How to modify models 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
Requirements
MUST need
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Java2-SDK 1.4.x from http://www.sun.com/
The simBio is developed on 1.4.2_01
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eclipse-SDK 2.1.x from http://eclipse.org/
The simBio is developed on built M20030924.
may need
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xml editor such as net.sf.solareclipse_0.4.0.bin.dist.zip from
http://sourceforge.net/projects/solareclipse/
Make new project "simBio"
- Eclipse menu, [File] -> [new] -> [Project]
- select [Java], [Java project] in the dialog, click [Next]
- input [Project Name] as "simBio", click [Next].
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click [Add Folder]
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click [Create New Folder]
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input [Folder name] as "src", click [OK]
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click [OK]
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the dialog will appear, click [Yes]
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now, source folders on build path is [simBio/src]
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default output folder must be [simBio/bin]
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click [Finish]
Import files
- click project [simBio] at the package explorer.
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right click, select [Import].
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select [Zip file] in the dialog, click [Next].
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click upper [Browse] in the dialog.
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select the attached Zip file "20031115_simBio.zip", click [Open].
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the check at the "/" in the left box of the dialog will appear.
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click [Finish]
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the dialog will appear, click [Yes to All]
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now you have a
simBio/org.simBio.bio/km
simBio/org.simBio.bio/nl
simBio/org.simBio.Run.java
simBio/org.simBio.RunGUI.java
simBio/org.simBio.*.jar
simBio/docs
simBio/xml
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select "simBio/org.simBio.*.jar", right click, select [property], select [javadoc location]
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click [Browse], select "simBio/docs/api", then [OK].
!!!!!!!!!!!!!!! IMPORTAMT NOTICE !!!!!!!!!!!!!!!
I have every rights of the files in this Zip file.
The package "jp.ac.kyotoU.med.biosim.*.jar" is private and closed at this moment.
Please Do NOT open the package.
Everything you need to calculate SA node Cell model is in the "src", and they are open. The lisence of them will be the CPL or something like that. Not yet determined.
Calculate the model
- open the folder "simBio" in the Package Explorer.
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open the folder "simBio/xml"
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click "SAnodeCell.xml", this file contains all parameters.
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click [Run] of the Eclipse menu, select [Run], the dialog will apear.
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Select [Java Application], click [New].
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input Name box as you like, for example "SAnodeCell.xml"
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Project box should be "simBio".
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input Main class box as "RunGUI"
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check the box "Include external jars when searching for a main class".
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click [Search]
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select "RunGUI" of the "jp.ac.kyotoU.med.biosim".
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click [OK].
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click [Arguments] tab.
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input [Program arguments] box as "xml/km/0006.xml".
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click [Run] at the bottom.
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congratulations, you will see like this
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click [start], the calculation will be done.
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you can change the every value in the table.
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If you need to change more, you need to modify the Java source in the "simBio/src/bio".
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After "exit" the program, select "simBio/xml" on the Eclipse and right click.
select [Reflesh], then the xml file named "xml/km/0006.bak?.xml" will be appeared.
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If you prefer the parameter set before calculation,
Delete "xml/km/0006.xml" which is the parameter set after calculation,
and Rename "xml/km/0006.bak?.xml" into "xml/km/0006.xml".
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If you don't need the parameter set before the calculation,
The file "xml/km/0006.bak?.xml" can be deleted or renamed.
If you want to calculate ventricular cell, please input [Program arguments] box as "xml/*.xml".
Let's try.
All rights are reserved by Nobuaki Sarai, Nov/15/2003.
If there are any trouble, mail me at sarai@card.med.kyoto-u.ac.jp