SimBiology

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I have a big and complicated model in SimBiology and when am running a simulation, it freezes. I have ran simple examples from the documentation and they run just fine. Why are my SimBiology simulations freezing in bigger and complex models? Can it be a mathematical instability in my model? kA00Z000001Dg8qSAC 000114207

R Andreev on 18 Mai 2021 asked, if it is possible to programmatically export the SimBiology model diagrams. I would like to do this programatically within MATLAB. A staff member replied that this was planned for the 2021 b release. Has this functionality been added yet? I cannot seem to find any documentation about it.

Matlab and modeling novice here. My ModelAnalyzer simulation abruptly stops graphing two species (IL-23 and Occupancy) of interest. I'm not sure what is causing this. Additionally, my RO (receptor occupancy) should never be a negative value since it's a %. How do I constrain this to a value from 0-100? Another question is how do I generate a plot of Free Drug vs. Occupancy values? I have attached my file to this question. Please let me know if I'm making mistakes that are leading to this output.

Hello team and community, I am currently working on a pharmacokinetic project that involves using a transit compartment model (DOI: 10.1007/s10928-007-9066-0) to describe drug absorption. I have constructed the model using the Simbiology app and have written a script for a specific function usede in the model (attached in the files). For the solver type, I have selected Sundials. However, I have encountered some strange results when carrying out simulations using the in-app model simulation functionality. I noticed that when I set the stop time from 1 to 7 hours, the simulation results appear to be fine. However, when I set the stop time to 8 hours or above, the simulation results show some unexpected behavior that I cannot comprehend. [stop time = 7 hour] [stop time = 8 hour] [stop time = 48 hour] I would greatly appreciate it if you could provide me with some insights into this problem. Thank you very much. Jesse

Hello team, I am trying to learn Bayesian parameter estimation in Simbiology from the shared file form the MatLab file exchange. After I ran the driver_PCSK9_script.m script, I would like to commit the best fit to the model and further carry out the best fitted simulation with following code. cs = getconfigset(pcsk9Model); variants_temp = sbiovariant('Variant'); variants_content = cell(1,height(mhSampler.ParameterEstimates)); for i = 1:numel(variants_content) param_name = split(mhSampler.ParameterEstimates.Parameter(i),'.'); param = sbioselect(pcsk9Model,'Where','Name','regexpi',param_name(end)); variants_content{i} = {param.Type,param.Name,'Value',mhSampler.ParameterEstimates{i,2}}; end variants_temp.Content = variants_content; commit(variants_temp,pcsk9Model) However, an error occured on the last line showed: Error using SimBiology.Variant/commit Component 'CholesterolIntakeDiet' does not exist in the model. Error in untitled8 (line 19) commit(variants_temp,pcsk9Model) Then I checked with the pcsk9Model model and I found that when I excuted "pcsk9Model" in the command line, I saw there are 47 parameters including parameter 'CholesterolIntakeDiet'. I also opened the model in the SimBiology Model Builder and was able to find parameter 'CholesterolIntakeDiet'. However, when I clicked into the pcsk9Model in the Workspace, it only showed 29 parameters. (showed in photo below) Do not know why and how this could happen or if have any misunderstanding of the model. Could you please showed me what could cause this problem and how to resolve it? Thank you very mch. Jesse

Hello, I am new to simbiology and would appreciate guidance on this issue! I am modeling several reactions inside a cell, which are affecteed by extracellular ligands & membrane bound receptors. Should the plasma membrane be its own compartment in my model? How should I deal with ligand gated receptors in the plasma membrane (I don't have 'concentrations' of those reeceptors in the PM, but do have intracellular mRNA values). Thanks in advance for everyone's time & help on this.

I'm building a mathematical model for a biological process. I have a set of ODE's ready for analysis, but I can't find a way to give these equations straight to the Simbiology analyser withouth first creating a diagram in the Simbiology model builder and hoping the ODE it spits out is the same as the one I already have. Is there a way to do this?

How do I change the range of the sliders in Simbiology? Used to be easy in prior versions.

