Leading Project for Biosimulation > Cell/Biodynamics Simulation > simBio

Frequently Asked Questions


1. Overall

1.1. Letters are malformed.


Please set the character encoding as UTF-8.

In Eclipse select Window -> Preferences... -> General -> Editors, selecting UTF-8 in "text file encoding".

When you use Eclipse 3.0, by right clicking on the project and selecting property, you can set the character code for the project.

The character code can be converted by using Java Cross Converter.

  1. Executing JavaCrossConverter.jar. Selecting the folder of your own project. In "character code before the converting" appropriate cord/code selection or automatic operation selection. In selecting "UTF-8" "the character code after the converting". Checking the "regular expression filter". ".*\.java" with input into the filter, "execution". The extension of the java file is converted to everything UTF-8 with this.
  2. When a Japanese comment has also been entered into xml, ".*\.xml" with input into the filter, "execution".

2. GUI

2.1. The result of continuous calculation is different from those which are obtained by sequential calculation by START commands every time.


It occurs when trying to renew the value, which is defined as public double in the Java class, from other classes while calculating. Define the value as public Node instead of double, and use getValue() for the place where a value is referred to, or setValue() for the place where a value is substituted.

Explanation. SimBio substitutes the value, which is defined as public double in Java class, for the same name parameter in the xml file, when executing START command. The value of this Parameter being modified while calculating, you do not perceive, and calculation advances at the value which is substituted at starting. When re-executing START command, in order to substitute the value which is renewed, the calculation result will differ.

To avoid this, please define variable as public Node in place of public double. When Node.setValue(x) is executed, the value of the Node is renewed by x instantaneously, Node.getValue() will give you the current value. A super class, when it exists, may also need modification. The method which utilizes Node becomes safe, but calculation speed becomes rather slow, there is also a demerit where description becomes troublesome.

2.2. The parameter table of the GUI cannot open on Mac OS X.


Please right click the node and select open or close from the pop-up menu.