E-CELL2 User's Manual
Chapter 6 Modeling Launcher
[Chapter 1:Chapter 2:Chapter 3:Chapter 4:Chapter 5][Top]

INDEX

1 Initial Settings
1.1 Options Tab
1.2 Directory Settings
2 Model Wizard
3 Rule File Wizard
3.1 Required Input
3.2 Process Scheme
4 Reactor Wizard
4.1 Required Input
4.2 Process Scheme
5 Import Wizard
5.1 Required Input
5.2 Process Scheme
6 Export Wizard
6.1 Required Input
6.2 Process Scheme
7 Editor/Viewer Window
7.1 Spreadsheet Editor
7.2 Text Editor
7.3 Message Viewer
8 Other Settings
8.1 Version Information

1 Initial Settings (Preference)

1.1 Options Tab (Options)

1.1.1 Behavior settings

./image/launcher/Preference1.jpg
Figure 1: Preference Options

While *.er files are the RULE files of E-CELL2 written in text format, *.eri files are in E-CELL2 executable format. Details can be found in Chapter 4 of the user's manual (Creating Rules section).
*.rd files are the Reactor files of E-CELL2. Details can be found in Chapter 5 of the user's manual (Creating Reactors section).

1.1.2 Other settings

1.2 Directory Settings (Directories)

Sets the paths to the programs and scripts, and the directories for saving the files. A warning message will be displayed if the target directory do not exist. If left blank, the directory of this launcher program will be used.

./image/launcher/Preference2.jpg
Figure 2: Preference Directories

1.2.1 Path settings (Programs)

1.2.2 Path settings for the Model and Script files (E-CELL2)

2 Model wizard(New Model) tab

Creates a new model directory.

./image/launcher/NewModel.jpg
Figure 3: New Model Wizard

Input the name of the model to create in the input field and press Execute to copy the temporally stored data (under Template directory) to that directory. The Model directory set at the Preference window will be changed with the execution of this process.

3 Rule file wizard (Rule file) tab

Creates an ERI file from a spreadsheet or an ER file.

./image/launcher/Rule.jpg
Figure 4: Rule File Wizard

3.1 Required Input

3.1.1 Spreadsheet file

Select the spreadsheet file via its path by directly typing its location or by browsing for the target by the "File..." button on the right. If the path is omitted, the Model directory set at the Preference window will be used. The process will terminate with a warning message if the target file do not exist.

  1. Select the target file(Choose...)
    A file selection dialog will open and users are to select the target file to open. The selected file will be displayed in the input field.
  2. Edit existing files (Edit...)
    A file selection dialog will open and users are to select the target file to edit. The selected file will be displayed in the input field.
  3. Create new file (New...)
    This will create new spreadsheet files to be edited. . The selected file will be displayed in the input field.

3.1.2 .er file(ER file)

Select the .er file via its path by directly typing its location or by browsing for the target by the "File..." button on the right. If the path is omitted, the Model directory set at the Preference window will be used.

  1. Select the target file(Choose...)
    A file selection dialog will open and users are to select the target file to open. The selected file will be displayed in the input field.
  2. Edit existing files (Edit...)
    A file selection dialog will open and users are to select the target file to edit. The selected file will be displayed in the input field.
  3. Create new file (New...)
    This will create new spreadsheet files to be edited. The selected file will be displayed in the input field.

3.1.3 .eri file (ERI file)

Select the .eri file or the path itself by directly typing its location or by browsing for the target by the "File..." button on the right. If the path is omitted, the Model directory set at the Preference window will be used. If only the path is designated, files will be created with the input spreadsheet (or the .er) file name with an .ERI extension. Model directory set at the preference window will be used if the field is left blank. A warning message will be displayed on overwriting existing files. The process will terminate with a warning message if the set directory do not exist.

  1. Select the target file(Choose...)
    A file selection dialog will open and users are to select the target file to open. The selected file will be displayed in the input field.

3.2 Process Scheme

3.2.1 Select the spreadsheet or .er file for input

Choose the input file under the following rules:

  1. If the Spreadsheet is selected
    Spreadsheet -> .er file -> .eri file conversion will be executed. A warning message will be displayed if the selected spreadsheet do not exist.
  2. If the Spreadsheet is not selected
    .er file selection is required for it will become the input for the scheme.
  3. Selecting .er files or their paths
    • If the Spreadsheet is selected
      Spreadsheet -> .er file -> .eri file conversion will be executed according to the data inputted. The output will be directory name + spreadsheet name + .ERI extension. A warning message will be displayed if the selected spreadsheet do not exist.
    • If the Spreadsheet is not selected
      .er file is required for it will be the input for the scheme. .er file -> .eri file conversion will be executed. A warning message will be displayed if the selected .er file do not exist.
  4. If neither .er files nor the directory are selected
    Spreadsheet -> .er file -> .eri file conversion will be executed according to the data inputted. The output will be directory name + spreadsheet name + .ERI extension under the Model directory set at the preference window. If neither the spreadsheet file nor .er files are selected, a warning message will be displayed.

If either "Translate immediately after editing spreadsheet" or "Translate immediately after editing .er file" is checked, the .eri conversion process will start immediately after each editing window is closed.

3.2.2 Set output rule file and directory

Set the filename or the directory name for the output .eri files according to the data inputted. .ERI files with inputted filename and directory (if any) will be created. If left blank, the file will be created under the Model directory set at the preference window. If the selected filename do not exist, a new file will be created with that name. A warning message will be displayed if the selected directory do not exist.

