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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...

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

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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...

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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...

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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 ...

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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...

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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...

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

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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...

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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...

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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...

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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...

presque 15 ans il y a | 0

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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)"...

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

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