How to run a model

Corresponding Author

Nobuaki Sarai, MD, PhD
e-mail: sarai@card.med.kyoto-u.ac.jp
http://www.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: +81-75-753-4349

  1. install java

    Java2-SDK 1.4.x from http://Sun.com/.
    The simBio is developed using Java2 SDK 1.4.2_01.
    Follow the instructions provided by http://Sun.com/.

  2. extract all

    includes are
    simBio.0.2/org.simBio.2.0.jar
    simBio.0.2/xml

    !!!!!!!!!!!!!!! IMPORTAMT NOTICE !!!!!!!!!!!

    I have every rights of the files in this Zip file. The package "org.simBio.*.jar" is private and closed at this moment. Please Do NOT open the package.


  3. check related files
    Please check that the file is placed as follows.

    simbio.0.2\
      + simbio.0.2.jar
      + lib\
      |   + commons-logging.jar
      |   + jh.jar
      |   + log4j-1.2.8.jar
      |
      + xml\...\
          + 0006.xml  (sample parameter file)
    

  4. open DOS prompt, and input

    > cd "simBio.0.2"
    > java -jar org.simBio.0.2.*.jar xml/km/0006.xml
    

  5. congratulations, you will see like the following picture.

    Start simBio

  6. calculate the model

    click [Model] -> [start], the calculation will be done. you can change the every value in the table. If you want to calculate other model, please apply argments such as "xml/gate/SingleNaChannel.xml". Let's try.