model-builder(1)					      General Commands Manual						  model-builder(1)

NAME

       model-builder - graphical ODE simulator

DESCRIPTION

	Model Builder is a graphical ODE simulator.  It allows the user to
	define, simulate and analyze arbitrary systems of Ordinary Diferential
	Equations.

Features
       * Equation-based model definition. No need to learn to program to
	 define and run your models. Just type-in you differential equations

       * Graphic output of simulation. You can save the graphics in the most
	 common formats: png, svg, pdf, etc.

       * Spreadsheet view of the results. From the spreadsheet you can make
	 customized plots from your variables. You can also export your data
	 to a .csv text file

       * Latex rendering of your system of equations. Check you equation in
	 clear mathematical notation.

       * Intuitive graphical interface.

       * Uncertainty analysis module. Implements a straightforward interface
	 for the Bayesian Melding method.

       * Sensitivity analysis. Find out how sensitive your model is to
	 variations in parameter values.

GETTING STARTED

	The best way to get started with ModelBuilder is open one of the
	models included with the distribution and look at it . Yes, it's that
	simple.

	So, if you have already intalled it, start Model-Builder by typing in
	the console:

	$ PyMB followed by <enter>.

	This will start Model-Buider . From now on I will assume that you
	know what a system of differential equations is, otherwise you
	probably should not be using Model-Builder.

	The larger box on the main frame, labeled "Differential Equations" is
	where we are going to start. On this text box you will write your
	system of equations (or a single equation) The syntax is that of
	python for mathematical expressions and functions and there are some
	conventions also, which I will explain below:

       * First of all, Model-Builder expects only the right-hand-side (RHS)
	 of you equations to be present one per line in the equations
	 box. The LHS is assumed to be of the form dy(t)/dt, dy_i/dt where i
	 is an index to the the number of equations in your model. This
	 number i will be used to refer to the state variables of the model (
	 y[i] ). This index, i, MUST start at 0, so if your model has 3
	 equations, their state variables will be y[0], y[1], and y[2] .

       * Another convention is the reference to model parameters. Any number
	 of parameters may be included in the equations by the using this
	 nomeclature: p[0], p[1], and so on. These parameter must the be
	 specified one per line and in ascending order in the "Parameters"
	 box. So the first line would be the definition of p[0], the second
	 of p[1] and so forth.

       * The mathematical expressions that make up the equations and the
	 parameters may include any function of the numpy python module. This
	 allows for the easy contruction of models with a level of
	 sophistication higher than that of a simple algebraic
	 expression. Time may be referenced in the equations or parameter
	 expressions by the variable "t". So if you want a parameter that is
	 a function of time, you can simply write in the parameter box.

       * The user familiar with python will also be able to include more
	 advanced structures in the model specification, such as Lambda
	 functions for instance.

	 Well, with that out of the way, it remains to explain the rest of
	 the interface which is pretty much self-explanatory:

       * The initial values box should include one number for each equation
	 (line) in the equations box. The numbers should be separated by
	 spaces.

       * The start time is the time value at which the equations begin to be
	 evaluated. The values of the state variables at this point in time
	 are those specified in the initial conditions.

       * End time: You can figure this one out...

       * Time step: this is the time-step used in reporting the output of the
	 simulation. The actual time step used by the numeric integrator is
	 variable and chosen on the fly. Its normally much finer that what
	 you specify here.

       * Critical time steps. Most user wil leave this box empty.

       * First Step: The size of the first step. Leave at 0 for automatic
	 determination.

       * Min Step Size and Max Step Size: Respectively the minimum and
	 maximum value for step sizes as chosen by variable step size
	 algorithm. Leave at zero for automatic determination.

       * Full Output check box: If this box is checked a lot of useful
	 information about the integration is included in the output. Check
	 out the output spreadsheet to see what they are.

       * Show convergence message: if this box is checked, ModelBuilder will
	 print "Integration successful" to the console after the integration
	 is completed. Useful for debugging purposes only. Uncheck if you are
	 doing uncertainty analyses. as it will slow things down.

       * Once you are done entering the necessary information for you model,
	 Just press the start button to calculate your model. Enjoy!

HOMEPAGE

       http://model-builder.sourceforge.net/

AUTHOR

	This manual page was written by Varun Hiremath
	<varunhiremath@gmail.com>, for the Debian project (but may be used by
	others).

								 December 4, 2006						  model-builder(1)