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New Zoomable Web Metabolic Network
And Regulatory Network Diagrams
Mario Latendresse
October 2010
Bioinformatics Research Group
SRI International
[email protected]
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Web Zoomable Overviews
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
Regulatory Overview
Currently available only for E. coli K12
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Cellular Overview
Available for over 1000 databases at BioCyc.org
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Both overviews have an Omics Viewer mode to
lay over expression data (e.g., experimental
data)
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A Demo of Regulatory Overview
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For E. coli at BioCyc.org
Tools->Regulatory Overview
The layout command
Nested ellipses: The three ellipses, grouping of genes on the outer ellipse.
Top to bottom: The rows have no genes that regulate each other
Zooming & panning
Adding relationship arrows (regulators and regulatees)
Searching for genes
Highlighting genes based on regulators and regulatees
Omics Viewer: animation of expression data
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Demo of Cellular Overview
 E.
coli at BioCyc.org
Tools -> Cellular Overview
 Zooming and panning
 Searching and highlighting
Based on genes, compounds, proteins, reactions, pathways
Can use names, substrings, biocyc unique identifiers (frame
ids)
 Omics Viewer: animation of expression data
 The permanent link mechanism
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Web Services for Cellular Overview
 The
Cellular Overview can be started with GET
and POST HTTP requests doing highlighting or
lay expression data over a specific diagram
 For
example, the Cellular Overview can be sent a
GET request to show a cellular diagram of E. coli
and highlight all the reactions in a specific
pathway
 Expression
data can be sent via a POST request
or refer to a file that resides on a server (URL
specified)
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Implementation
 Entirely
in JavaScript on the client browser
 Uses OpenLayers for graphics and highlighting
 All the base images are generated by the Web
server
 All the base images are tiled
 Use Yahoo User Interface package (YUI) for
dialogs, mouse over popups, some
communications between the client browser and
Web server (Ajax)
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Future Plans
 Tooltips
with histogram of time-series data
 Integration
of the Regulatory and Cellular
Overview Omics Viewers
 Allow
comparative analysis between organisms
based on the Cellular Overview
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Questions?
Questions?
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