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Ingrid Tigges

MathWorks

Attivo dal 2013

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Technical Support
DISCLAIMER: Any advice or opinions posted here are my own, and in no way reflect that of MathWorks.
Professional Interests: SimBiology, Bioinformatics, Graphics, GUIs

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Risposto
How to repeatedly assign the concentration to a species
The following describes how you can do a repeated assignment for a dataset. If you compare this to the link in my comment you wi...

circa 9 anni fa | 0

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Risposto
How can I use Matlab Compiler to make a stand alone script including simFunction Objects
Steven is right with respect to the link he is refering to. After the loading of your simfunction in your file TEST, you need th...

circa 9 anni fa | 0

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Risposto
Simbiology general stability and speed
I have simulated models with more than 150 reactions myself in SimBiology and this works without problem. Have you seen the "ac...

circa 9 anni fa | 1

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Risposto
How to drive model in simbiology from values on data file?
Do you want a kind of lookup table for your data? If yes you can do it as follows: 1) Create a repeated rule that calls an ex...

oltre 9 anni fa | 0

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Risposto
Error in sbmlimport - Conversion from SBML/XML to stochiometric matrix
Hi Namrata, The files from KEGG are not in the SBML format but in the KGML format (see <http://www.genome.jp/kegg/xml/ KGML s...

oltre 9 anni fa | 1

Risposto
SimBiology and the parallel toolbox
Have a look at this link <http://www.mathworks.com/matlabcentral/answers/93471-is-it-possible-to-use-simbiology-model-objects-wi...

oltre 9 anni fa | 1

Risposto
bug: extra space before greek letter if rendered with painters
There is a workaround for this issue. Due to the disadvantages of the workaround, please contact technical support in order to g...

oltre 9 anni fa | 0

Risposto
How can I define a time-dependent reaction rate for an SIR model in Simbiology
Hello Nicolas, You can use rate rules to define parameters that are dependent on time. This link of the documentation explain...

oltre 9 anni fa | 1

Risposto
Find the steady states of a system.
Given that the steady state is defined as dx/dt=0 which is approximately delta x/delta t you can check whether the difference in...

quasi 10 anni fa | 0

Risposto
Triggering Events In SimBiology toolbox
I have attached a .zip file which contains a .sbproj file with a small example. In this example species_1 is created with consta...

circa 10 anni fa | 1

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Risposto
How to load simbiology project object and children from m file?
Hello Zetty, in your code you are using the line simData = sbiosimulate(m1, cs, Dose) ; This way you create a S...

oltre 10 anni fa | 1

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Risposto
crash at pcolor, surf, etc..
Don't be afraid to ask technical support in those cases. In worst case the answer will be sorry, you do not have a license with ...

oltre 10 anni fa | 0

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Risposto
Concentration in each compartment at a fixed time
Hi Rakesh, Since I do not know whether you are using the SimBiology Desktop, let me explain the Desktop and Command Line appr...

oltre 10 anni fa | 0

Risposto
SimBiology calling a function
Have a look at the attached code. simbiology_ml_answers is the main script. The steps are as follows: * Get species names w...

oltre 10 anni fa | 0

Risposto
simbiology competition and inhibition
You can find an explanation on how to fit parameters that should be within certain limits here: <http://www.mathworks.com/matlab...

circa 11 anni fa | 0

Risposto
simbiology competition and inhibition
Hi, here are my quick replies to your questions: 1) Create the reaction as you normally do in the SimBiology desktop and then...

circa 11 anni fa | 0

Risposto
Estimate global and local parameters
You can find an example explaining the combination of pooled (global) and unpooled (local) parameters here <http://www.mathworks...

circa 11 anni fa | 0

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Risposto
Newbie questions in Simbiology
I am not sure how much I can help you with your first two questions, but let me help you with the other three. There is no need...

circa 11 anni fa | 1

Risposto
Simbiology simulation and fit tasks give different outputs
Are you sure that you are using the same simulation settings, initial values etc. in both situations? It might be worth contacti...

circa 11 anni fa | 1

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Risposto
Regarding PK modelling in Simbiology!
Hi, I do not know your model so keep this in mind when reading my answers. 1) In a typical PK model, the input is likely to ...

circa 11 anni fa | 0

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Risposto
Diagram layout in Simbiology
The issue you describe is an issue of "forward compatibility". To my best knowledge MathWorks trys to ensure that projects from ...

circa 11 anni fa | 2

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Risposto
Upper limit or saturation
Should the upper limit come into play when running a simulation? In this case, you could set the upper limit using an event. Ha...

circa 11 anni fa | 1

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Risposto
for and if loops question
Is there a reason you are supposed to use 3 for loops? A hint: Have a look at the function INTERSECT. Using this function the ta...

circa 11 anni fa | 0

Risposto
How does oligoprop calculate melting temperature? I can't get it to match.
The oligoprop function uses the calculation from this site: < http://www.basic.northwestern.edu/biotools/oligocalc.html> (scro...

oltre 11 anni fa | 0

Risposto
sbionlinfit Grouping Experimental Data Replicates For Parameter Fitting
Are you using the SimBiology Desktop? Do you want to get one set of parameters for all replicates? For each replicate set th...

oltre 11 anni fa | 1

Risposto
Simbiology how to simulate multiple doses in different groups
I have two questions: 1) Are you using the SimBiology Desktop? 2) Is the only difference between the two groups the dosing...

oltre 11 anni fa | 1

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Risposto
Generate dose response curve with Simbiology
Yes, it is possible. Have a look at this entry from the file exchange: <http://www.mathworks.com/matlabcentral/fileexchange/359...

oltre 11 anni fa | 1

Risposto
i am using minspantree function of matlab.i need to convert tree output of this function to an array.output tree looks like as (1.2) 1....(3,4) 1....(5,8) 1...first digit in parentheis indicates destination node and second digit is source
Did I understand you correctly that you want to have a "normal" matrix rather than a sparse matrix? If this is the case you ...

oltre 11 anni fa | 0

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Risposto
Calculating Senstivities with SimBiology GUI and from 'sbiosimuate' - How do I deal with NaNs and Infs
The results between the GUI based calculation and your calculation in the command line differ because of a difference in the cal...

oltre 11 anni fa | 0

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Risposto
Out of memory at the end of simulation
Out of memory issues can have many different root causes. Bart has valid points with the questions he asked. There are some more...

oltre 11 anni fa | 0

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