About SE





How to import a configuration file for SE ?

&size(18){To analyze a dynamical system, you have to produce programs depending on the problem. In addition, you may need to restart a previous produced project. Then, you can import a file that saves the configuration for SE. The configuration for SE is saved as a XML formatted file*1. The following explanation is an example of the SE configuration file for Hodgkin-Huxley equation.

index.php?plugin=attach&refer=aboutSE&openfile=importSE.png

  1. Starts up SE. The below is a situation of the initial start-up when a new project is generated.

    index.php?plugin=attach&refer=aboutSE&openfile=importSE2.png

  2. Select File -> Import -> SE save file

    index.php?plugin=attach&refer=aboutSE&openfile=importSE3.png

  3. Starts up SE save file select window

    index.php?plugin=attach&refer=aboutSE&openfile=importSE4.png

  4. Select the SE save file that saves previously the configuration for SE

    index.php?plugin=attach&refer=aboutSE&openfile=importSE5.png

  5. If the Import is completed, the several data are reflected to each field.

    index.php?plugin=attach&refer=aboutSE&openfile=importSE6.png



How to save the configured state of SE ?

  1. Select File -> Export -> SE save file

    index.php?plugin=attach&refer=aboutSE&openfile=exportSE.png

  2. Write the save file name. The default extension is .sed. It's also able to change the extension.

    index.php?plugin=attach&refer=aboutSE&openfile=exportSE2.png

  3. The produced file is a XML formatted file as follows:

    index.php?plugin=attach&refer=aboutSE&openfile=exportSE3.png



How to import the system equation edited as a text file ?

SE can import the system equation edited as a text file. You produce a equation file using a suitable editor. For instance, by using MATLAB editor, the equation file is produced as follows:

  1. Starts up MATLAB Editor. The below is a situation when the Hodgkin-Huxley equation is edited as a HH.eq.

    index.php?plugin=attach&refer=aboutSE&openfile=importSE7.png

  2. Equations are input according to the number of state variables. Note these two requirements:
    1. State variables are denoted in the form, x[n] (n = 1,2・・・).
    2. Parameters are inserted between two “$”.
      • The following variables should be used with caution when they are used as parameters.
        epsconstant meaning relative precision of floating point
        iimaginary unit quantity
        Infinfinitely large, ∞
        jimaginary unit quantity
        NaNNot-a-Number
        piRatio of circumference and diameter of a circle
        realmaxMaximum positive floating point value
        realminMinimum positive floating point value
        These are constants or variables prepared by MATLAB with the noted meanings. If these names are to be explicitly used as parameters, they must be used in the form $・・・$ as in $eps$. If not inserted between two $, MATLAB will consider these parameters as constants or variables, and system generation will be successful. However, there is no guarantee that the generated tools will work as intended.
      • When handling non-autonomous system equations, external forces that can be applied are limited to sinusoidal forces with single frequency. In this case, in the equations, the force is described as cos(t) or sin(t)*2.

        index.php?plugin=attach&refer=aboutSE&openfile=importSE8.png

  3. Import the text file from SE, if the edit of the equation file is finished. First, starts up SE. The below is a situation of the initial start-up when a new project is generated.

    index.php?plugin=attach&refer=aboutSE&openfile=importSE2.png

  4. Select File -> Import -> Equation Text

    index.php?plugin=attach&refer=aboutSE&openfile=importSE9.png

  5. Starts up Equation Text file select window

    index.php?plugin=attach&refer=aboutSE&openfile=importSE10.png

  6. Select the saved Text file

    index.php?plugin=attach&refer=aboutSE&openfile=importSE11.png

  7. If the Import is completed, the equation data are inserted to each equation field.

    index.php?plugin=attach&refer=aboutSE&openfile=importSE12.png

    • At default settings, the dimension is 2 and the type of system equation is Non-autonomous. Thus, you have to change the dimension, the type of system equation depending on the system equation.



How to save the data of the system equation as a text file

If you want to save the system equation as a text file, you will able to utilize the following command.

  1. Select File -> Export -> Equation text

    index.php?plugin=attach&refer=aboutSE&openfile=exportSE4.png

  2. Write the save file name. The default extension is .eq. It's also able to change the extension.

    index.php?plugin=attach&refer=aboutSE&openfile=exportSE5.png

  3. The generated file is the following text file.

    index.php?plugin=attach&refer=aboutSE&openfile=exportSE6.png



How to check the generated system ?

When you analyze a dynamical system, it is necessary to check the system equation. A mistake of the description and the difference of the value of the system parameters may produce serious symptoms. Thus, the confirmation of the system equation is absolutely imperative. To easily check the equation, you can utilize various Web browsers.

  1. After the project is produced, a XML Document, which is named Equation, is generated in the project directory.

    index.php?plugin=attach&refer=aboutSE&openfile=checkEq.png

    • In the following, an example of the Equation.xml when an analysis tools for Hodgkin-Huxley equation is produced.

      index.php?plugin=attach&refer=aboutSE&openfile=checkEq2.png

  2. To browes the Equation.xml by using various Web browsers for example IE, firefox, Netscape, etc., you can check the system equation and parameters.

    index.php?plugin=attach&refer=aboutSE&openfile=checkEq3.png




*1 For detailed see How to save the configured state of SE ?
*2 Parameters such as angular frequency or frequency are not written. These parameters are automatically added during tool generation.

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Last-modified: 2009-07-23 (Thu) 20:13:30 (3431d)