Time-dependent rate laws?

Hi everyone! Apologies if this isn't the right place to put this.

I'm interested in applying a time-dependent rate law for one of my reactions. Currently what I've found to work is a structure like this, where I create a pseudo-species that increases linearly with time as a reaction and then define my time-varying rate law using that.

begin seed species
  A 100
  B 100
  C 0
  T 0
end seed species
begin observables
  Molecules A A()
  Molecules B B()
  Molecules C C()
  Molecules T T()
end observables
begin functions
tfunc() = sin(T)+1
end functions
begin reaction rules
  A() + B() <-> C() tfunc(), 1
  0 -> T    1
end reaction rules
simulate({method=>"ode",t_end=>100,n_steps=>1000})

But, is there a better way to do this? Is it possible to just access the current time state from within the BioNetGen file without having to do this workaround? I noticed that there's a "time" constant reserved in the syntax file in the VSCode extension, and what I know of cvode I'd expect there should be a way to access time from inside the problem function that's passed to it.

I do the same thing but this approach becomes problematic for a stochastic model, as the time counter does not change smoothly I recall trying to use the built-in time function a long time ago and I was dissatisfied with it for some reason that I now forget It would be nice to have a simple way to access the current time in function definitions, no matter which simulator is being used Sent from my iPhoneOn May 17, 2024, at 10:20 AM, hodgensc @.***> wrote: Hi everyone! Apologies if this isn't the right place to put this. I'm interested in applying a time-dependent rate law for one of my reactions. Currently what I've found to work is a structure like this, where I create a pseudo-species that increases linearly with time as a reaction and then define my time-varying rate law using that. begin seed species A 100 B 100 C 0 T 0 end seed species begin observables Molecules A A() Molecules B B() Molecules C C() Molecules T T() end observables begin functions tfunc() = sin(T)+1 end functions begin reaction rules A() + B() <-> C() tfunc(), 1 0 -> T 1 end reaction rules simulate({method=>"ode",t_end=>100,n_steps=>1000})

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>

RuleWorld / bionetgen

Time-dependent rate laws? #275