Retrieve run-time threshold condition

Hi folks, I am experimenting with implementing the non-Markovian Gillespie Algorithm (nMGA) in Brian based on Vestergaard and Genois (PLoS Comput. Biol. 2015, p9). Is there a way to retrieve real-time evaluations of the threshold/reset conditions?

At the moment my method is implemented by reaction=NeuronGroup(1,code=nMGA,...) where

nMGA = '''
       tau : 1
       Q   : 1
       transition = tau<Q*dt : boolean

Say I have a reaction in the nMGA scheme every time tau<Q*dt where tau and Q are set inside my nMGA implementation (within reaction=NeuronGroup(...). This reaction is detected passing threshold='tau<Q*dt to the NeuronGroup.

Because the nMGA requires some tricks for multiple transitions within the same time step, I am using reaction.run_regularly(code=code_after_transition) as well, where

code_after_transition = '''
                        if not transition:

I want to avoid defining transition in the reaction equations and have it instead directly passed from the reaction.thresholder or whatever evaluates the threshold condition. Something in the spirit of lastspike.

Hi Maurizio,
we don’t have a variable that is explicitly set by the thresholder, spikes are stored in a dedicated data structure. I have to admit that I do not exactly understand the issue: why do you not want to define transtion in the equations? If you wanted to set a variable after each spike (or transition), you could set it in the reset. Or the same for a custom event and run_on_event.

@mstimberg You are totally right. Sorry. I was caught in a classic loop-of-thoughts. To answer your question. The idea is that I have a transition = tau<Q*dt : boolean in the equations. And then if (not transition): <do some stuff> else: <do some other stuff upon transition>. This is the case of the nMGA, with the complication, that upon a transition, the algorithm requires to do some additional stuff after the reset and before updating to the next time step.

On a side note, following up on to your reply, do the reset or threshold code strings allow specification of complex code in the form of if (...) : else : ... or for or while loops (the latter for example in the reset code)? Or do I need to resort run_on_event in these cases?

You cannot use control structures like if/else or for/while in Brian code, the only direct way to implement it would be in C++/Cython code as part of user-defined functions. If you want to assign two different values to a variable depending on a condition, you can use the workaround var = int(condition)*value_1 + int(not condition)*value_2. Otherwise you’ll need to do everything with custom events and run_on_event, e.g. you can do stuff like:

group = NeuronGroup(..., events={'transitioned': 'transition',
                                 'no_transition': 'not transition'})
group.run_on_event('transitioned', 'do something')
group.run_on_event('no_transition', 'do something else')
1 Like