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version (14.4 KB) by Jeremy Huard
Imports ODE models in the BerkeleyMadonna(TM) format into a SimBiology(R) model


Updated 25 Apr 2019

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This function enables you to import systems of ODEs described using BerkeleyMadonna syntax into SimBiology. Just pass in the file name of the BerkeleyMadonna model and get the SimBiology model object as output.
Some elements of BerkeleyMadonna are not supported, however:
(i) difference equations
(ii) higher-order equations
(iii) ODEs in STELLA notation
(iv) if/then constructs and logical operators among others
Please check the code to see a complete listing of unsupported elements.

Step functions in the BerkeleyMadonna model are converted into equivalent SimBiology constructs (doses or events).

Comments and Ratings (3)

Jeremy Huard

Thanks Peter for your positive comment and your feedback.
I have updated this function and the update fixes the two issues you were having.

There are quite a few more changes, including a conversion of the ODEs into a reaction network that is activated by default but can be deactivated. This conversion is quite naive though and won't work for intercompartmental transport.
Please give it a try and let me know if you have issues.

Peter Bloomingdale

This is awesome! Just a few words of advice from my experiences, which may be helpful to some...

(1) There should only be one space between "INIT" and the initial condition for the species you are defining. For example...

INIT Cp=Dose/V

(2) Differential equations should be written in one line. If the differential equation is written in multiple lines, only the first line will be imported.

Peter Bloomingdale

MATLAB Release Compatibility
Created with R2019a
Compatible with any release
Platform Compatibility
Windows macOS Linux
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