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simbiology competition and inhibition

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Michael on 15 Nov 2013
Answered: Ingrid Tigges on 19 Nov 2013
I am exploring suitability of simbiology for my application : exploring both desktop and direct coding: Quick pointers appreciated!
Within the desktop environment 1) is there anyway to express competitive binding or pathway inhibition processes? I have not discovered this in graphical interface? presumably this means coding model directly in matlab? 2) how to port desktop generated code back to matlab for all configured components? (must it be done screen by screen?) 3) how to set parameter (k) constraints? (limit range) or select specific parameters to vary in model: is this possible in desktop? 4) how to merge building block models into integrated models most efficiently? capability within desktop?


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Answers (2)

Ingrid Tigges
Ingrid Tigges on 18 Nov 2013
Hi, here are my quick replies to your questions:
1) Create the reaction as you normally do in the SimBiology desktop and then enter as reaction, choose as kinetic law "Unknown" and enter the kinetics in "ReactionRate". This way you can use any kind of Reaction rate you can imagine.
2) Click on the small, downwards facing triangle next to the Navigation bar and select "Export Model to Workspace"
3) Can you please be more specific about this? Do you want to limit the range in which parameters can be? If yes, please have a look at this link Specifying upper and lower limits for species
4) I am sorry, but I don't understand your question. Can you please explain this a bit more in detail?
I hope this helps.

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Michael on 18 Nov 2013
Thank you for the very rapid answer to my first two questions. Very helpful.
To clarify: 3) My question specifically related to limiting the range of rate constants to something physiologically plausible or preventing specific constants from being varied during the optimisation phase (to prevent over- flexibility in potentially over-prametised models). ie we may fix components of a model/compartment from one set of experimental data and then require model to fit elements of a separate set of equations / compartment. Limiting species concentrations is of course also likely to be useful useful: so this would also be useful to know)
4) This relates to building models based on experimental data separately before integrating separate models into a larger model. Is it possible to import several models into the graphical interface and connect (ie add compartment or model)? I can see how this can be done in code, but maybe it is possible to some extent in the graphical interface too?
With Thanks

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Ingrid Tigges
Ingrid Tigges on 19 Nov 2013
You can find an explanation on how to fit parameters that should be within certain limits here: Specifying bounds of parameters during parameter fitting in SimBiology
Regarding your 4th question you can copy and paste elements from one model to another in the SimBiology Desktop. From the command-line, there is also limited support for copying using a method called copyobj.


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