FACSIMILE

FACSIMILE Features

Model Templates

The user can store the environment for a given modelling session in a template file. This defines the model file and the results files that the user would like to either view or graph after the run is completed. Using the template the results files will be available in a window after each run.

Batch Instructions

A facility is available to allow the user to set up instructions, either manually or using a custom dialogue, to cause the model to be run repeatedly using a specified set of different input parameters. The combined results from these runs can subsequently be tabulated and graphed using other features of the package.

The Model Wizard

The model wizard allows the user to create a working FACSIMILE kinetic model without writing any FACSIMILE code. The reactions and rate constants are entered via an easy to use dialogue which also requests any other parameters (such as temperature, pressure, pH etc.), the time steps at which output is required, and the termination criteria. The wizard will generate a standard FACSIMILE model file which can then be edited and enhanced as any other model.

Graphics Facilities

This release of FACSIMILE incorporates better graphics facilities than previous versions. The emphasis has moved away from having to define the data you wish to graph before you run your model (i.e. in the FACSIMILE code) towards the interactive graphing of the output data once the simulation is complete. Standard graphs can also be defined in the template file so they are instantly available after each run.

The graph interface allows users to choose any of the variables defined in the model and plot them against time or any other linearly varying value in the output set.

The interface also allows users to take data from any time point in a series of runs of the same model and plot against whatever parameter was varied between each run.

Other Features

Features are available to allow users to:

• specify chemical reactions and initial value problems through an easy-to-use high-level input language
• solve both differential and algebraic equations
• use state-of-the-art numerical methods with automatic time stepping
• fit parameters to experimental data
• perform a sensitivity analysis to identify the most important reactions
• use a simple command language for input and output