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Hi All,
I'm attempting to put a set of simbiology global sensitivity analysis plots into my thesis and I'm running into some issues with the GSA plots. Firstly, the figures are very large, it would be quite beneficial to grab a set of the plots and arrange them myself, is there any documentation on how to mess around with the '1x1 Sobol' produced by sbiosobol? Or just GSA plots in general.
The second problem is that the results appear to be relative to the most sensitive parameter in that run. Is it recommended to have a resonably sensitive 'baseline' parameter in each run? I find it difficult to compare plots when a not so sensitive parameter is being recorded as near '1' for the whole run because it's being stacked against a set of very insensitive parameters. I.e. if i have multiple sets of GSAs due to a large model, how can I easily compare results? If I could do some single run through with every parameter that would be the ideal, I imagine, but then the default plot would be half a mile off the bottom of my screen, haha! Perhaps there is a solution to the first question that might help there?
Thank you for your help,
Dan
Hi all,
I've translated a model from another piece of software (monolix) into simbio programmatically to make use of your very easy global sensitivity analysis system.
It looks a little something like this, for a 'single' line example:
r1 = addreaction(model,'InsI -> InsP');
r1.ReactionRate = 'InsI*kip/vi'; %- is + panc
k1 = addkineticlaw(r1, 'Unknown');
Multiplied about 20 fold, as you can see I have included my volumes within the reaction rates myself (vi). The model functions perfectly and I have corrected the outputs at the end:
[time, x, names] = sbiosimulate(model,csObj,dObj1);
x(:,1) = x(:,1)/vi;
So that they are in concentration, as needed. However, when it comes to sensitivity analysis because I have corrected them post-model it is technically incorrect, it is analysing the absolute quantities. This is quite noticible in the sensitivity to the volumes.
Is there an easy fix to this, I've had to fight dimensionality with units in the past using simbio and I'd be great if there was some way of dividing a compartment output by a volume, for example. It is a functionality that exists in monolix, so I was hopeful it might here!
Thank you for your time.
EDIT:
I think I've worked it out, I had to refactor my model to operate in concentrations, just refitting it now. Now I should just be able to use unitless compartments.
I am trying to simulate model of blood lymphocyte count from a paper using Simbiology. The rate of in or out following circadian rythym is kp(t)=km + kb cos [(t-tpeak)*2pi/24] Where and how do I write the expression ? I dont think I can write in repeated assignment ?
I am currently facing a compatibility issue when attempting to load a SimBiology model created in MATLAB 2021a into MATLAB 2023a. Specifically, the code capture functionality does not seem to be working.
If anyone has encountered a similar situation or has insights on how to capture the code for a SimBiology model created in an older version of MATLAB, I would greatly appreciate your guidance. Are there any alternative methods or specific steps that can be followed to ensure successful code capture?
Thank you in advance for your time and expertise.
I've now seen linear programming questions pop up on Answers recently, with some common failure modes for linprog that people seem not to understand.
One basic failure mode is an infeasible problem. What does this mean, and can it be resolved?
The most common failure mode seems to be a unbounded problem. What does this mean? How can it be avoided/solved/fixed? Is there some direction I can move where the objective obviously grows without bounds towards +/- inf?
Finally, I also see questions where someone wants the tool to produce all possible solutions.
A truly good exposition about linear programming would probably result in a complete course on the subject, and Aswers is limited in how much I can write (plus I'll only have a finite amount of energy to keep writing.) I'll try to answer each sub-question as separate answers, but if someone else would like to offer their own take, feel free to do so as an answer, since it has been many years for me since I learned linear programming.
Dear community,
I would like to develop a fermentation model with 4 ODEs, one of which contains variable y. A "repeated assignment", e. g. y=5x+5, contains variable x that has been measured each second. These data (columns with time and corresponding value x in each row) are recorded in the Excel file.
Does anyone have any suggestion how to implement this in symbiology?
Thank you very much in advance,
Tetiana
Hi,
I want to develop a PK model based on some PK data. The PK data seems to display 2 peaks when one initial dose is given.
I would like to give one dose. A fraction of this dose (fr) is absorbed following the linear relationship - ka*Drug the other fraction (1-fr) is absorbed following a linear absorption (ka1*Drug) with a Tlag (it maybe a zero order). The fraction fr is unknown so it must be estimate.
Does anyone have can provide any suggestion to implement this in symbiology or provide a link where I can look?
Thank you very much in advance,
Ferran
I have a species which is absorbed in a zero-order manner. I want to model the reaction rate as "UptakeRate*ActiveState". So I can give value of 1 or 0 to ActivateState to control the active state of this process. The species itself is under control multiple processes, so I want to use Event to automatically change the active state of absorption.
However, when I use these two events:
Event 1，trigger: species > 0, Function: ActiveState =1; Event 2, trigger: species <=0, Function: ActiveState=0
The simulation seems to be stuck without stop.
Is there any way to solve this ? Thanks
Hi,
Im a new user of simbiology, can any one tell me How to fix a parameters to a known constant when estimating models.
Hello,
In the previous versions, we were able to change the reaction line properties to Reactant, Product, or Reactant and Product. This option is not available in 2021b. How do we change the proerpties if we reaction line is both Reactant and Product?
