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Web-based metabolic network visualization with a zooming user interface.

Latendresse M, Karp PD - BMC Bioinformatics (2011)

Bottom Line: It uses the OpenLayers library to display tiled diagrams.This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner.This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA. latendre@ai.sri.com

ABSTRACT

Background: Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging.

Description: We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams.

Conclusions: This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu.

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Related in: MedlinePlus

The Cellular Overview after Three Searches. The Cellular Overview after three searches. It created three highlighted overlays, one for each search. Highlighting can be activated and deactivated by toggling the radio buttons in the blue Layer Switcher panel on the right. When a 'List' button is clicked, a small window opens up to list the objects found in the overview. Such a window is opened for the list "Gene 'arg' " (the list is long so that the window is scrollable). A gene search finds reactions, RNAs, transporters, and enzymes in the overview. Clicking an item in the list places a marker in the diagram to better locate it.
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Figure 2: The Cellular Overview after Three Searches. The Cellular Overview after three searches. It created three highlighted overlays, one for each search. Highlighting can be activated and deactivated by toggling the radio buttons in the blue Layer Switcher panel on the right. When a 'List' button is clicked, a small window opens up to list the objects found in the overview. Such a window is opened for the list "Gene 'arg' " (the list is long so that the window is scrollable). A gene search finds reactions, RNAs, transporters, and enzymes in the overview. Clicking an item in the list places a marker in the diagram to better locate it.

Mentions: When a search is done (see Figure 2), the objects found are highlighted in the Cellular Overview diagram using a graphical overlay, which is a separate graphical plane in which JavaScript code can draw rectangles, circles, and lines of different colors. The list of overlays is shown in the Layer Switcher panel on the right of the Overview Web page. From this panel you can activate or deactivate (render invisible) specific overlays.


Web-based metabolic network visualization with a zooming user interface.

Latendresse M, Karp PD - BMC Bioinformatics (2011)

The Cellular Overview after Three Searches. The Cellular Overview after three searches. It created three highlighted overlays, one for each search. Highlighting can be activated and deactivated by toggling the radio buttons in the blue Layer Switcher panel on the right. When a 'List' button is clicked, a small window opens up to list the objects found in the overview. Such a window is opened for the list "Gene 'arg' " (the list is long so that the window is scrollable). A gene search finds reactions, RNAs, transporters, and enzymes in the overview. Clicking an item in the list places a marker in the diagram to better locate it.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113945&req=5

Figure 2: The Cellular Overview after Three Searches. The Cellular Overview after three searches. It created three highlighted overlays, one for each search. Highlighting can be activated and deactivated by toggling the radio buttons in the blue Layer Switcher panel on the right. When a 'List' button is clicked, a small window opens up to list the objects found in the overview. Such a window is opened for the list "Gene 'arg' " (the list is long so that the window is scrollable). A gene search finds reactions, RNAs, transporters, and enzymes in the overview. Clicking an item in the list places a marker in the diagram to better locate it.
Mentions: When a search is done (see Figure 2), the objects found are highlighted in the Cellular Overview diagram using a graphical overlay, which is a separate graphical plane in which JavaScript code can draw rectangles, circles, and lines of different colors. The list of overlays is shown in the Layer Switcher panel on the right of the Overview Web page. From this panel you can activate or deactivate (render invisible) specific overlays.

Bottom Line: It uses the OpenLayers library to display tiled diagrams.This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner.This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA. latendre@ai.sri.com

ABSTRACT

Background: Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging.

Description: We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams.

Conclusions: This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu.

Show MeSH
Related in: MedlinePlus