I have two models, one made in Simbiology and the other in COMSOL, that I am trying to get to work in conjunction with eachother. I know there are resources like Livelink and Simulink, but what is the best approach to integrate these two models which both are observed in time studies?

Hello! I'm a PhD student from EPFL, I'm currently working with Matlab to try to model a simple double feedback loop in order to observe bistability, for this purpose I've built this set of ODEs: function dy = model_equation(t,y) dy = zeros(4,1); sCDC2i=1.0; dCDC2i=1.0; sWEE1i=1.0; dWEE1i=1.0; a1=1.0; a2=1.0; b1=200.0; b2=10.0; v=1.0; g1=4.0; g2=4.0; k1=30.0; k2=1.0; CDC2a=y(1); CDC2i=y(2); WEE1a=y(3); WEE1i=y(4); dy(1)=a1*CDC2i-b1*CDC2a*(v*WEE1a)^g1/(k1+(v*WEE1a)^g1); dy(2)=sCDC2i-dCDC2i*CDC2i-a1*CDC2i+b1*CDC2a*(v*WEE1a)^g1/(k1+(v*WEE1a)^g1); dy(3)=a2*WEE1i-b2*WEE1a*CDC2a^g2/(k2+CDC2a^g2); dy(4)=sWEE1i-dWEE1i*WEE1i-a2*WEE1i+b2*WEE1a*CDC2a^g2/(k2+CDC2a^g2); this set of ODEs is solved and plotted with the following commands: function A = modelSim(time) [T,Y]=ode15s(@model_equation,[0 time],[0 1.0 0 1.0]); plot(T,Y(:,1),T,Y(:,2),T,Y(:,3),T,Y(:,4));hold on; hleg1=legend('CDC2a','CDC2i','WEE1a','WEE1i'); set(hleg1,'Location','NorthEastOutside'); hold off; A=[T,Y]; Now the problem is that the system is not bistable, but I've a species (CDC2a) that tends to accumulate and never reaches steady state. I was thinking that I had made some mistake while I was writing the model, but after several controls, I found that there aren't mistakes in the model. So I've tried to use simbiology, I copied and pasted the ODEs from the .m file to Simbiology, set all the parameters as in the ODEs file, and the model started to work correctly, I got exactly the results I wanted! So I started to check for difference between the Simbiology model and the .m file, this is what I've found: * ODEs are exactly the same * parameters and costants are exactly the same * ode solver and its options are equal * the ODEs system in the .m file is solved trough "[T,Y]=ode15s(@model_equation,[0 time],[0 1.0 0 1.0],options);" while in simbiology the given command is "data = sbiosimulate(m2, cs, [], []);" (where m2 is the model and cs the options for the solver) Now I can't figure out what is happening, I've tried in many different ways to get those results to be the same but I wasn't able to do it. In order to continue my project I need to know at least why I obtain different results, and which one to trust. Any help will be much appreciated because at this point I'm running out of ideas! thank you very much in advance!

I am trying to transfer a model from COPASI to Matlab Simbiology by exporting it as an SBML (.xml) file. When I try to import this file into Matlab through either the command window or Simbiology Load Model function I get the following 'Invalid Reaction' error (after renaming the species to fit the naming convention): Invalid Reaction value. Spaces are required before and after species names and stoichiometric values, for example, 2 A + B -> 2 C. Stoichiometric values must be greater than zero. Type 'help SimBiology.Model.addreaction' for more information. Error in privatesbmlio How do I resolve this issue and is there a better way to go about this transfer?

