1 / 9

Pathway Tools: Desktop vs. Web Mode - Comparative Genomics Tools

Explore the differences between using Pathway Tools in Desktop vs. Web mode for bioinformatics research. Learn about advanced query tools, pathway prediction, editing options, and ongoing efforts to transition Desktop features to the Web. Get detailed guides on configuring the Web server and interacting with databases effectively.

april-casey
Télécharger la présentation

Pathway Tools: Desktop vs. Web Mode - Comparative Genomics Tools

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related