Answered
Estimating PKPD model in simbiology
Hi Brandon, There are a number of examples available on the MathWorks site. Here are <http://www.mathworks.com/matlabcentr...

11 years ago | 0

Answered
How does Matlab Simbiology calculate pharmacokinetic (PK) non-compartmental (NCA) area under the curve (AUC)?
Hi, Some of the details of SimBiology's non-compartmental analysis (NCA) depend on the type of data and type of dose. However...

11 years ago | 1

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Answered
Questions in Simbilogy Please help me
(1) I'm not sure what you need to do, but you can save a model to an .sbproj file via the desktop or the command line and then l...

11 years ago | 1

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Answered
Integration tolerance not met in SimBiology?
[Updated on January 22, 2024: The Model Debugger for SimBiology is a great tool for deubgging all sorts of simulation failures. ...

11 years ago | 4

Answered
I looking for to generate the pulses (similar to binary pattern ex.011010)over a certain time interval.
Hi, I see two different ways to interpret your question. I'll try to show you how to implement solutions for both from the MA...

11 years ago | 1

11 years ago | 1

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Answered
How to use the 'exist' function for a SimBiology built-in function?
Hi Ciaran, The list of built-in and user-defined kinetic laws are stored on something called the SimBiology root object. You ...

11 years ago | 0

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Answered
How to use the 'exist' function for a SimBiology built-in function?
Hi Ciaran The MassAction kinetic law is always included in SimBiology, so you can always use it in a SimBiology model. It's a...

11 years ago | 0

Answered
How to view differential equations produced by SimBiology?
Hi Ciaran, In addition to exporting to equations within the desktop, you can get a text version of the equations from the com...

11 years ago | 3

Answered
Synax for species generation in SimBiology.
Hi Ciaran, 'null -> protein' is the syntax used in SimBiology. However, you will also need to specify the reaction rate. W...

11 years ago | 0

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Answered
How can I get species B = cummax(species A) in SimBiology?
Hi Dooyoung, In SimBiology, you cannot create a species or parameter that is a vector. You can however analyze a simulation a...

11 years ago | 1

Answered
Formatdb has been deprecated by BLAST in favor makeblastdb, yet matlab 2014b still tries to use formatdb when using the blastformat.. is there any way around this?
Hi, MATLAB doesn't actually ship with |formatdb|. |blastformat| required you to download |formatdb|, and the MATLAB function ...

11 years ago | 0

Answered
parameter estimation in a model when we have some time courses
Hi Ali, The short answers to your questions are: Yes, Yes, Yes, Yes, and Yes. The long answer is that these are extremely ...

11 years ago | 0

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Answered
chromosomeplot conflict with legend
Can explain in more detail what exactly you're trying to do? It's not clear to me exactly what you are trying to add a legend fo...

11 years ago | 0

Answered
GO = geneont('live', 'false'); stopped working
It looks like this problem was also fixed in the latest update to the Gene Ontology database. It sounds like maybe there was a p...

11 years ago | 0

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Answered
simbiology problem with ode solvers
Hi, This problem occurs when SimBiology cannot find a necessary MATLAB function, coder.extrinsic. See if you have a file name...

11 years ago | 1

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Answered
rankfeatures,algorithm,microarray,gene selection
The |rankfeatures| function help lists the following references: # Theodoridis, S. and Koutroumbas, K. (1999) Pattern Recog...

11 years ago | 1

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Answered
Simbiology: definining multiple parameters from output of single function
Hi, SimBiology doesn't have an easy way to do this. As you guessed, I think the best option is to use get the nth output. The...

11 years ago | 0

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Answered
getnewickstr does not work on the output of getmatrix
<http://www.mathworks.com/help/search.html?qdoc=newick&submitsearch=Search A quick search> of the documentation for the term New...

11 years ago | 0

Solved

Return the Nth Output from an Input Command
*Description* Given _F_, a cell array whose first element is a function handle and subsequent elements are arguments, return ...

11 years ago

Answered
how to use stoichiometry matrix in matlab simbiology to construct model?
SimBiology allows you to *view* the stoichiometric matrix for a model using <http://www.mathworks.com/help/simbio/ref/getstoichm...

11 years ago | 0

Answered
Using sbiofit to estimate/fit a complex model based on multiple measurments
Hi Vincent, You can fit multiple experiments with the same set of parameters using |sbiofit|, but you will need to make sever...

11 years ago | 1

Answered
How to compile and deploy SimBiology file on the web
Hi Zetty, You need to take two additional steps to update this example to work with MATLAB Builder JA. First, you need to ...

11 years ago | 0

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Answered
Using Simbiology to estimate parameters based on several variables/rules
Hi Corey, No, I think you're doing the right thing by using a repeated assignment rule to define the compartment total. What ...

11 years ago | 0

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Answered
Parameter Estimation of Kinetic Model
<http://www.mathworks.com/help/simbio/examples/parameter-scanning-parameter-estimation-and-sensitivity-analysis-in-the-yeast-het...

12 years ago | 0

Answered
Importing SBML with MCR
Hi Paul, With restrictions, SimBiology is supported with the MATLAB Compiler as of R2012b. However, one of those restrictions...

12 years ago | 0

Answered
Fitting kinetic parameters for a chemical reaction model without experimental data
I don't think it's possible for anyone to answer that question without knowing the details of your reaction scheme. It's quite p...

12 years ago | 0

Answered
How to limit the range of a parameter in Simbiology?
Hi Rajith, You're calling normrnd in an initial assignment rule, right? I would be very careful using random numbers in the m...

12 years ago | 0

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Answered
SimBiology or sbmlimport crashing MATLAB
Hi Richard, The problem is that some of the compartments have a size of 0. This is not supported in SimBiology. Even though t...

12 years ago | 0

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Answered
MATLAB (R2012a) with SimBiology installed won't run biograph (Cannot find a license for SR_Bioinformatics_Toolbox.)
Hi Phil, First off, I'm sorry to hear about all the hassles you and your students are having. It sounds to me like you hav...

12 years ago | 0