRI International"— Presentation transcript:

1 WWW Server Operation Markus Krummenacker Fred Gilham Bioinformatics Research Group SRI International

2 SRI International Bioinformatics WWW vs. Desktop 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 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 Database Links: Link to/from PGDB and external web site UG section  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:

6 SRI International Bioinformatics Lab Exercise Start up Pathway Tools in web server mode Connect to it with your browser: 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 guide/released/mysql.html 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


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