SimBiology

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Hi! So I saved a run when I was doing fitting for my data, and put the results in a folder on the Simbiology model analzyer dashboard. I wanted to replicate that saved data but I can't seem to find where the initial parameters for that run are stored? If anyone could help or if there's any way I can further clarify please let me know!

Hi, I am new to using MATLAB and SIMBIOLOGY. I am trying to fit 6 binding curves where the ligand is the same throughout the experiment and only the analyte concentrations are different. I want to globally fit all 6 curves to one model, sharing the rate parameters but not sharing the concentration parameters. Is there a way to do this in simbiology? When I am setting up the Data Map I have my independent variable as Time, since binding is measured over time, and I have 6 responses each corresponding to my binding response generated for each analyte concentration. I get an error of "The same model component appears in the left-hand side of multiple elements of the responseMap input argument. The responseMap cannot contain any duplicates." Any help would be great! Attached is the data I am trying to fit.

Hi, I built a PBPK model and fitted a few parameters to the model by using observed data. Next I created a variant of the fitted parameters and simulated the model with the variant values. Based on my previous experience, I expect to see same predcition profile as then fitted plot when using the same model, but the predcitions from "Simulate Model" program are different. On the other hand when I add sensitivity calculation in the "Simulate model" program, then the predicted curve obtained matches with the fitted curve. I am not sure of this behavior of the model in Simbiology. May I get some help on figuring out this issue? Thank you in advance

Is there a way to set UseParallel to true directly on Simbiology Model Analyzer for performing fitting with global solvers (e.g., particleswarm)? I know it is doable programatically (https://www.mathworks.com/matlabcentral/answers/881998-apply-parallel-computing-to-simbiology), but I couldn't find this option on Simbiology Model Analyzer.

I have a simbiology model and want to fit the model to an expected cmax value. The problem is that I don't know the time of the cmax in the data so I don't know how to set up the fitting problem in simbiology. How could I do this?

I have a dataset that contains one independent variable, time and four dependent concentration variables. These are kinetic traces. Two of these variables are titrated concentrations that change from one trace to the next. I would like to fit the entire dataset to my model however Simbiology does not allow datasets where the independent variable increases non monotonically. How do I fit the entire dataset globally? Attached is a 3D plot of the different traces. I would like to create surface with my model on it. Is this possible in simbiology. I suppose if I get the parameters I can do it manually using meshgrid and surf. However the parameters need to come from a global fit. There are no analytical solutions to the 6 set of coupled ODEs. It has to be done numerically. I have also attached the dataset.

Hello everyone, I'm doing fits in Simbiology in order to estimate parameters (Isqnonlin, constant error). The problem is that I got unusual result once. I checked everything (iniatial values, programm and so on) and tried again. It hasn't changed. So I tried also on my friend's PC. The Matlab version and the project are the same. The results on my friend's PC are different and look better. What is the reason for such outcomes? What should I do to get the same results?

I'm fitting a simbiology model to experimental data. After the fit I can see that the model fits the data pretty well. However, the MSE property in the optimresults object returns Inf even though the residuals are not Inf (as shown from the optimresults Output property).

Hi everyone, I have been using SimBiology to fit my data and have came up with a model. I would like to compare the predicted graph to experimental results. Is there a way to do so in the app itself? Thank you.

Hi all, I am using SimBio to build a signaling model and I am trying to fit the model to my own data. The fitting works well for some of my targets (signaling pathway kinases). However, for 2 of the targets, after I click run botton in the fit data program, the program will just stop and I can see a blue indicator next to the "DATA" box. I didn't see any other error messages. When I simulate the model using the initial conditions of my estimated parameters, the simulated profile is close to my actual data so I am very confused why the fitting cannot proceed. Any suggestion is greatly appreciated!!!

I can fit to individual dose data using pooled fiting or mixed effects no problem. However, for some compounds I have multiple doses and I wish to fit to these simultaneously to obtain a single parameter set. %% PREPARE MODEL gData = groupedData(data); gData.Properties.IndependentVariableName = 'Var1'; gData.Properties.GroupVariableName = 'Var3'; gData.Properties.VariableUnits = {'hour','nanogram/milliliter','',''}; gData.Properties; % One-Compartment Extravascular pkmd = PKModelDesign; pkc1 = addCompartment(pkmd,'Central'); pkc1.DosingType = 'FirstOrder'; pkc1.EliminationType = 'linear-clearance'; pkc1.HasResponseVariable = true; model = construct(pkmd); configset = getconfigset(model); configset.CompileOptions.UnitConversion = true; % Single dose dose = sbiodose('dose'); dose.TargetName = 'Dose_Central'; dose.StartTime = 0; dose.Amount = 75; dose.AmountUnits = 'milligram'; dose.TimeUnits = 'hour'; responseMap = {'Drug_Central = Var2'}; % Use NCA parameter estimates as initial parameter guess NCA.Central = mean(ncaparameters.V_z,'omitnan'); NCA.CL = mean(ncaparameters.CL,'omitnan'); NCA.ka = 1; paramsToEstimate = {'log(Central)','log(Cl_Central)','log(ka_Central)'}; % estimatedParams = estimatedInfo(paramsToEstimate,'InitialValue',[5e-4 1e-6 1],'Bounds',[1 5;0.5 2; 1e-3 10]); estimatedParams = estimatedInfo(paramsToEstimate,'InitialValue',[NCA.Central NCA.CL NCA.ka]); % Fit [Individual, Pooled, Mixed Effects] fitConst = sbiofit(model,gData,responseMap,estimatedParams,dose); pooledFit = sbiofit(model,gData,responseMap,estimatedParams,dose,'Pooled',true); Here is my code for 1 dose. The multiple dose data is in a table similar to the tutorial for phenobarbital, where the next dose and corresponding data follows the previous dose. I wish to do this using PK models and the sbiofit or similar commands that utilise simbiology. Please can someone shed some light on this? Cheers

Hello, I have simbiology 2019a. I am trying to fit ka using a one compartment PK model (I have Vd and Cl fixed). I had previously scanned my model for ka and found that ka should be approximate 0.5. When I compared simulations to observed data, 0.5 allowed for the model to fit the data well. I next tried fitting the data using the same concentrations in the model simulations. The ka's were much larger than expected. Upon further expection, the generated simulated concentration vs time profile doesn't produce a curve. It appears as if the model fittings are not generating a concentration profile. I checked if I was making a mistake in the dosing information or response information, but my fitting screen is similar to the example (https://www.mathworks.com/help/simbio/gs/fit-data.html) Any input or additional references to compare would be greatly appreciated. Thanks

Hi, My current problem is to fit a theoretical model for a chemical reaction (with 2 unknown parameters) to a bench of data. TO do that, I use Simbiology, where I define my reaction. Then I run the simulation with the function sbiosimulate. I have written an handle function @to_fit, wich gives me this theoretical solution. Then, I use the function lsqcurvefit to fit my function to_fit to the data. But my problem is that the vector returned by @to_fit doesn't have the same size than my data vector (it is the same time interval [0 90], but not the same number of points) . How could I choose the vector time in the function sbiosimulate ? I hope my description is clear enough, Thanks