Ken Webb 2010-03-28T16:25:33Z
In 2006-2007 I developed a model of the cell mitochondrion using MagicDraw UML and Xholon. It was based on a paper by Daniel Beard. <pre>Beard DA (2005) A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation . PLoS Comput Biol 1(4)</pre>
The UML and Xholon model also benefited from a brief correspondence with Patrick Hannaert and Francois Guillaud, the authors of another model based on the Beard paper. They kindly provided an early copy of their Simulink model. Their work has subsequently been published as a paper.
The MagicDraw and Xholon model is described in a set of PDF files, in which I detail the steps that can be followed to produce the Xholon version. The steps are based on the steps in my published paper UML as a cell and biochemistry modeling language which appeared in BioSystems in 2005. The software system described in the BioSystems paper was called CellAK, and was based on Rational Rose RealTime.
The following links go to pages in a version control system. Select download.
Steps 3 and 4
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