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Contents 1 CellML 1.1 JSim 1.2 Models developed 1.3 External links

CellML

CellML is a language which stores and exchanges computer-based mathematical models. It is an open standard based on the XML markup language, and is being developed by the Auckland Bioengineering Institute at the University of Auckland. To develop models in CellML we used the COR and OpenCell programs.

The Newcastle team used CellML for their Gold award winning project last year, so we have decided to once again use this technology.

JSim

To bridge the gap between agent based models (Java) and cellular models (CellML), the Newcastle team are using a software product called JSim, developed by the University of Washington.

Models developed

The following are models which we have developed using CellML:

• Sin Operon Model
• Metal Intake Model

In addition to CellML, JSim has been used to access models written in CellML in:

• Population Simulation Model

External links

• [http://www.cellml.org/ CellML.org]
  • [http://www.cellml.org/about/news/newcastle-university-team-wins-gold-in-igem-synthetic-biology-competition-cellml-technology-plays-important-role An article about last year's CellML usage]
• [http://nsr.bioeng.washington.edu/jsim/ JSim]
• [http://cor.physiol.ox.ac.uk/ COR]
• [http://www.cellml.org/tools/opencell/ OpenCell]