Signal Transduction
Author:
Catherine Lloyd (Bioengineering Institute, University of Auckland)
This part of the CellML website contains some examples that demonstrate how CellML can be used to mark up biochemical pathway models. The basic theoretical examples we have used are designed to help clarify the specification contained in the main part of the site and demonstrate what the CellML developers regard as “best practice” for model design. The metadata associated with the models provide structured contextual information and facilitate searches of collections of models and model components. Currently all metadata are optional, however the CellML team strongly recommends that the modeller provides as much metadata as possible. All models have the same basic constituents and structure. This facilitates the creation of complex models from simpler ones by combining models and/or adding detail to existing models.
Each example includes a description explaining the CellML, several versions of the CellML description of the model available for download, and a PDF of the equations used in the CellML description. The PDF of each model's equations was generated using the MathML Renderer, a tool which extracts the MathML from the CellML and transforms it to LaTeX.
The currently available example biochemical pathway models are:
Demonstration
reaction element examples: gives examples demonstrating the use of the
<reaction>element and its subelements.basic reaction model: introduces the
<reaction>element and its subelements, and the recommended method for dividing a reaction model into components.two reaction example: demonstrates the use of one chemical species in more than one reaction.
two reaction with encapsulation example: demonstrates how a simple reaction can encapsulate a multiple-reaction pathway.
A Full Published Model
