SimBiology

Segui

I am building a model that requires a user defined kinetic law. My code: Mobj = sbiomodel('u_PA_parameter_generation'); %create model object comp_obj = addcompartment(Mobj, 'plasma'); %create compartment object Robj2 = addreaction(Mobj, 'PLS + Pro_u_PA -> PLS + u_PA'); %create reaction object abskineticlawObj2 = sbioabstractkineticlaw('reaction_2','PLS*Pro_u_PA^ci*keff_PLS'); %create kinetic law sbioaddtolibrary(abskineticlawObj2) %add kinetic law to the library. The last line above is the causing my problem. In the absence of sbioaddtolibrary function I get an error: 'Error using SimBiology.Reaction/addkineticlaw The kinetic law named 'abskineticlawObj2' does not exist in the user-defined library. Use SBIOADDTOLIBRARY to add to the library before using it.' ...and when I do as the error suggests (adding the sbioaddtolibrary line above) I get a different error: 'Error using SimBiology.Root/addtolibrary The kinetic law 'reaction_2' already exists as a user-defined. Rename by changing the Name property or re-create by using SBIOABSTRACTKINETICLAW.' Since these errors are basically a paradox I was wondering if anyone knew if this is a problem with the software or is there a problem with my code. The rest of the reaction is listed below: Kobj2= addkineticlaw(Robj2, 'abskineticlawObj2'); Pobj2a = addparameter(Kobj2, 'keff_PLS',40); %This rate needs a hill coefiscient!!! Pobj2b = addparameter(Kobj2, 'ci',2); set(Kobj2, 'ParameterVariableNames','keff_PLS'); set(Kobj2, 'ParameterVariableNames','ci') Thanks

I am reproducing a published model and need to view the differential equations produced by the SimBiology functions. I am using a script (rather than the GUI interface) though I can import the model into the SimBiology GUI if the solution requires. Does anybody know how to see the differential equations from a SimBiology model. Thanks in advance.

In other modelling software I can simple use: ' -> protein' for fist order production of a protein however this doesn't seem to be excepted in SimBiology. I have also tried: 'null -> protein' but this also does not work. What is the syntax for producing a species out of nothing in simbiolgy? Thanks

I have a function which will calculate the values for multiple parameters within my model in Simbiology. I know I can define a rule that calls functions with a single output and use this to define a parameter value, however I don't know how to do this for multiple parameters. In Matlab it could be accomplished by: [par1,par2,par3]=function(a,b,c), where a,b,c are inputs for the function. However as Simbiology does not allow vectors as parameters this will not work. Alternatively if there was some way to retrieve (say) the 3rd output from the function this would be enough, e.g. par3=function(a,b,c){3}, however as far as I am aware this is not possible. Any help appreciated. Thanks