Thanks
Simulations and model results do not get exported to the MATLAB workspace automatically. 2021b. Under Model Analyzer preferences, I checked "export results when model run is complete", but to no effect. I have to manually expert simulations after each run. Please advise. Thanks RD
Introduction
Comma-separated lists are really very simple. You use them all the time. Here is one:
a,b,c,d
That is a comma-separated list containing four variables, the variables a, b, c, and d. Every time you write a list separated by commas then you are writing a comma-separated list. Most commonly you would write a comma-separated list as inputs when calling a function:
fun(a,b,c,d)
or as arguments to the concatenation operator or cell construction operator:
[a,b,c,d]
{a,b,c,d}
or as function outputs:
[a,b,c,d] = fun();
It is very important to understand that in general a comma-separated list is NOT one variable (but it could be). However, sometimes it is useful to create a comma-separated list from one variable (or define one variable from a comma-separated list), and MATLAB has several ways of doing this from various container array types:
struct_array.field % all elements
struct_array(idx).field % selected elements
cell_array{:} % all elements
cell_array{idx} % selected elements
string_array{:} % all elements
string_array{idx} % selected elements
Note that in all cases, the comma-separated list consists of the content of the container array, not subsets (or "slices") of the container array itself (use parentheses to "slice" any array). In other words, they will be equivalent to writing this comma-separated list of the container array content:
content1, content2, content3, .. , contentN
and will return as many content arrays as the original container array has elements (or that you select using indexing, in the requested order). A comma-separated list of one element is just one array, but in general there can be any number of separate arrays in the comma-separated list (zero, one, two, three, four, or more). Here is an example showing that a comma-separated list generated from the content of a cell array is the same as a comma-separated list written explicitly:
>> C = {1,0,Inf};
>> C{:}
ans =
1
ans =
0
ans =
Inf
>> 1,0,Inf
ans =
1
ans =
0
ans =
Inf
How to Use Comma-Separated Lists
Function Inputs: Remember that every time you call a function with multiple input arguments you are using a comma-separated list:
fun(a,b,c,d)
and this is exactly why they are useful: because you can specify the arguments for a function or operator without knowing anything about the arguments (even how many there are). Using the example cell array from above:
>> vertcat(C{:})
ans =
1
0
Inf
which, as we should know by now, is exactly equivalent to writing the same comma-separated list directly into the function call:
>> vertcat(1,0,Inf)
ans =
1
0
Inf
How can we use this? Commonly these are used to generate vectors of values from a structure or cell array, e.g. to concatenate the filenames which are in the output structure of dir:
S = dir(..);
F = {S.name}
which is simply equivalent to
F = {S(1).name, S(2).name, S(3).name, .. , S(end).name}
Or, consider a function with multiple optional input arguments:
opt = {'HeaderLines',2, 'Delimiter',',', 'CollectOutputs',true);
fid = fopen(..);
C = textscan(fid,'%f%f',opt{:});
fclose(fid);
Note how we can pass the optional arguments as a comma-separated list. Remember how a comma-separated list is equivalent to writing var1,var2,var3,..., then the above example is really just this:
C = textscan(fid,'%f%f', 'HeaderLines',2, 'Delimiter',',', 'CollectOutputs',true)
with the added advantage that we can specify all of the optional arguments elsewhere and handle them as one cell array (e.g. as a function input, or at the top of the file). Or we could select which options we want simply by using indexing on that cell array. Note that varargin and varargout can also be useful here.
Function Outputs: In much the same way that the input arguments can be specified, so can an arbitrary number of output arguments. This is commonly used for functions which return a variable number of output arguments, specifically ind2sub and gradient and ndgrid. For example we can easily get all outputs of ndgrid, for any number of inputs (in this example three inputs and three outputs, determined by the number of elements in the cell array):
C = {1:3,4:7,8:9};
[C{:}] = ndgrid(C{:});
which is thus equivalent to:
[C{1},C{2},C{3}] = ndgrid(C{1},C{2},C{3});
Further Topics:
MATLAB documentation:
Click on these links to jump to relevant comments below:
Dynamic Indexing (indexing into arrays with arbitrary numbers of dimensions)
Summary
Just remember that in general a comma-separated list is not one variable (although they can be), and that they are exactly what they say: a list (of arrays) separated with commas. You use them all the time without even realizing it, every time you write this:
fun(a,b,c,d)
Hello
I would like to pulse an input species. I read in the forums that repeated assignments can be used for this, but I am not exactly sure how to implement this. This is the MATLAB code that resembles what I would like the input pattern to be:
t = 0:1/1e3:60; d = [10:2:30]'; x = @rectpuls; y = pulstran(t,d,x);
plot(t,y)
hold off
xlabel('Time (s)')
ylabel('Waveform')
Thanks for any help! Aaron
Hello, We would like to share one of our QSP models with non-modeler colleagues for them to play with. Is there a simple way to generate a standalone app from a SimBiology model, with sliders allowing the user to change various parameter values?
Thank you,
Abed
Hello, Does the 'sbiofit' function have functionality implemented for likelihood=based handling of BLoQ censored data, similar to functionality in NONMEM and other softwares? If not, are there plans to implement this?
Thanks,
Abed
Hello,
I recently downloaded the GlobalSensitivityAnalysisApp. I am trying to perform a GSA using a simbiology model. I try running the App, but I get the error "No Sobol Indices Available to Plot. Configure the Sobol section and click the Compute button." I'm not sure if there is a step I'm overlooking. I'm following the instructional video for this app on the Matlab website, and I'm not sure what Configure the Sobol section is referring to. Any guidance would be greatly appreciated.
How can I add the value of the error for each estimated parameter?
