1. Bioinformatics Research Group SRI International latendre@ai.sri.com
New Zoomable Web Metabolic Network
And Regulatory Network Diagrams
Mario Latendresse
October 2010
Bioinformatics Research Group
SRI International

2. Web Zoomable Overviews
Regulatory Overview
Currently available only for E. coli K12
Cellular Overview
Available for over 1000 databases at BioCyc.org
Both overviews have an Omics Viewer mode to lay over expression data (e.g., experimental data)

3. A Demo of Regulatory Overview
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

4. 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

5. 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)

6. 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)

7. 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

8. Questions?
Questions?