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Advanced Comparative Genomics Tools for Bioinformatics Server Operations

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This document outlines the setup and operation of advanced comparative genomics tools in a web server environment. It details the configuration of the Pathway Tools server and discusses the transition from desktop applications to web-based interfaces. Key topics include organism selection, database link management, and command-line arguments for customizing server operations. Users can access tools such as BioVelo for BLAST searching and Pathologic for PGDB curation. Guidelines for MySQL database setup, configuration parameters, and troubleshooting common issues are also provided.

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Advanced Comparative Genomics Tools for Bioinformatics Server Operations

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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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