Ingrid Tigges
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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...
etwa 10 Jahre vor | 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...
etwa 10 Jahre vor | 0
| akzeptiert
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...
etwa 10 Jahre vor | 1
| akzeptiert
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...
mehr als 10 Jahre vor | 0
| akzeptiert
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...
mehr als 10 Jahre vor | 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...
mehr als 10 Jahre vor | 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...
mehr als 10 Jahre vor | 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...
mehr als 10 Jahre vor | 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...
fast 11 Jahre vor | 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...
etwa 11 Jahre vor | 1
| akzeptiert
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...
mehr als 11 Jahre vor | 1
| akzeptiert
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 ...
mehr als 11 Jahre vor | 0
| akzeptiert
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...
mehr als 11 Jahre vor | 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...
mehr als 11 Jahre vor | 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...
fast 12 Jahre vor | 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...
fast 12 Jahre vor | 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...
fast 12 Jahre vor | 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...
etwa 12 Jahre vor | 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...
etwa 12 Jahre vor | 1
| akzeptiert
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 ...
etwa 12 Jahre vor | 0
| akzeptiert
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 ...
etwa 12 Jahre vor | 2
| akzeptiert
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...
etwa 12 Jahre vor | 1
| akzeptiert
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...
etwa 12 Jahre vor | 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...
mehr als 12 Jahre vor | 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...
mehr als 12 Jahre vor | 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...
mehr als 12 Jahre vor | 1
| akzeptiert
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...
mehr als 12 Jahre vor | 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 ...
mehr als 12 Jahre vor | 0
| akzeptiert
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...
mehr als 12 Jahre vor | 0
| akzeptiert
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...
mehr als 12 Jahre vor | 0
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