How can I define a time-dependent (species) reaction rate for an model in SimBiology?

I want to define that a specie A is being produced given by 2 degree quardratic equation as a function of time. How to define it ?

[Jeremy Huard]

Hi Puru,

I would recommend you to create a reaction null -> A with a custom reaction rate defined by the quadratic equation. In this reaction rate you can use the variable time, which is a reserved word in SimBiology and corresponds to the current time of the simulation.

Best regards,

Jérémy

[Puru Raj]

Hi Jérémy,

Thanks for your help. It worked . Just one more doubt should i put rate as 2*a*time+b or a*time^2+b*time+c?

Regards,

Puru

[Jeremy Huard]

Hi Puruj,

I guess it depends on how the equation should look like.

If you want something like then the reaction rate should indeed be . That said, if x is not involved in any other reactionthat involve other species, it might be easier to define this equation as a repeated assignment.

If you would rather want then the reaction rate should be .

Best regards,

Jérémy

[Puru Raj]

Thank you.

Answer 1

[Jeremy Huard]

Hi Puru,

I would recommend you to create a reaction null -> A with a custom reaction rate defined by the quadratic equation. In this reaction rate you can use the variable time, which is a reserved word in SimBiology and corresponds to the current time of the simulation.

Best regards,

Jérémy

[Cristina]

Hi Jeremy,

Does Simbiology allows to run the SSA when the model has time dependent rates? If yes, how can they be written?

Thanks,

Cristina

[Jeremy Huard]

Hi @Cristina,

For SSA in SimBiology all reactions in the model must have their KineticLaw property set to MassAction.

You can find more details about the requirements for stochastic simulations and about the different solvers available here: https://www.mathworks.com/help/simbio/ug/stochastic-solvers.html

Best regards,

Jérémy

[Cristina]

Thanks for the reply! I guess that means that the reaction propensities need to be constant if I want to simulate my model stochastically using SimBiology. Do you know if there is any Matlab package that would allow me to have a rate as a funtion of time?

Best regards,

Cristina