Leading Project for Biosimulation > Cell/Biodynamics Simulation > simBio

Contents of the simBio package

simBio folders follow the standard folder arrangement of Apache Maven


Java source is put here.

  • In org.simBio, there are starting classes which have a main method.
  • In org.simBio.bio there are classes which calculate biological models.

    Below the org.simBio.bio package, they are generally shown as cited in papers. Except for these, please create suitable packages.

    • org.simBio.bio.hodgkin_huxley_1952
    • org.simBio.bio.matsuoka_et_al_2003
    • org.simBio.bio.matsuoka_et_al_2004
  • The base classes in org.simBio.core use integral calculus.
  • In org.simBio.sim there are GUI and analysis classes.


Documents which are referred to from Javadoc in the doc-files folder of Java source and the same folder go here.


Java source for the test classes are put here.


Resources which are used by the test classes are put here.


Used Java class libraries are put here.


This is where model xml files go.

Model xml files which operate on this go below the xml folder of the same name as the Java source project folder. If there is just one xml file, an xml file of the same name is created.

  • xml/hodgkin_huxley_1952.xml
  • xml/matsuoka_et_al_2003/model.xml
  • xml/matsuoka_et_al_2004/model.xml


Documents go here.