simBio

simBio is a Java package designed to help biologists and other researchers create biological models with ease. The software includes pre-built models for cardiac cells, epithelial cells, and pancreatic β cells, making it a versatile tool for those working in medical biology.

Since much of the research in medical biology pertains to molecular and cellular level functions, simBio helps integrate experimental data into dynamic models that accurately replicate these functions on a computer. The software achieves this by using object-oriented principles that split mathematical models into discrete function elements and variables, which can be classified according to biological relationships. These relationships can also be visualized through a graph.

With simBio, it is easy to combine various cellular functions and mechanisms based on experimental results to create complex models with ease. Additionally, simBio supports the creation of models with ordinary differential equations, integral calculation, result graph display, and file data extraction.

The software's structure is composed of three main elements: mathematical model calculation using Java, the initialization of model parameter values and their structure with XML files, and the solving of initial value problems with an integration engine. This comprehensive structure allows researchers to build and adjust models quickly and easily.

Overall, simBio is a valuable tool for biologists and other medical researchers looking to create complex, dynamic biological models with ease.