Berkeley Madonna is a widely used commercial modeling and simulation tool for the Windows and Mac OS X operating systems. The input to Berkeley Madonna is a file that basically consists of a set of parameters, initial values, function definitions and ordinary differential equations. COPASI can generate these ordinary differential equations from the reactions of the model and export them together with the needed parameters in a format suitable to be read into Berkeley Madonna.
Since the way ordinary differential equations are specified is similar between different programs that take such input, it should be rather easy to adjust the exported file for import in other programs as for example the free
XPPaut program or even
Mathematica.
Warning: Berkeley Madonna does not support all mathematical functions available in COPASI if such a function is used in a model, COPASI will write the string "ILLEGAL FUNCTION" to the exported file instead of the name of the function. Naturally this will lead to an error message when one tries to load the file in Berkeley Madonna. Functions currently not supported by Berkeley Madonna are: sec, csc, cot, sech, csch, coth, arcsec, arccsc, arccot, arcsech, arccsch, arccoth, floor, ceil, factorial, modulus and logical xor.
The Constants for TRUE, FALSE, and Euler's number will be exported as numerical values where FALSE will be exported as 0 and TRUE will be exported as 1. Likewise infinity and "not a number" are exported as the strings "inf" and "nan" respectively.
COPASI adds comments to variables in the ODE by using the semicolon to separate the comment from the actual code. Since this feature has been added to Berkeley Madonna in Version 7.0 the exported code cannot be used with older versions of Berkeley Madonna.
In order to export the set of differential equations to a Berkeley Madonna file, you select the Export ODEs menu entry from COPASI's File menu. In the save dialog that shows up, you select
Berkeley Madonna Files (*.mmd) from the File type drop down and specify the name of the file you want to write the ODEs to. After clicking on the Save the ODEs will be saved to the specified file.
