SimBiology

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I built a simple drug and dose model, I try to use GSA and mpgsa method, but when I finished setting up and pressed run, it says that "unable to plot gsa empty result"

I am trying to run a sensitivity analysis where I vary one parameter for a data set/variants activated by orders of magnitude (say -5 to 5), and obtain the peak value for a species in order to compare the % change from the original (order of magnitude of 0). In principle, it makes sense in my head how to do this, but I don't know how to go about writing a custom code in symbiology.. Any help would strongly be appreciated. I have a program in symbiology for running multiple data set and single data set simulations, but not sure how to define a custom one like this.

Hi All, I need to use IDA solver in MATLAB but I am not able to use it. I have downloaded the installation folder which contains the SUNDIALS package but I do not know the further steps in order to be able to use IDA on MATLAB. Do you know how can I do? PS: I need to run it on my Mac, are there any problems of compatibility? Thank you so much in advance! Gabri

I am encountering a "MATLAB:UndefinedFunction" error with the message, "Undefined function handle" when running a MATLAB script in conjunction with a SimBiology program in MATLAB R2024b. The program performs a set of model fits to experimental data by submitting each model fit to a cluster using "parfeval". The cluster consists of the host computer (running a MATLAB SimBiology Model Analyzer interface and runs the program) and five additional compute nodes. This issue only occurs after the SimBiology program has been run at least once with the parallel pool generated by the cluster. How can I resolve this error? kA0UU0000003wNd0AI 000575480

Dear staff, I'm learning how to implement a TGI model in Simbiology using a scripting approach. For that purpose I started to implement my model (based on the example tumor_growth_fitPKPD_completed.sbproj) just with a modified growth component and I'm trying to fit a dataset. Attached you can find the dataset (synth_data.mat) and the TGI script (test_code.m). As you can see the initial tumor mass of different patients varies quite a lot so I can't use a unique initialization for the variable w0. I would like to understand if (and how) it is possible to pass to the model the initial tumor mass for each ID, in order to avoid to fit this parameter. Thank you very much for your help.

Hello, I have a simbiology PBPK model, to which I successfully fit several organ data (liver, kidneys, spleen, blood, ...) simulatenously using the proportional error model. I would like now to switch to numeric weights (1/SD²) for the error model to account for the experimental variability in the model, as I have concentrations and SDs data for each compartment/organ. My data is now formatted in a "wide" format: time points in rows, organ concentrations as columns. I've done some tests on a two-compartment model (GI + Central), based on the example bioavailabilty.sbproj file to remove complexity and enable quick testing of the approach: I managed to implement the numeric weights when fitting only one compartment, by adding a column SD (and even Weights) to the dataset (see files beginning with "fit1comp_"). However when fitting data of two compartments and keeping the wide format of the data, with then Conc_Central, Conc_GI, SD_Central and SD_GI columns, this approach doesn't seem to work because of the multi-column format of the Weights (see files beginning with "fit2comp_wide_"). I also tried to have data in a "long" format, with Time, Conc, SD and Group as columns, where the groups represent my compartment (central, GI). However when mapping the responses, I didn't manage to assign properly the Blood_Plasma.Drug_Central and GI_Compartment.Drug_Oral to the groups in the model analyzer application. The group-specific properties seem only to be variants and doses and not response. I understood from the documentation this groupping is mostly foreseen to map different individuals for the same type of response, so I am not sure how this can be implemented. Do you have any advice on how to implement the mutli-compartment fit with numeric weights? Thanks in advance! Best regards

Sometimes when I try to create and compile a SimFunction, the following error happens: Unable to create SimFunction: --> Error reported from ODE Compilation: Not enough input arguments. Caused by: Error using SimBiology.internal.compile --> Error reported from ODE Compilation: Not enough input arguments. The code file will run in other versions of MATLAB (e.g. I just got this error in R2023a, but it runs fine on R2022b).

I cannot seem to find ribbon buttons for undo/redo operations in SimBiology. In Matlab I find them in the "Quick Access Toolbar" - in fact I can change the toolbar layout through Matlab preferences. In the SimBiology desktop quick access toolbar there are no undo/redo buttons nor is there any option in the does not show undo/redo buttons nor does the SimBiology preferences allow for the customization of the quick access toolbar.

i doesnt respond to any commands related to simbiology and it gives a massage of missing contents.m file

Dear all, I am trying to build a PBPK model of a radioactive probe, and the proposed drug dose unit is Bq (becquerel), but the becquerel unit in current simbiology is not a drug dose category. The error is as follows：Quantity named Dose_Central references a unit that dose not exist or is not a valid unit. In addition, do you have any experience in building PBPK models of radioactive probes? If so, can you share it? Thanks！ Miya

I tried to open the SimBiology file via SimBiology MATLAB 2024b, which was created on 21 Mar by the version 2024b, but failed to open Model Analyzer while successfully opened Model Builder. Alert was popped up as attached in this inquery. This phenomenon has happened only recently. Also, it is reproduced several times. An old file I saved on 12 Mar can be opened without any issues.

