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Presentation transcript:

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 latendre@ai.sri.com

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)

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

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

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)

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)

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

Questions? Questions?