Answered
Is it possible to use an output function with sbiosimulate as with the ODE solver suite?
Hi Kevin, In SimBiology you can set the maximum number of seconds that a simulation should take by setting the configset prop...

9 years ago | 0

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Answered
How to use resolve griddedinterpolant error in the msbackadj in bioinformatics toobox?
Hi, The problem is that your variable |MZ| does not span a large enough range for the default algorithm options of |msbackadj...

10 years ago | 2

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Answered
How do I convert .sbproj files to matlab code?
Hi Kannan, I'm not sure what you mean by "seeing the MATLAB code of the model." Here are some things that might be related to...

10 years ago | 0

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Answered
Error Using mzxml read
Hi, I believe the mzXML file is invalid. |mzxmlread| could give a more helpful error message, but the error occurs when the p...

10 years ago | 0

Answered
How to fix an mzxmlread error?
Hi, I believe the mzXML file is invalid. |mzxmlread| could give a more helpful error message, but the error occurs when the p...

10 years ago | 0

Answered
Does SimBiology support loading SBML with math ci elements referencing a reaction id?
Hi Jason, You are correct that SimBiology does not yet support the ability to reference a reaction rate in mathematical expre...

10 years ago | 0

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Answered
Simbiology Desktop: Why my parameter is not recognized in the EventFcns (I would like to change its value at a precise timepoint) ?
Hi Raphaelle, SimBiology allows you to create 2 kinds of parameters: model-scoped and reaction-scoped. Reaction-scoped parame...

10 years ago | 1

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Answered
Cant run or getequations from simbiology file from publication
You are getting errors because this is basically an incomplete model. The SBML file does not specify rates for any of the reacti...

10 years ago | 0

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Answered
Is there a way of performing a nlinfit with 2 independent variables in SimBiology?
Hi, SimBiology does not support this kind of problem in the desktop GUI or in the command-line functions like sbiofit. Today,...

10 years ago | 2

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Answered
Changing data in a simbiology model
You haven't really given us enough information to provide much help. Based on the limited information you've provided, all I can...

10 years ago | 0

Answered
Where is the undo/redo function in SimBiology
Hi, Unfortunately, you cannot find the buttons because the SimBiology Desktop does not yet support undo or redo. I am one ...

10 years ago | 0

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Answered
Inputting a genetic circuit into SimBiology to get ODEs
Hi, The diagrams in the SimBiology Desktop do not currently support graphical notation for activation and repression. However...

10 years ago | 0

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Answered
Create an arbitrary event function that updates a model variable on every time loop in Simbiology 5.3?
Your question sounds quite similar to another one asked a while back: <http://www.mathworks.com/matlabcentral/answers/7982-fluct...

10 years ago | 0

Answered
Simbiology - Copying "quantities used by this rule"
Unfortunately, SimBiology does not have a publicly documented way to access the quantities used by a rule from a MATLAB function...

10 years ago | 0

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Answered
Error when trying to use Create App feature within SimBiology
Hi Sean, I think this indicates that an unexpected MATLAB error occurred while trying to create the app. However, it's diffic...

10 years ago | 0

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Answered
In SimBiology, can you change the Capacity of a compartment using an Event or Assignment (and still pass dimensional analysis)?
Hi Bernard, Yes, it's possible to change the capacity of a compartment using an event or assignment. To do this, set the corr...

10 years ago | 1

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Answered
"Simulating a group with an initial condition failed" Why am I getting this error when Simbiology Data Fitting?
Hi Justin, I'm one of the SimBiology developers, and I wrote the code that issues this error. This error is reported because ...

10 years ago | 0

Answered
Use the Simbiology diagram feature in a graphical interface
Hi Martin, I'm happy to hear that you find SimBiology useful. (I'm one of the developers on the team.) But to answer your ...

10 years ago | 0

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Answered
Parsing undefined variables in the Simbiology toolbox
Hi Adam, I think you're taking a reasonable enough approach, but there are several additional things you need to consider: ...

10 years ago | 1

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Answered
How do I calculate a derivative of a time-variable parameter in SimBiology ?
Hi Sergey, There is no way to directly access the time derivative or previous value of state in SimBiology. There are differe...

10 years ago | 0

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Answered
symbiology new project (Estimating the Bioavailability of a Drug)
Hi, The files are located under the "examples\simbio" folder of your MATLAB installation. You can open the project in the Sim...

10 years ago | 0

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Answered
Bioinformatics Toolbox - 'blastall' is not recognized as an internal or external command
Have you installed the BLAST+ executables? As stated on the <http://www.mathworks.com/help/bioinfo/ref/blastlocal.html blastloca...

10 years ago | 0

Answered
How can I use Matlab Compiler to make a stand alone script including simFunction Objects
Hi Christoph, I believe you misread the compiler support <http://www.mathworks.com/products/compiler/supported/compiler_suppo...

10 years ago | 0

10 years ago | 0

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Solved

Free passes for everyone!
_Simply return the name of the coolest numerical computation software ever_ *Extra reward* (get a _freepass_): As an addit...

10 years ago

Solved

This is a palindrome and so am I
A palindrome is a sequence of characters which reads the same backward or forward, for instance 'a man a plan a canal panama'...

10 years ago

Answered
Conservation laws in Simbiology
Hi Debora, I can (and will) tell you a way you can explicitly enforce conservation laws, but I think it's first worth asking ...

10 years ago | 0

Answered
How to add a partial differential equation to lotka volterra equation
Hi, SimBiology does not currently support PDEs. If you want to model this system in SimBiology, you would need to discretize the...

10 years ago | 0

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Answered
Simbiology "Fatal Error" while trying to import xml sbml model
I believe you are referring to <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260002/ this paper> . The ZIP file that you attache...

10 years ago | 0

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Answered
Estimating PKPD model in simbiology
I reread your question, and I see that the above answer didn't really address your question about transforming concentrations th...

11 years ago | 1

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