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This is the main repository for the Synapse simulation package written in Julia language. The associated publication is on BiorXiv.
Yuri Rodrigues, Cian O'Donnell and Romain Veltz wrote the code.
You need at least Julia v1.5.0 to run this code
To run the package Synapse, we need some bleeding edge versions of other packages.
To install the package, please run
pkg> add SynapseElifeNote that this has to be done only once! You don't need to do it for every session
You can then use it like
using SynapseElifeYou can build the website associated with this package by running make.jl in the folder path/Synapse/docs
If you want to have information about a function use ?. For example, you can type ?SynapseParams to get
help?> SynapseParams
search: SynapseParams
struct SynapseParams
Postsynaptic parameters
Units
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• time: ms
• length: µm (area µm^2, volume µm^3)
• voltage: mV
...In order to know the parameters used in the model, you can do for example (for the presynaptic ones):
using SynapseElife
?PreSynapseParamswhich gives
help?> PreSynapseParams
search: PreSynapseParams
struct PreSynapseParams
Presynaptic parameters
• Firing events are processed separately from the main simulation (at /Users/rveltz/only_stp.jl) it takes the firing
structure as input from the function [compilation][/Users/rveltz/utils_data.jl:672].
• Using the EPSP times vesicle depletion and AP induced by EPSP is estimated, however one can use a tag in order to
deactivate it (covering subthreshold EPSP cases).
• The presynaptic part of our model is phenomelogical, for instance, soma variable was made to have intended to
represent the voltage and is able to accumulate for faster frequencies but has an abstract unit.
Equations
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based on D. Sterratt et al book; Principles of Computational Modelling in Neuroscience (https://www.compneuroprinciples.org/
) page 183
raterec = (n_rec_t0 - rec) * rec_dt * rrp
raterrp = (n_rrp_t0 - rrp) * rrp_dt * rec
rateref = (n_rec_t0 - rec) * ref_dt
Fields
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• trec_ca::Float64
recovery constant of pre calcium decay function Default: 20000
• delta_ca::Float64
fraction of decay constant of pre calcium decay f Default: 0.0004
• tau_pre::Float64
decay time constant of pre calcium Default: 20
• tau_soma::Float64
decay time constant for AP induced by EPSP Default: 40
• n_rrp_t0::Int64
initial conditions ready releaseble pool Default: 25
• n_rec_t0::Int64
initial conditions recovery pool Default: 30
• rec_dt::Float64
rate rrp -> rec Default: 1 / 5000
• rrp_dt::Float64
rate rec -> rrp Default: 1 / 45000
• ref_dt::Float64
rate infinite reservoir -> rec Default: 1 / 40000
• slope::Float64
sigmoid parameter for release probability Default: 2.0
• half::Float64
sigmoid parameter for release probability Default: 0.7
• ap_slope::Float64
sigmoid parameter for AP-by-EPSP probability Default: 2.0
• ap_half::Float64
sigmoid parameter for AP-by-EPSP probability Default: 0.7If you want to alter the default value of a parameter, you can create a variable as follows
param_synapse = SynapseParams(
t_end = 1000.,
soma_dist = 200.,)