SimBiology

Segui

I have a reaction network model built using simbiology. This includes reactions for synthesis and degradation of various species. So, generally I run steadystate and update the model state before running any simulations. Now, I would like to estimate some of the parameters in the model using sbiofit. My questions is whether sbiofit equilibrates model state for each parameter sample during fitting? Thanks and regards.

I'm trying to develop the QSP model for endogenous biomarker dynamics in the body with simbiology app (R2021). This biomarker remains to be 5 mM in the tissue under untreatment condition, whereas the concentration is gradually increased up to 10 mM and deacreased to 5mM by administrating the some precursor molecules. I would like to fit the parameter for the production and metabolism of this biomarker. How can I set the steady state concentation (in this case; 5mM) in simbiology app?

I am trying to use SimBiology to fit a simple model of receptor binding, consisting of a ligand, a receptor, and a complex. The reaction uses reversible mass action kinetics. I can fit this system to time course data, but have not been able to figure out how to use steady state data to find the forward and reverse kinetic rate constants. For example, the data I am trying to fit can be simulated by the following table: Ligand concentration (nM) | Resulting complex concentration (normalized) 0.01 | 0.01 0.03 | 0.05 0.20 | 0.15 1.00 | 0.35 3.00 | 0.70 11.0 | 0.85 110 | 1.00 I have tried to estimate parameters by having a bolus of ligand "injected" and then some (long) time later reporting the normalized complex concentration. However, this results in values which do not return the initial logistic curve. I would prefer to use SimBiology Desktop as I am new to the program, but I am willing to learn how to program a model in the workspace. Any help or tips would be appreciated. Thank you!

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