How to create a biological model on simBio

Author

Nobuaki Sarai, M.D., PhD.
Department of Physiology and Biophysics, Kyoto University Graduate School of Medicine, Kyoto, Japan
e-mail: sarai@card.med.kyoto-u.ac.jp
http://www.card.med.kyoto-u.ac.jp

  1. disolove the biological system

    In simBio, the ordinary differential equations are separated into a set of equations and variables according to the biological knowledge. A set of equations are defined as a Reactor, in other words, or functional module. Variables are defined as Nodes. A biological model is represented as a graph composed of Reactors and Nodes.

  2. write ODE in the Method "calculate(double)"

    Create your Reactor which inherits core.Reactor and override Method "protected void calculate(double)". A set of equations are written in this Method. Node.getValue() is used to get current value. Node.setValue(double) is used to set current value. Node.addDyDt(double) is used to calculate ODE.

  3. define class field in Java source code

    Nodes are separated into 2 groups in Java source code. One is "public Node" that is linked or calculated by ODE. Another is "public double" that is NOT linked from anywhere eles, constant during integration. The name of the field must be the same as is in the xml.

  4. write model description file in xml format

    There must be at least 4 tags in the XML file.

    1. yourClass (= Reactor, set of equations)
    2. link (= Node outside of your Class, make complete links in the XML, which is analogs to the file system)
    3. variable (= Node which is calculated by ODE)
    4. parameter (=Node which is NOT calculated by ODE)

    Nodes are separated into 2 groups. One is variable that is calculated by ODE. Another is parameter that is NOT calculated by ODE.

    link everything properly in the xml. The structure is analogus to the file system.

  5. The core create instance tree and graph

    The core package create instance tree and automatically link everything as in the xml.

  6. You may get the results

    Every parameter can be edited and 2D graph is available through GUI.

All rights are reserved by Nobuaki Sarai, Dec/10/2003.
If there are any trouble, mail me at sarai@card.med.kyoto-u.ac.jp