SimBiology

フォロー

Would be useful to know. I believe 2020b only supports level 2, correct? Has anyone else run into having to use an sblm level 3 model? How do you handle this? Thanks.

I am having troubles installing libSBML, which I need to use GenSSI for parameter identifiability in Simbiology. I am following the instructions in this documentation, but I cannot use SBML in either case: when I add 'manually' the folder to the path and try to run the command `TranslateSBML('test.xml')`, the following error pops up: Execution of script TranslateSBML as a function is not supported: C:\Users\elisa\libsbml\src\bindings\matlab\TranslateSBML.m And if I try to run installSBML.m, the following error occurs: Error using installSBML Executables were not found.Please make sure they are in the same directory as the installSBML and other scripts. I opened an issue on github, but haven't received an answer yet.

I'm trying to run this model with SimBiology but see an error message. BIOMD0000000268_url.xml SBML L2V4 representation of Reed2008_Glutathione_Metabolism Reed2008_Glutathione_Metabolism | BioModels (ebi.ac.uk) "piecewise" is a function in matlab but it seems SimBiology model bulider recognizes it as a variable... Any idea? --------- RULE Aminoacid_input = piecewise(breakfast,and(le(7,daytime),le(daytime,10)),lunch,and(le(12,daytime),le(daytime,15)),dinner,and(le(18,daytime),le(daytime,21)),fasting) error message: "Rule include varaibles that are unidentified." with red higllight for "piecewise" ---------------------------------

Hello, I am new to Matlab/SimBiology. I have an SBML Model that I am loading into the Model Builder. Upon doing this, I have the following error reported in the main Matlab Command window. Warning: Error posting 'expressionStatus' for ''. Error from MATLAB: 'Error using SimBiology.web.diagramhandler Input argument 'element' is invalid.'.' > In SimBiology.web.modelhandler In SimBiology.web.modelhandler In SimBiology.web.modelhandler In sbiojsgate (line 27) In connector.internal.fevalMatlab In connector.internal.fevalJSON The model does complete loading, but the diagram is completely blank. I would like to know what I can do to resolve this, since seeing the diagram would be nice. I would share the SBML file, but it is proprietary, and I do not know what I would do to create an SBML model that produces the same issue. One other thing that might be helpful is that I am on macOS with an M1 chip. Thank you

I have an .sbml model I want to simulate using ssa. It works for small timespans, and when using ode simulations. However, in this example matlab simply crashes. Why is this? is there a way of preventing this? % Load model. model_egfr_net = sbmlimport('egfr_net.xml'); % Prepare model for SSA simulations. clean_ssa_sbml_model(model_egfr_net) cs = getconfigset(model_egfr_net); cs.SolverType = 'ssa'; cs.StopTime = 100.0; % Simulate model. [t, x, names] = sbiosimulate(model_egfr_net); I have attached the model. Also, per https://uk.mathworks.com/matlabcentral/answers/1582584-simbio-running-stochastic-ssa-simulation-of-sbml-imported-model the model has to be modified to enable ssa simulations. The attached function (used in the script) is provided here: function [] = clean_ssa_sbml_model(model) parameters = sbioselect(model, 'Type', 'parameter'); for paramIndex = 1:numel(parameters) parameter = parameters(paramIndex); [~, usageTable] = findUsages(parameter); % Update any reaction that uses this parameter in its rate. if isempty(usageTable) % if check added by Torkel. continue end reactions = usageTable.Component(usageTable.Property == "ReactionRate"); for reactionIndex = 1:numel(reactions) reaction = reactions(reactionIndex); oldRate = reaction.ReactionRate; kineticLaw = reaction.KineticLaw; if isempty(kineticLaw) % Add a kinetic law kineticLaw = addkineticlaw(reaction, 'MassAction'); else % Update the existing kinetic law to mass action kineticLaw.KineticLawName = 'MassAction'; end kineticLaw.ParameterVariableNames = parameter.Name; newRate = reaction.ReactionRate; if ~strcmp(oldRate, newRate) warning("Reaction rate for reaction %s changed from %s to %s.", ... reaction.Name, oldRate, newRate); end end end end

In a description of the SBML standard, namely Hucka et al., The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core, J Integr Bioinform. ; 12(2): 266. doi:10.2390/biecoll-jib-2015-266, a point of the specification is stated: "4.11.2 SimpleSpeciesReference As mentioned above, every species that enters into a given reaction must appear in that reaction’s lists of reactants, products and/or modifiers. " One maddening element of this is that a species can apparently be all three things! A self growth of A to increase the amount A, self-catalyzed by A. Does anyone know if appearance of a species in one list is sufficient, or (for example) if I have a mass action expression of compound A, does A have to be in both the reactants AND the modifer list? More to the point: As far as I can tell, sbmlexport does not export modifers. They're just not there. So if one has reactions like A->B, but the reaction rate expresssion is r=k*A*C, where C is a species, then sbml isn't conformal. Am I missing something? Improperly using sbmlexport? If modifiers are NOT there, will modifers be included in a future release? Right now I have a python script that captures all of the species in reactions that are not reactants or products, but it would be nice to have. This brings up a question. Suppose I have a function dependent upon species, but indirectly. For example, A parameter defined by a repeat assignment: Glut4 = f(Plasma.Insulin); for a reaction of Plasma.Glucose --> muscle.Glucose I have the reaction rate rp2m = k * Glut4 * Plasma.Glucose; Given those equations, is Plasma.Insulin a modifier of the reaction defined by rp2m?