I am building a SimBiology Model. I want to simulate from randomly generated initial conditions numerous times and find the steady state of a particular specie (PLS). MY current code does this in a graphical sense but I need the actual numbers in a vector (for example) for subsequent use. Does anybody know how to do this? My current code is: %Random Number Generations and Assignment No_of_simulations = 10; %i.e. points number_of_parameters = 4; %i.e. dimenions lb=[1e-3]; ub=[0.1]; x = lhsdesign(number_of_parameters ,No_of_simulations); D = bsxfun(@plus,lb,bsxfun(@times,x,(ub-lb))); for i=x, n1 = i(1); n2 = i(2); n3 = i(3); n4 = i(4); %Model generation. Mobj = sbiomodel('u-PA_parameter_generation'); comp_obj = addcompartment(Mobj, 'plasma'); %Reaction 1 Robj1 = addreaction(Mobj, 'Pro-u-PA + PLG -> PLS + Pro-u-PA'); Kobj1= addkineticlaw(Robj1, 'MassAction'); Pobj1 = addparameter(Kobj1, 'keff_zymogen',0.035); set(Kobj1, 'ParameterVariableNames','keff_zymogen'); %Reaction 2 Robj2 = addreaction(Mobj, 'PLS + Pro-u-PA -> PLS + u-PA'); Kobj2= addkineticlaw(Robj2, 'MassAction'); Pobj2 = addparameter(Kobj2, 'keff_PLS',40); set(Kobj2, 'ParameterVariableNames','keff_PLS'); %Reaction 3 Robj3 = addreaction(Mobj, 'u-PA + PLG -> u-PA + PLS'); Kobj3= addkineticlaw(Robj3, 'MassAction'); Pobj3 = addparameter(Kobj3, 'keff_pos',0.9); set(Kobj3, 'ParameterVariableNames','keff_pos'); %Reaction 4 Robj4 = addreaction(Mobj, 'Pro-u-PA -> null'); Kobj4= addkineticlaw(Robj4, 'MassAction'); Pobj4 = addparameter(Kobj4, 'u1',0.084); set(Kobj4, 'ParameterVariableNames','u1'); %Reaction 5 Robj5 = addreaction(Mobj, 'PLG -> null'); Kobj5= addkineticlaw(Robj5, 'MassAction'); Pobj5 = addparameter(Kobj5, 'u2',0.032); set(Kobj5, 'ParameterVariableNames','u2'); %Reaction 6 Robj6 = addreaction(Mobj, 'PLS -> null'); Kobj6= addkineticlaw(Robj6, 'MassAction'); Pobj6 = addparameter(Kobj6, 'u1',0.084); %Same as R4 set(Kobj6, 'ParameterVariableNames','u1'); %Reaction 7 Robj7 = addreaction(Mobj, 'u-PA -> null'); Kobj7= addkineticlaw(Robj7, 'MassAction'); Pobj7 = addparameter(Kobj7, 'u1',0.084); %Same as R4 set(Kobj7, 'ParameterVariableNames','u1'); %Reaction 8 Robj8 = addreaction(Mobj, 'null -> Pro-u-PA'); Kobj8= addkineticlaw(Robj8, 'MassAction'); Pobj8 = addparameter(Kobj8, 'a1',0.0032); set(Kobj8, 'ParameterVariableNames','a1'); %Reaction 9 Robj9 = addreaction(Mobj, 'null -> PLG'); Kobj9= addkineticlaw(Robj9, 'MassAction'); Pobj9 = addparameter(Kobj9, 'a2',0.01); set(Kobj9, 'ParameterVariableNames','a2'); %setting species concentrations Sobj1 = sbioselect(Mobj,'Type','species','Name','Pro-u-PA'); set(Sobj1, 'InitialAmount',n1) Sobj2 = sbioselect(Mobj,'Type','species','Name','PLG'); set(Sobj2, 'InitialAmount',n2) Sobj3 = sbioselect(Mobj,'Type','species','Name','PLS'); set(Sobj3, 'InitialAmount',n3) Sobj4 = sbioselect(Mobj,'Type','species','Name','u-PA'); set(Sobj4, 'InitialAmount',n4) %simulate config = getconfigset(Mobj); set(config,'StopTime',1000) [t_ode, x_ode, names] = sbiosimulate(Mobj); hold on figure; set(gcf, 'color','white'); plot(t_ode, x_ode(:,1:end)); legend(names) end Thanks in Advance