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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

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Bioinformatics Research Group SRI International latendre@ai.sri.com

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

  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?

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