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
either a desktop application or a Web Server. 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.
Whether you run in desktop mode or web server mode,
installing Pathway Tools locally at your site (versus accessing the public BioCyc.org
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
more Pathway/Genome Databases (PGDBs), 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:
- The official BioCyc.org Web site, where the entire BioCyc collection of
PGDBs is available to the general public.
- An internal Web site at your organization, which makes the BioCyc collection of PGDBs accessible to users within your institution.
- An internal 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.
For information on downloading the software for local installation, click here.
Feature Comparison Highlights
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
- Pathway/Genome Editors: All functionality
- Pathway/Genome Navigator:
- Ability to generate genome posters from a PGDB (see example)
- Ability to generate metabolic-map posters from a PGDB (see example)
- Ability to magnify the cellular overview diagram to see compound and enzyme names
- Ability to export PGDB data in many formats
- Many additional query options are provided in desktop mode, including:
- Search for metabolic pathways by substrates
- Search for proteins by pI, molecular weight, and regulation
- Search for chemical compounds by SMILES substructure
- Many additional Cellular Overview queries are provided, such as:
- Compare full metabolic maps of two or more PGDBs
- Find and highlight compounds, reactions, and genes on the metabolic map according to many criteria
- Highlight enzymes controlled by a specified transcription factor
- Trace the path of a particular metabolite through the metabolic network
using the new metabolite tracing tool (below):
 Click for larger image
- A new Genome Overview (below) provides a picture of the entire genome of an organism, with an icon for each gene.
Omics data can be painted onto this diagram so that the color assigned to each gene reflects its expression level.
 Click for larger image
- A new Regulatory Overview (below) shows the entire transcriptional regulation network of a PGDB, or can be customized to show a designated subset of the network. This tool requires that the transcriptional regulatory network be defined in a PGDB, which currently must be done manually. EcoCyc is currently the best PGDB in which to try this tool. In future releases of Pathway Tools it will be possible to paint omics data onto the Regulatory Overview.
 Click for larger image
- Additional Omics Viewer options, such as:
- The ability to superimpose omics datasets on the Genome and Regulatory Overviews as well as or instead of the Cellular Overview.
- The ability to superimpose multiple omics datasets on a single display
- Greater control over the color scheme
- Display of SAM data files
- Starting from a PGDB object such as a pathway, reaction, or chemical compound, navigate
through one command to the same object in another organism's PGDB
- User interface customization, including display colors, fonts, and content of various display features
- Application Programming Interfaces (API's) for software developers
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 for complex queries to be devised through a search form
- 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 BioCyc.org)
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