3.2.3 Batch Process

Clicking the Execute button starts the conversion process. The log of the process will be displayed in the message window during the process with errors if any (where the process will be terminated at that point). If the error occurred while script execution, the error details will be in the message window.

4 Reactor wizard tab (Reactors)

Creates the Reactor source files (C/C++ and header files) and DLL from .rd files.

./image/launcher/Reactor.jpg
Figure 5: Reactors Wizard

4.1 Required Input

4.1.1 .rd file (RD file)

Select the .rd file via its path by directly typing its location or by browsing for the target by the "File..." button on the right. If the path is omitted, the RD directory under Model set at the Preference window will be used. The process will terminate with a warning message if the target file do not exist. If the filename is omitted, all .rd files under the target path will be converted.

  1. Select the target file(Choose...)
    A file selection dialog will open and users are to select the target file to open. The selected file will be displayed in the input field.
  2. Edit existing files (Edit...)
    A file selection dialog will open and users are to select the target file to edit. The selected file will be displayed in the input field.
  3. Create new file (New...)
    This will create new spreadsheet files to be edited. The selected file will be displayed in the input field.

4.2 Process Scheme

4.2.1 Designating the .rd files for input

Designate the input .rd file via its path. A warning message will be displayed during the conversion process if non-existing files are selected. The RD directory under the Model directory designated under the Preference window will be chosen if the path information is not included in the input.

If a directory name is selected, all .rd files under that directory will be converted. If no input, the RD directory under the Model directory in the Preference window will be the target.

If "Translate Immediately after editing .rd file" is checked in the Preference window, Reactor file conversion process will start immediately after closing the editor window.

4.2.2 Batch Process

Conversion Process will start when the Execute button is pressed. Log will be displayed in the message window during the conversion process. The process will terminate with a warning message if an error occurs during the process. If the error occurred when loading script, error details will be displayed in the message window.

Note that the Makefile for creating Reactor modules is required for this conversion process to succeed. A warning message will be displayed if this Makefile do not exist under the DLL output directory set at the Preference window. Please also make sure that the permission settings for the Makefile is set in writable mode, for the list of the Reactor modules (DLL) to be created will be appended to the file under the DLLFILESR section.

This process creates the Reactor source files in the format set at "Output source Extension" in the Preference window. The extensions for the header files are always .h.

Reactor Source files and DLL files will be saved under the directories set at the Preference window.

5 Import wizard tab (Import)

Imports models that are created externally to this system.

./image/launcher/Import.jpg
Figure 6: Import Wizard

5.1 Required Input

5.1.1 Model name

Designate the location of the .jar file of the model to import via its path, by directly typing its location or by browsing for it using the "File..." button on the right. The installation directory of E-CELL2 will be chosen if only a file name is designated.

5.2 Process Scheme

5.2.1 Designating the .jar file (Java Archive file) for imput

Designate the input .jar file via its path. If a nonexistent file name is designated, a warning message will be displayed upon execution, and the import process will not be executed.

5.2.2 Batch Process

The import process will start when the Execute button is clicked. A log will be displayed in the message window during the import process. If an error occurs during the import process, a warning message will be displayed and the process will be terminated.

This process creates a new directory with the name of the imported model, under the installation directory of E-CELL2.

6 Export wizard tab (Export)

Exports models that are created by this system so that they can be loaded by other E-CELL2 users.

./image/launcher/Export.jpg
Figure 7: Export Wizard

6.1 Required Input

6.1.1 Model name

Designate the directory of the model to export by directly typing its location or by browsing for it using the "File..." button on the right.

6.2 Process Scheme

6.2.1 Designation of the model to export

Designate the directory of the model to export. If a nonexistent file name is designated, a warning message will be displayed upon execution, and the export process will not be executed.

6.2.2 Batch Process

The export process will start when the Execute button is clicked. A log will be displayed in the message window during the export process. If an error occurs during the export process, a warning message will be displayed and the process will be terminated.

This process creates a model archive file in ".jar" format under the installation directory of E-CELL2.

7 Editor/Viewer Window

Two simple editors and one viewer window is included in this launcher.

Each window has a common command set of the following:

1. Save File

Saves the edited (or displayed) text onto a file. If the file was newly created, a file selection dialog will open during save. The editing file will be the save target elsewise. When in message viewer mode, the displayed text file will be saved. A file selection dialog will always appear in this mode. A warning message will be displayed on overwriting existing files.

2. Refresh

Performs an "undo" and refreshes the data back to its saved or last opened position. When in message viewer mode, any displayed message will be cleared. If any changes were to be made to the saved data, A warning message will be displayed before altering the data.

7.1 Spreadsheet Editor

Simple editor to edit CSV files in tab format.

./image/launcher/SpreadSheetEditor.jpg
Figure 8: Spreadsheet Editor

Right-clicking inside the cell displays the following menu:

7.2 Text Editor

Simple editor for editing files in text format.

./image/launcher/TextEditor.jpg
Figure 9: Text Editor

7.3 Message Viewer

Message window to display errors and process logs. Read only.

./image/launcher/Message.jpg
Figure 10: Message Viewer

8 Other Settings

8.1 Current Version

Displays the version of this launcher.

./image/launcher/Version.jpg
Figure 11: Version Information


E-CELL2 User's Manual
Last Update $Date: 2003/3/25 $.
Copyright: Keio University and Mitsui Knowledge Industry Co., Ltd. 2000-2003
Chapter 6 Modeling Launcher
[Chapter 1:Chapter 2:Chapter 3:Chapter 4:Chapter 5][Top]