I have some .SBPROJ files I created using MATLAB R2020a SimBiology App. When I attempt to open these saved project files using MATLAB R2019b SimBiology, the GUI freezes, and MATLAB has to be killed manually through Task Manager. How can I open SimBiology SBPROJ files using older releases of MATLAB? kA03q000001HpUZCA0 000150493

I am using the simbiology QSP model from H Wang et al., "Dynamics of tumor-associated macrophages in a quantitative systems pharmacology model of immunotherapy in triple-negative breast cancer", iScience, 2022. The model includes a drug treatment that works fine with both the SUNDIALS and ODE15s solvers when the dose start time is set to day 0. However, when the dose start time is set to a value later than 0, I encounter the 'Integration Tolerance Not Met' error. The error appears earlier with SUNDIALS; for example, it occurs when the dose start time is set to 7 days. In contrast, the simulation runs without issues using ODE15s until the dose start time is set to 15 days. Surprisingly, with ODE15s, when I reduce the dose amount from 100 units to 20 units, the simulation runs fine with the delayed dose start time set to 40 days. However, if I further delay the dose start time to 50 days, the simulation fails again. Any help will be higly appreciated.

When I run the Simbiology debugger, it runs for a bit and then stops. The simulation is not run. I get the following output in the command line. >> startSimBiologyDebugger(model,cs,model_variant,doses_sim) The debugger is currently running. Stop debugging to unblock MATLAB command line. ans = 'Dimensions of arrays being concatenated are not consistent.' ans = struct with fields: file: '[insert my directory here]' name: 'Debugger.simulationCallback' line: 0 The debugger has stopped. MATLAB command line is unblocked.

Hello all, First, I used SimBiology Model Builder to restore the PPK model that had been established in NONMEM. Since SimBiology Model Builder cannot add parameters for inter-individual variation and error models, I added them using code. But I found that the exponential error model has not been added to the model. I would like to ask how to add the exponential error model to the following code and how to optimize the simulation process code? Thank you for your help! opts = spreadsheetImportOptions("NumVariables", 3); opts.Sheet = "Sheet1"; opts.DataRange = "A2:C237"; opts.VariableNames = ["ID", "TIME", "DV"]; opts.VariableTypes = ["double", "double", "double"]; Dose = readtable("Dose.xls", opts, "UseExcel", false) data = groupedData(Dose); sbiotrellis(data,@semilogy,"ID","TIME","DV",Marker="+",LineStyle="--");%%@semilogy % Extract the model overall model file s = sbioloadproject("Version-2-20241218.sbproj"); model = s.m1; covModel = CovariateModel; covModel.Expression = {'V1 = exp(theta1 + eta1)',' V2 = exp(theta2 + eta2)','F1 = exp(theta3 + eta3)','CL = exp(theta4 + eta4)'}; covModel.FixedEffectNames covModel.FixedEffectDescription options.ErrorModel = 'exponential'; options.ErrorModelParameters = struct('sigma', 1.0928) thetas = table(4.0056,-20.3634,-7.9054,7.0873,'VariableNames',["theta1","theta2","theta3","theta4"]) omega = table([2.4432;0;0;0],[0;0.0534;0;0],[0;0;9.4391;0],[0;0;0;0.0729],'VariableNames',["eta1","eta2","eta3","eta4"]) phi = sbiosampleparameters(covModel.Expression,thetas,omega,Dose) f = createSimFunction(model,covModel.ParameterNames,'Drug_Central',[]) simresults = f(phi,24) t = sbiotrellis(simresults,[],'Time',' Drug_Central'); t.hFig.Position(3:4) = [800 500]; set(t.plots,'XGrid','on','YGrid','on'); set(t.plots,'YScale','log'); lh = findobj(t.plots,'Type','line'); set(lh,'LineWidth',2);

Hello, I am having some trouble fitting a model to data using Simbiology. The error message seem to indicate simulation failure when using initial parameter estimates. But when I use exactly the same model, dose, Configset, and set parameters to be idential to the initial parameter estimate for fitting to run "sbiosimulate", the simulation finished without error. Could you please advise how to deal with this error. Thank you very much in advance! The error I got is attached below (there is a dose delay of 2000): Error using SimBiology.fit.internal.validateSimFunctionWithDoseInputs One or more simulations failed when using the initial values of estimated parameters. Check your model for errors or try different initial values for estimated parameters. Error in SimBiology.fit.internal.FitObject/fit (line 216) obj.SimFunctionDoseInputs = SimBiology.fit.internal.validateSimFunctionWithDoseInputs(obj.SimFunction, values, obj.Dosing, obj.OutputTimesCell, tfEmptyDose); Error in sbiofit (line 318) [varargout{1:nargout}] = fitObject.fit(modelObj, data, responseMap, estimInfo, varargin{:}); Error in fitproblem/fit (line 650) [varargout{1:max(1,nargout)}] = feval(argCell{:}); Caused by: Unable to complete simulation for input parameters [0.5 0.1 1e-09] because: CVODES returned -4 from module CVODES function CVode: At t = 2000 and h = 7.28377e-15, the corrector convergence test failed repeatedly or with |h| = hmin. Empty results have been returned for this simulation.

