Cell Electrophysiology Simulation Environment is a software tool designed for simulation of electrophysiology in a virtual environment. It provides a platform for the study of cellular systems, allowing researchers to better understand the complexities of electrophysiological processes.
The Cell Electrophysiology Simulation Environment (CESE) is a powerful software package specifically designed for performing computational electrophysiological simulations, such as simulations of cardiac myocyte electrical activity. It is ideal for simulating action potentials, individual ionic currents, and changes in ionic concentrations. The software is cross-platform and runs on any system that has Java runtime environment (JRE) version 1.4 or above, making it accessible to users across a wide range of platforms.
CESE is an integrated environment for performing computational simulations using a variety of electrophysiological models. At this stage, it allows the creation and execution of single-cell models that contain both Hodgkin-Huxley (HH) and Markovian current formulations. Models of the electrical activity of cardiac myocytes with source code are included in the CESE distribution. In the future, the developers plan to extend the number of available models and add certain neuronal models.
The main strength of CESE lies in its uniformity; the program interface remains the same for different types of models. Users can easily switch between models and compare simulation outputs. Model parameters can be modified, selected for output, and/or clamped in the same, standard way. CESE extends the conventional electrophysiological meaning of the "voltage clamp". Users can clamp virtually any model variable, including voltage (membrane potential), total or individual ionic currents, ionic concentrations, temperature, gating variables, etc.
CESE also provides simple but efficient data visualizations. Simulation results can be presented in graphic and tabulated forms, with plots that can be customized and regions of interest zoomed. While CESE was not designed to be a data analysis tool, users can generate current-voltage relationships (I-Vs) and calculate statistical parameters for a given signal within the program. Data can also be exported to ASCII, Axon Text File (ATF), and NetCDF formats for analysis in other packages.
The CESE software was created using the best programming practices available to Java developers, with a focus on user interface consistency and code clarity and reuse. Wherever possible, CESE relies on available Java APIs (such as Java2D, JavaBeans, and JAXP) to simplify the code. Model creation requires a number of house-keeping functions to be coded, such as ODE integrators, routines for handling model parameters, saving/restoring model state, visualizing simulation results, etc. CESE provides implementation for these routines so that users can concentrate on writing concrete ionic current(s), while CESE handles the rest.
Finally, the latest release of CESE includes a GUI for changing plot types, improves performance, and contains several important bugfixes.
CESE is an integrated environment for performing computational simulations using a variety of electrophysiological models. At this stage, it allows the creation and execution of single-cell models that contain both Hodgkin-Huxley (HH) and Markovian current formulations. Models of the electrical activity of cardiac myocytes with source code are included in the CESE distribution. In the future, the developers plan to extend the number of available models and add certain neuronal models.
The main strength of CESE lies in its uniformity; the program interface remains the same for different types of models. Users can easily switch between models and compare simulation outputs. Model parameters can be modified, selected for output, and/or clamped in the same, standard way. CESE extends the conventional electrophysiological meaning of the "voltage clamp". Users can clamp virtually any model variable, including voltage (membrane potential), total or individual ionic currents, ionic concentrations, temperature, gating variables, etc.
CESE also provides simple but efficient data visualizations. Simulation results can be presented in graphic and tabulated forms, with plots that can be customized and regions of interest zoomed. While CESE was not designed to be a data analysis tool, users can generate current-voltage relationships (I-Vs) and calculate statistical parameters for a given signal within the program. Data can also be exported to ASCII, Axon Text File (ATF), and NetCDF formats for analysis in other packages.
The CESE software was created using the best programming practices available to Java developers, with a focus on user interface consistency and code clarity and reuse. Wherever possible, CESE relies on available Java APIs (such as Java2D, JavaBeans, and JAXP) to simplify the code. Model creation requires a number of house-keeping functions to be coded, such as ODE integrators, routines for handling model parameters, saving/restoring model state, visualizing simulation results, etc. CESE provides implementation for these routines so that users can concentrate on writing concrete ionic current(s), while CESE handles the rest.
Finally, the latest release of CESE includes a GUI for changing plot types, improves performance, and contains several important bugfixes.
What's New
Version 1.4.7: N/A