simBio

simBio is a simulator for biological systems such as cardiac cells, epithelial cells, and pancreatic beta cells. simBio is written in Java, uses XML and can solve ordinary differential equations.

Changes from previous version are

1. LGPL is applied.
2. GUI has been improved.
3. The volume regulation model of the ventricular myocyte (Terashima et al, 2006, in press) is included.
4. Comments in xml files will be kept after calculation.

Available model list: http://www.sim-bio.org/docs/bio/

Download: http://sourceforge.net/projects/simbio/

Users' mailing list: http://sourceforge.net/projects/simbio/

In an attempt to mimic biological functional structures, a cell model is, in simBio, composed of independent functional modules called Reactors, such as ion channels and the sarcoplasmic reticulum, and dynamic variables called Nodes, such as ion concentrations. The interactions between Reactors and Nodes are described by the graph theory and the resulting graph represents a blueprint of an intricate cellular system. Reactors are prepared in a hierarchical order, in analogy to the biological classification. Each Reactor can be composed or improved independently, and can easily be reused for different models.

For more information, see
Nobuaki Sarai, Satoshi Matsuoka and Akinori Noma
simBio: a Java package for the development of detailed cell models
Progress in Biophysics and Molecular Biology, 2005, in press