Fabien Campagne^4,*, 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