I want to fit a PK model with multiple datasets; every dataset has concentration time courses for different species in the model - how do I do this? The time points in each dataset are not consistent, if that matters. I'm using MATLAB R2024b and the SimBiology Model Analyzer app. My model has multiple compartments, and Compartment1 has two species called "RNA" and "PROTEIN". The datasets look something like this: Dataset1 which corresponds to RNA values in the plasma: Dataset2 which corresponds to protein levels in the plasma: I want to fit the model parameters to both the datasets, where I'm mapping PLASMA_RNA from dataset1 to 'RNA" and SERUM_PROTEIN from dataset2 to "PROTEIN".

In SimBiology, there is a limited set of units one case use. Amount, or concentration. This is often inconvenient, as (for example) I might want to use timers (units of time), or surrogates for concentration (like MFI for nanomoles/milliliter). Too, many sbml models use units that aren't in the set of acceptable ones. One can use user-defined units, but these generally link with defined units and this means that one could have unit conversions that have no bearing on reality. What is the recommended work-around for this? What progress has been made with respect to allowing species units that are neither amounts nor concentrations? Thanks!

Hello I would like to add digestibility to a model I created in SimBiology Model Builder. I know I should add digestibility to Variants, but I don't know how to do that in detail. Please let me know. RW

Hello, I'm looking for alternatives for simplifying some biological network models I have in simbiology (the actual way this simplification will be is still TBD, but the overall goal is to be able to reduce the number of eqs. and parameters to facilitate data fitting, preferably in a supervised automated way), and I was wondering if there's any way of using this Model Order Reduction toolbox for simbiology models. Thank you, Paulo

Hi everyone! I'm plotting data using SimBiology, but I'm having trouble plotting simple data with error bars. I don't have access to the raw data, but I do have the mean and standard deviation for each time point. My table is structured as follows: ID | Time | Conc | SD I want to plot these data on the Percentile plot, displaying the means with error bars based on their standard deviation. However, I haven't been able to achieve this simple task. Even after adding two columns with the maximum and minimum values by calculating [Conc+SD] and [Conc−SD], it seems that SimBiology requires values in the same column. Basically I wish to do on Simbiology what the matlab errorbar function does (https://it.mathworks.com/help/matlab/ref/errorbar.html#d126e478849). Please help!

What is the BEST way to get the simulation data out of simbiology and into excel or some other program? I have found a brief explanation on how to export to Matlab area and then convert to XLS but its not working terrible well

I have three supplements that I would like to compare (bioavailability). For each of the three, we will have whole bood, serum, and urine measurements done at timed intervals in a day. Supplements will be given orally and it will be a single dose (three different days for each). I am exploring the best way to calculate area under the curve using trapezoidal rule, finding tmax, and cmax. I have explored Simbiology and the examples I have seen are far more complex than what I need. I will appreciate any help on getting this done. Thank you.

I've used Matlab extensively to model biochemical networks with systems of ODEs, though I'm new to using SimBiology. I've imported a calcium channel model into SimBiology and can execute it, plot the results, etc. What I'd like to do now is take one of the species, Ca — currently with its InitialAmount set to 0.5 millimole/litre, and its BoundaryCondition and ConstantAmount attributes set to on — and control its concentration as a function of time, treating it as an input function to the rest of the system. (I'm investigating how different ways of pulsing Ca concentration will affect downstream production of autonomous CaMKII.) What is the best way to accomplish building such an input function in SimBiology? I found <https://www.mathworks.com/help/simbio/ug/example--creating-a-model-that-uses-a-user-defined-function-in-an-expression.html this> article, which describes how to create a custom user-defined function and use it in reaction, rule, and event expressions. But I don't think this is what I need to do. I'd appreciate any guidance. Thanks.

Hi, In simbiology design app, is there a way to define a species like a step fucntion so that it increases to a constant after a specific time point? I tried to use 'events' to trigger a species increase after a time piont, but the species is not a constant and changed during reactions. I also tried to 'dose', which behaved same as 'event' triggered species increase. There are examples of codes where a user defined function was used in conjunction with repeated assignments. However, in design app, code can't seem to be edited. Thank you very much! -Ji