Leading Project for Biosimulation > Cell/Biodynamics Simulation > simBio


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 free software. You may redistribute or modify it based on the conditions stipulated below in the GNU Lesser General Public License, which has been issued by the Free Software Foundation.

The simBio is distributed in the hope that it will be useful, but with * absolutely no guarantee *. Absolutely no guarantee, expressed or implied, exists of merchantability or fitness for a particular purpose. For details, please look at the GNU Lesser General Public License.

The LGPL original text is http://www.gnu.org/copyleft/lesser.html.


  1. Nobuaki Sarai, Satoshi Matsuoka and Akinori Noma
    simBio: a Java package for the development of detailed cell models
    Progress in Biophysics and Molecular Biology 90: 360-377,2006


simBio wouldn't be half the library that it is today without the contributions that have been made by the developers listed below:

  • Akinori Noma
  • Akira Amano
  • Ayako Takeuchi
  • Bong Ju Kim
  • Chiaki Oka
  • Hiroyuki Kawano
  • Keisuke Terashima
  • Kenta Hori
  • Mikael Wing
  • Ryuta Saito
  • Satoshi Matsuoka
  • Syohei Hido
  • Takao Shimayoshi
  • Tetsuya Matsuda
  • Toshifumi Nishi
  • Tsukasa Shibayama

It is possible that we have missed someone on this list, if that applies to you, please send an e-mail.

Corresponding Author

Nobuaki Sarai, MD, PhD
e-mail: sarai at card.med.kyoto-u.ac.jp
Department of Physiology and Biophysics,
Kyoto University Graduate School of Medicine
Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
phone: +81-75-753-4357
fax: +81-75-753-9448