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Comparison of Desktop and Web Modes of Pathway Tools

On each of the platforms under which it runs (Macintosh, Windows/x86, Linux/x86), the same Pathway Tools binary program can run as a desktop application or as a Web Server (or both -- these options are not exclusive). Although the software shares most of its functionality between these two modes of operation, some functionality is available in only one mode or the other. Therefore, by installing Pathway Tools locally, you will gain access to desktop operations that are not available through the Web site. Some sites run Pathway Tools in both desktop and Web mode so that they have access to all Pathway Tools capabilities (usually both modes would be configured to access the same PGDBs).

Whether you run in desktop mode or web server mode, installing Pathway Tools locally at your site (versus accessing the public server) is likely to speed up many operations because it eliminates network delays and sharing of computer resources. In addition, installing Pathway Tools at your site enables comparisons across Pathway/Genome Databases (PGDBs) created at your site, because the many comparative operations within Pathway Tools require that all PGDBs to be compared reside within the same Pathway Tools server.

By a desktop application, we Pathway Tools running as an application on a computer's desktop window system.

By a Web server, we Pathway Tools running in a mode in which it functions as a Web server, and all interactions with it are through a Web browser. Pathway Tools Web servers could include:

  • A private Web site at your organization, which makes the BioCyc collection of PGDBs accessible to users within your institution.
  • A private Web site at your organization, which makes PGDBs that you have created, or that other Pathway Tools users have created, accessible to users within your institution.
  • An external Web site at your organization, which makes PGDBs that you have created using Pathway Tools available to the the general public.
  • The official Web site, where the entire BioCyc collection of PGDBs is available to the general public.

To download the software for local installation, click here.

Features Available in Desktop Mode Only

  • PathoLogic: All PathoLogic functionality including
    • Creation of new PGDBs
    • Use of Pathologic inference tools, such as pathway prediction, pathway hole filling, operon prediction, and the Transport Inference Parser

  • MetaFlux: All MetaFlux functionality including
    • Development of flux-balance analysis (FBA) models
    • Execution of FBA models
    • Gene knock-out analysis of FBA models

  • Pathway/Genome Editors: All PGDB editing functionality is available in desktop mode only

  • Pathway/Genome Navigator:
    • Omics analysis tools:
      • The ability to superimpose omics datasets on the Regulatory Overview
      • Omics graphing capabilities are available, such as graphing the levels of individual genes or metabolites, or of all genes or metabolites within a pathway
      • Greater control is available for the omics viewer color scheme
      • Ability to input SAM data files
    • Desktop-only Cellular Overview (metabolic map diagram):
      • Compare full metabolic maps of two or more PGDBs
      • Find and highlight compounds, reactions, and genes on the metabolic map according to more criteria than using the Web version
      • Highlight enzymes controlled by a specified transcription factor
    • Ability to generate genome posters from a PGDB (see example)
    • Ability to generate metabolic-map posters from a PGDB (see example)
    • Ability to export PGDB data in many formats
    • Application Programming Interfaces (APIs) for software developers in Java, Perl, and Lisp
    • Network reachability analysis: define a known or hypothetical growth medium for an organism. The software then computes whether, starting from that growth medium, the metabolic reaction network is capable of producing expected product compounds.
    • Trace the path of a particular metabolite through the metabolic network using the metabolite tracing tool (below):

        Click for larger image


      Features Available in Web Mode Only

      • Pathway/Genome Navigator:
        • Comparative genomics tools are available to generate summary tables comparing metabolic networks across a user-specified set of PGDBs
        • An advanced query tool allows users to formulate precise queries through an interactive form
        • Customize pathway diagrams for Powerpoint or publications
        • BLAST searching allows the user to query a desired sequence against an organism's complete genome
        • Full-text searches are available if the Web site is indexed by Google (as is