I have a .sbml model stored in an .xml file. It contains a couple of observables. When I plto the simulation results, these are uniformly set to "1" when I use the ssa simulation, however, observables seems to work fine with ode simulations. This is the code: % Fetch model. model = sbmlimport('multistate.xml'); % Run simulation. cs = getconfigset(model); cs.SolverType = 'sundials'; cs.StopTime = 10.0; [t_ode, x_ode, names] = sbiosimulate(model); % Plot observables. plot(t_ode, x_ode(:,end-3:end)) xlabel('Time') ylabel('States') legend(names(end-3:end)) % Prepare model for SSA simulations (see https://uk.mathworks.com/matlabcentral/answers/1582584-simbio-running-stochastic-ssa-simulation-of-sbml-imported-model). parameters = sbioselect(model, 'Type', 'parameter'); for paramIndex = 1:numel(parameters) parameter = parameters(paramIndex); [~, usageTable] = findUsages(parameter); % Update any reaction that uses this parameter in its rate. if isempty(usageTable) % if check added by Torkel. continue end reactions = usageTable.Component(usageTable.Property == "ReactionRate"); for reactionIndex = 1:numel(reactions) reaction = reactions(reactionIndex); oldRate = reaction.ReactionRate; kineticLaw = reaction.KineticLaw; if isempty(kineticLaw) % Add a kinetic law kineticLaw = addkineticlaw(reaction, 'MassAction'); else % Update the existing kinetic law to mass action kineticLaw.KineticLawName = 'MassAction'; end kineticLaw.ParameterVariableNames = parameter.Name; newRate = reaction.ReactionRate; if ~strcmp(oldRate, newRate) warning("Reaction rate for reaction %s changed from %s to %s.", ... reaction.Name, oldRate, newRate); end end end % Run simulation. cs = getconfigset(model); cs.SolverType = 'ssa'; cs.StopTime = 10.0; [t_ssa, x_ssa, names] = sbiosimulate(model); % Plot observables. plot(t_ssa, x_ssa(:,end-3:end)) xlabel('Time') ylabel('States') legend(names(end-3:end)) % Non-observables plot still work. plot(t_ssa, x_ssa(:,1:end-4)) xlabel('Time') ylabel('States') legend(names(1:end-4)) % Observable plotting still work for the modified model when using ode. cs = getconfigset(model); cs.SolverType = 'sundials'; cs.StopTime = 10.0; [t_ode_2, x_ode_2, names] = sbiosimulate(model); plot(t_ode_2, x_ode_2(:,end-3:end)) xlabel('Time') ylabel('States') legend(names(end-3:end)) Which produces these plots: The observables can be plotted when the mode is simulated via ode: The observables are all "1" when simualted via ssa: The other species can be plotted without problem though: Finnaly, plotting the observables when the system has been simualted via ode still work, even after the model have been modified. There is something wrong where the observables values are not set when the ssa algorithm is used. Finally, I have attached the model file (extension changed to .txt so that mathworks website would accept it).

Hello, I have a biochemical reaction network model defined in the SBML format (attached). I can load the model using the sbmlimport: sbml_mod = sbmlimport('multistate.xml'); I can perform ODE simulations of this model using sbiosimulate: [time,x,names] = sbiosimulate(sbml_mod); However, if I want to perform stochastic SSA (GIllespie) simulations (https://uk.mathworks.com/help/simbio/ug/stochastic-solvers.html), I get problems. Running cs = getconfigset(sbml_mod,'active'); cs.SolverType = 'ssa'; cs.StopTime = 30; [t_ssa, x_ssa] = sbiosimulate(sbml_mod); I get errors: --> Error reported from Stochastic Compilation: Reaction named 'Reaction_2' has an empty kinetic law. For stochastic simulation all kinetic laws must be MassAction. (one for each of my 18 reactions) It turns out that when loading SBML models each reactions get no KineticLaw, which is needed for SSA simulations. E.g. sbml_mod.Reactions(1).KineticLaw simply returns []. However, all reactions in the SBML file are simple MassAction reactions, e.g. sbml_mod.Reactions(1).ReactionRate is 'kon*[R(a,l)]*[L(r)]'. I tried simply looping through all reactions and setting their KineticLaw field to 'MassAction'. But this still yields errors like --> Error reported from KineticLaw Validation: Parameter variable name on kinetic law '' is empty. The number of parameters on the kinetic law must match the number in its definition, and all parameter names must be set. So I somehow need to ftech the right parameters and att that to the MassAction kinetic law. It seems like this should be fairly straightforward (e.g. many other packages, like Copasi can do SSA simulations directly from SBML files). Is there some automatic way of setting all reactions to MassAction kinetic law, or some other way which would enable me to do an SSA simulation of the model?

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?

When trying to import an SBML file to use in SimBiology, I am getting the following error >> x = sbmlimport('http://www.netpath.org/netslim/EGFR1/EGFR1_SBML.xml') Error using SimBiology.SBMLReadWrite/sbmlread A fatal error occurred reading in this file. Error in sbmlimport (line 96) ret = sbmlRW.sbmlread(modelString, {'stream'}); A similar error occurs if the linked file above is downloaded and added to the path instead. ( Throwing an error on line 89: ret = privatesbmlio('read',nargout,{tempFileName}); ) Why is this happening? How can I fix it?

Functions to import SBML files containing function definitions into SimBiology.

I'm trying to import this SBML model into SimBiology using the sbmlimport function. Unfortunately this results in an immediate crashing of MATLAB (2010b and 2013a) - does anyone have any suggestions on how to proceed or diagnose the issue? Many thanks, Richard