Answered
strange error in Simbiology
From looking at the Java error log, I suspect it's a bug and/or memory leak in Java's handling of zip files. I'm still trying to...

14 years ago | 0

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Answered
SimBiology parameter fit
sbionlinfit uses a local optimization routine that does not support parameter bounds. Even fmincon, which does support parameter...

14 years ago | 0

Answered
How to output reaction rates for each time step in Simbiology?
Hi Frank, Unfortunately, SimBiology does not currently provide direct access to the calculated rates. There are a couple of o...

14 years ago | 1

Answered
sbiosimulate with events
Hi Omar, Are there any other obvious difference in the simulations? If the model appears to be the same in both cases, then p...

14 years ago | 0

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Answered
simbiology: how to combine multiple species when plotting a graph?
Hi Molly, Regarding part 1: Probably the easiest way to do what you want is to add an pseudo-species to represent the sum ...

14 years ago | 0

Answered
get initial amounts of some species
As of R2011a, you can use sbioparamestim to estimate the initial amount of a species. If you can't easily upgrade to R2011a, you...

14 years ago | 0

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Answered
Matlab crash; Java HotSpot(TM) 64-Bit Server VM warning
Per Walter's suggestion, you can try increasing the Java heap via a MATLAB <http://www.mathworks.com/help/techdoc/matlab_env/brj...

14 years ago | 0

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Answered
SBML import in Matlab
Hi Razvan, The problem is that three species in the file (Gpr1Glucout, Gpa2a, and Gpa2aKrh) have a negative concentration, whic...

15 years ago | 0

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Answered
Fluctuations in Simbiology
Hi Razvan, I think the answer will ultimately depend on what you know about the fluctuations and what sort of questions you'r...

15 years ago | 0

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Answered
Events which introduce dicontinuities (Simbiology toolbox)
Hi Razvan, There's a SimBiology demo on this topic. Execute the following from the MATLAB prompt and see if that answers your...

15 years ago | 0

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Answered
Parameter estimation with more data sets
Hi Razvan, Here's additional information on how you can fit simulations to the same data set using lsqnonlin. You can also fi...

15 years ago | 0

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Answered
Parameter estimation with more data sets
Hi Razvan, sbioparamestim only allows you to estimate one set of parameters using one set of data. I think the easiest way to...

15 years ago | 0

Answered
Accessing a simbiology class
Hi Omar, In the code you typed above, "msp" should be a vector of species objects that you can index using "msp(1)", "msp(2)"...

15 years ago | 0

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Answered
Problems with a simbiology model
Question 1: First, a little background. In SimBiology, parameters can be associated either with a model (sometimes called "model...

15 years ago | 0

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