Ingrid Tigges
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Feeds
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...
oltre 10 anni fa | 0
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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...
oltre 10 anni fa | 0
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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...
oltre 10 anni fa | 1
| accettato
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...
quasi 11 anni fa | 0
| accettato
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...
quasi 11 anni fa | 1
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...
quasi 11 anni fa | 1
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...
quasi 11 anni fa | 0
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...
circa 11 anni fa | 1
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...
oltre 11 anni fa | 0
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...
oltre 11 anni fa | 1
| accettato
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...
quasi 12 anni fa | 1
| accettato
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 ...
quasi 12 anni fa | 0
| accettato
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...
quasi 12 anni fa | 0
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...
circa 12 anni fa | 0
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...
oltre 12 anni fa | 0
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...
oltre 12 anni fa | 0
Estimate global and local parameters
You can find an example explaining the combination of pooled (global) and unpooled (local) parameters here <http://www.mathworks...
oltre 12 anni fa | 0
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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...
oltre 12 anni fa | 1
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...
oltre 12 anni fa | 1
| accettato
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 ...
oltre 12 anni fa | 0
| accettato
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 ...
oltre 12 anni fa | 2
| accettato
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...
oltre 12 anni fa | 1
| accettato
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...
oltre 12 anni fa | 0
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...
quasi 13 anni fa | 0
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...
quasi 13 anni fa | 1
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...
quasi 13 anni fa | 1
| accettato
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...
quasi 13 anni fa | 1
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 ...
quasi 13 anni fa | 0
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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...
circa 13 anni fa | 0
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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...
circa 13 anni fa | 0
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