Cell Electrophysiology Simulation Environment (CESE)

About this document

This document is a brief description of the Cell Electrophysiology Simulation Environment (CESE). Visit official CESE website at cese.sourceforge.net to get most recent version of documentation and release notes.

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Getting help

The online documentation is included in CESE distribution. Press F1 or select Help/Contents in the menu at any time to access information about the current state of a program. Use "What's this" feature to get help on a particular interface element.

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Installing models

All models located in the /bin/models directory of the distribution and in the /cese-1.4/models local installation directory will be installed automatically during CESE startup. To install models from another location, use Model/Install Model command in the main menu.

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Controlling model parameters

After the normal application startup you will see certain data in the table and tree in the right part of the main application window.

You can set model parameters values in the table ("Value" column). Click on the parameter you want to change, enter new value, and press <Enter>. If the new value is valid, it will be updated. You can save current model parameters at any time using File/Save Parameters command. The saved model parameters can be loaded later using File/Open Parameters command. To reset model to its initial state use File/New Parameters.

Below the parameters table is a display tree. Here you can select model parameters that will be displayed as simulation results. You can select more than one variable -- press <Ctrl> or <Shift> while selecting variables.

Above the table you can see a combobox where you can switch between the installed models.

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Performing simulations

After setting models parameters as desired and choosing variables for display you can press Start Simulation (F5) button to begin simulations.

To select where to put the results (into the new or top window) use Select new/top window (rightmost) button on the main tool bar.

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Viewing results

When simulation is finished the data will be displayed in the new/top Results View window.

Each Results View window contains a data area, 2 axis, and corners ("units" and "ms").

To zoom data in the data area press Ctrl and while keep pressing drag with a mouse (pressing left mouse button) -- you will see a rectangle representing zooming area. Release a mouse button (still keeping Ctrl depressed), and changes became effective.

Dragging with a mouse from top left to bottom right will set a Zoom In mode, whereas dragging in the opposite direction will change it to Zoom Out mode.

Return to the full scale is simple -- press Ctrl and double click with a left mouse button. You can also click with a right mouse button and select Full Scale from the context menu.

To zoom data for one axis only, drag with a mouse in the axis area, not in the main data area. You can also use Ctrl-double-click or use context menu to return to the full scale.

On a left side of each Results View window you will find a legend panel (hidden by a split pane). In the Legend Tree you can select a channel and change its color/visibility. You can also specify comment which will be printed with the data.

Press right mouse button to activate context menu for the data area or axis.

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Printing and saving results

To print results select a Results View window and choose File/Print Results command in the main menu. Select File/Print Preview to get a preview dialog where you can change different page setup options.

To save results into the ASCII, ATF (Axon Text File, recognized by Axon's pClampTM software), NetCDF data files, or PNG image files, select a Results View window and choose File/Export Results command in the main menu.

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Clamp mode and clamping signals

You can specify a command that will control certain model parameter during simulation run.

All signals and records are stored as XML documents and can be opened in any text editor. Simple XML editor is built into the environment, select Record/Record Editor to invoke.

To use a clamp command, open a record file (Record/Open Record command in the main menu). The environment will go into the clamp mode, and certain variables will be marked as clamped in the model properties table (based on the information in the record file). Start simulation as usual, using Model/Start Simulation (F5).

After you selected a record file, you can test its content by selecting Record/Test Record command in the main menu.

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Feedback

CESE is hosted at cese.sourceforge.net

Mail support@simulogic.com with feedback and questions. Visit our SourceForge page to obtain access to the bug database, mailing lists, CVS repository, files, and forums.

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Copyright © CESE and Simulogic Inc., 1999 - 2007.
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