simBio iconsimBio 1.0PR2

simBio is a Java package to create biological models for biologist and others.
simBio is a Java package to create biological models for biologist and others. Cardiac cell models are available.

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

In the field of medical biology, extensive research results regarding molecular and cellular level functions have been accumulated, but the mechanisms of these complex cell functions cannot be explained quantitatively. Due to this fact, a quantitative dynamic model that can integrate experimental data and reproduce biological mechanisms on computers is important. We developed simBio in order to have a tool for an easy creation of cell models employing object-oriented principles. In simBio, mathematical models such as a myocyte model that are described using ordinary differential equations are split into function elements such as ion channels and variables such as ion concentrations. In this new way of developing cell models, function elements are equally independent, and can be grouped according to biological classifications. Moreover, the correlations of variables and function elements can be described as a graph. The aim is a tool with which various cellular functions and mechanisms based on the experimental results can easily be combined to a more complex cellular structure or even a whole cell which is suitable for exploring new hypotheses.

simBio is a tool for making it easier to build cell organism models, and for promoting the sharing/reuse of models. It provides the necessary features to create models which use ordinary differential equations and mathematical models, do integral calculation, display result graphs, extract results to files, change parameters and do calculations.

The structure of simBio is divided into 3 main elements. The first describes calculations of mathematical models with Java. The second describes the initial values of parameters and the structure of mathematical models with XML files. The third solves initial value problems of ordinary differential equations with an integration engine.

last updated on:
March 28th, 2008, 19:10 GMT
developed by:
simBio Team
license type:
GPL (GNU General Public License) 
ROOT \ Science and Engineering \ Bioinformatics


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