Administering Pathway Tools

1
Administering Pathway Tools
2
Obtaining Pathway Tools

• Free for non-commercial use
• To obtain license agreement send email to
• ptools-info_at_ai.sri.com

3
Information Sources

• Pathway Tools Users Guide
• aic-export/ecocyc/genopath/released/doc/userguide1
  .pdf
• Pathway/Genome Navigator
• Appendix A Guide to the Pathway Tools Schema
• aic-export/ecocyc/genopath/released/doc/userguide2
  .pdf
• PathoLogic, Editing Tools
• Pathway Tools Web Site
• http//bioinformatics.ai.sri.com/ptools/
• Publications, programming examples, etc.
• Pathway Tools Tutorial
• http//bioinformatics.ai.sri.com/ptools/tutorial/

4
Reporting Problems

• E-mail to ptools-support_at_ai.sri.com
• Include
• Error message
• Result of typing zoom count all
• What version and platform you are running
• What operation were you performing when the error
  occurred?
• Tools -gt Instant Patch

5
Additional Pathway Tools Functionality
6
Napster Comes to Bioinformatics

• Public sharing of Pathway/Genome Databases
• PGDB registry maintained by SRI at URL
  http//biocyc.org/registry.html
• Registry operations
• List contents of registry
• Download PGDBs listed in the registry
• Register PGDBs you have created

7
Registry Details

• Why register your PGDB?
• Declare existence of your PGDB in a central
  location
• Facilitate download by other scientists
• Why download a PGDB?
• Desktop Navigator provides more functionality
  than Web
• Comparative operations
• Programmatic querying and processing of PGDB
• Registration process
• Registered PGDBs have open availability by
  default
• Authors can provide their own license agreements
• Registered PGDBs reside on authors FTP site