Comparison of Desktop and Web Modes of Pathway Tools

The same Pathway Tools binary program can run as a desktop application (Mac, Windows, and Linux) or as a Web Server (Mac and Linux). 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 mean Pathway Tools running as an application on a computer's desktop window system.

By a Web server, we mean 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:
    • Creation and gap filling of flux-balance analysis (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 Genome Overview
      • Greater control is available for the omics viewer color scheme
      • Ability to input SAM data files
    • Ability to compare full metabolic maps of two or more PGDBs on Cellular Overview (metabolic map diagram)
    • Ability to export PGDB data in many formats
    • Application Programming Interfaces (APIs) for software developers in Python, Java, Perl, and Lisp
    • MultiOmics Explainer -- This tool constructs explanations for how some condition might cause some effect (e.g., how an increase in a metabolite level might alter a level of gene expression) by searching across a joint metabolic/regulatory network.
    • 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.

Features Available in Web Mode Only

  • Pathway/Genome Navigator:
    • Comparative genomics tools are available to generate summary tables comparing genome and metabolic network information across a user-specified set of PGDBs
    • The Metabolic Route Search tool allows users to search for routes through an organism's metabolic network, possibly including additional reactions from the MetaCyc database
    • Web mode includes more extensive SmartTable functionality
    • Web mode provides several organism-selection criteria that are not available in desktop mode
    • Web mode includes an expanded set of search operations under the Search menu, many of which are not available under desktop mode
    • An advanced query tool allows users to formulate precise queries through an interactive form
    • Customize pathway diagrams for Powerpoint or publications
    • BLAST searching and sequence pattern searching allow the user to perform searches against an organism's complete genome or proteome
    • Users can construct sequence alignments in web mode
    • Full-text searches are available if the Web site is indexed by Google (as is
    • Web mode provides a metabolite translation service
    • Web mode provides a web services API