The output produced in this mode will be a text (e.g., ASCII) file. The contents of this file can be pasted into a Berkeley Madonna Equation window and run. It is not a "clickable" Berkeley Madonna file.

Parameters and initial conditions that are not set in the model will default to zero.

Example

SBMLWrite[inputfile -> "rep.xml", 
          format -> "BerkeleyMadonna", 
          outputfile -> "foo.txt"]

This example is illustrated on the sbml file rep.xml, which can be downloaded as zipped XML | HTML Encapsulated XML | Raw XML (Note that most browsers will not display raw xml files correctly). The MathSBML commands that were used to create this XML file are here.

The following output file is generate by this example:

{ Model Name:    Repressilator Model }
{ Creation Time: 27-May-2004 13:56:44.549466 }
{ User:          jamestkirk }
{ Machine:       slartibartifast }
{ System:        PowerPC PowerMac MacOSX    }
{ Generated by MathSBML 2.3.8 (27-May-2004) }
METHOD RK4
STARTTIME = 0
STOPTIME = 10
DT = 0.02
{ Differential Equations }
d/dt (repressilator_px) = 5.*(-repressilator_px+repressilator_x)
d/dt (repressilator_py) = 5.*(-repressilator_py+repressilator_y)
d/dt (repressilator_pz) = 5.*(-repressilator_pz+repressilator_z)
d/dt (repressilator_x) = 250./(1.+repressilator_pz^2.1)-1.*repressilator_x
d/dt (repressilator_y) = 250./(1.+repressilator_px^2.1)-1.*repressilator_y
d/dt (repressilator_z) = 250./(1.+repressilator_py^2.1)-1.*repressilator_z
{ Parameters }
repressilator_alpha = 250.
repressilator_beta = 5.
repressilator_alpha0 = 0
repressilator_alpha1 = 0
repressilator_n = 2.1
repressilator_k1 = 1.
repressilator_K = 1.
{ Initial Conditions }
init repressilator_x = 0
init repressilator_y = 0
init repressilator_z = 0
init repressilator_py = 0
init repressilator_px = 5.
init repressilator_pz = 15.

[05-27-2004]