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Sci. STKE, 31 August 2004
[DOI: 10.1126/stke.2482004pl11]

Quantitative Information Management for the Biochemical Computation of Cellular Networks
(Animated Tutorials)

Fabien Campagne4,*, Susana Neves2, Chiung-wen Chang2, Lucy Skrabanek4, Prahlad T. Ram4, Ravi Iyengar4, Harel Weinstein 1,3,4

1Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York NY 10029.
2Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York NY 10029.
3Institute for Computational Biomedicine, Mount Sinai School of Medicine, New York NY 10029.
4Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York NY, 10021

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*Corresponding author. Address Weill Medical College of Cornell University, c/o Rockefeller University, Smith Hall 410, Box 270; 1230 York Avenue, New York, NY 10021; USA; E-mail: fac2003{at}med.cornell.edu

These animated tutorials, or viewlets, demonstrate how to interact with the search, submission, or export options at SigPath. The viewlets require the Macromedia Flash Player browser plug-in, which is available free from Macromedia (http://www.macromedia.com/downloads/).

Background information for searching SigPath and understanding the molecule records. This viewlet demonstrates how to search SigPath, then provides the user an overview of the information that is available for a particular record. [Background information viewlet]

Querying Sigpath. These viewlets demonstrate how to search SigPath for small molecules, proteins, or reactions that are already saved in SigPath. Relevant details about the records are explained. [Search for small molecules viewlet] [Search for proteins viewlet] [Search for reactions viewlet]

Phosphorylation Biowizard. This viewlet demonstrates how to submit the necessary information to create a phosphorylation reaction in SigPath. [Phosphorylation Biowizard viewlet]

Binding Biowizard. This viewlet demonstrates how to submit the necessary information to create a binding reaction in SigPath. [Binding Biowizard viewlet]

XML submission. This viewlet demonstrates how to format reactions based on the SigPath XML schema and how to upload XML-formatted data into SigPath. [XML submission viewlet]

Model assembly. This viewlet demonstrates how to create a model representing a set of reactions by choosing the reactions and setting or choosing the kinetic and biochemical parameters, how to save the model, and how to view it through SigPath. [Model assembly viewlet]

Export models in JSim format. This viewlet demonstrates how to export a model that is already saved in Sigpath in a format acceptable for computational analysis by JSim software. [JSim-formatted model export viewlet]

Export models in Kinetikit format. This viewlet demonstrates how to export a model that is already saved in Sigpath in a format acceptable for computational analysis by Kinetikit software. [Kinetikit-formatted model export viewlet]

Export models in XML format. This viewlet demonstrates how to export a model that is already saved in Sigpath in an XML format. [XML-formatted model export viewlet]

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Citation: F. Campagne, S. Neves, C. Chang, L. Skrabanek, P. T. Ram, R. Iyengar, H. Weinstein, Quantitative information management for the biochemical computation of cellular networks. Sci. STKE 2004 pl11 (2004).

© 2004 American Association for the Advancement of Science


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