/* Copyright (c) 2015 EPFL-BBP, All rights reserved.
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*/
/*
* @file synapses.hoc
* @brief Template that store the synapses
* @author Werner Van Geit @ BBP
* @date 2015
*/
begintemplate synapses_863902f300
public load_synapses, synapse_list, netcon_list, netstim_list, \
pre_mtypes_bitmap, n_of_pre_mtypes, id_mtype_map, pre_mtypes, \
active_pre_mtypes, update_synapses, pre_mtype_netconlists, \
pre_mtype_freqs, pre_mtype_netstimlists, reset_synapses, \
weights, delays, synconf_list
objref synapse_list, netcon_list, netstim_list, pre_mtypes_bitmap, \
id_mtype_map, pre_mtypes, active_pre_mtypes, pre_mtype_netconlists, \
pre_cell_ids, pre_mtype_freqs, pre_mtype_netstimlists, rng_list, \
pre_mtype_weightlists, pre_mtype_synapselists, \
were_active_pre_mtypes, pre_mtypes_excinh, weights, delays, \
synconf_list, stringtools, tmp_synapse, this
/** Constructor */
proc init() { local mtype_id localobj mtype_map_file, mtype_name_string
strdef line, mtype_name
// Number of m-types
n_of_mtypes = 55
synapse_list = new List()
rng_list = new List()
netcon_list = new List()
netstim_list = new List()
weights = new Vector()
delays = new Vector()
pre_mtype_netconlists = new List()
pre_mtype_netstimlists = new List()
pre_mtype_weightlists = new List()
pre_mtype_synapselists = new List()
pre_mtypes_bitmap = new Vector(n_of_mtypes, 0)
pre_mtypes_excinh = new Vector(n_of_mtypes, 1)
active_pre_mtypes = new Vector(n_of_mtypes, 0)
were_active_pre_mtypes = new Vector(n_of_mtypes, 0)
pre_mtype_freqs = new Vector(n_of_mtypes, 10.0)
pre_mtypes = new Vector()
pre_cell_ids = new Vector()
for i=0, n_of_mtypes-1 {
pre_mtype_netconlists.append(new List())
pre_mtype_netstimlists.append(new List())
pre_mtype_synapselists.append(new List())
pre_mtype_weightlists.append(new Vector())
}
id_mtype_map = new List()
// Read the mapping between m-type names and m-type IDs
mtype_map_file = new File("synapses/mtype_map.tsv")
mtype_map_file.ropen()
for i=0, n_of_mtypes-1 {
mtype_map_file.gets(line)
sscanf(line, "%d\t%s", &mtype_id, mtype_name)
mtype_name_string = new String(mtype_name)
id_mtype_map.append(mtype_name_string)
}
mtype_map_file.close()
stringtools = new StringFunctions()
}
/** Update the active synapses in the GUI
Arguments:
synapse_plot: synapse plot object
*/
proc update_synapses() { localobj pre_mtype_netcons, pre_mtype_netstims, \
pre_mtype_weights, pre_mtype_synapses, synapse_plot
synapse_plot = $o1
for i=0, n_of_mtypes-1 {
pre_mtype_netcons = pre_mtype_netconlists.o(i)
pre_mtype_weights = pre_mtype_weightlists.o(i)
pre_mtype_synapses = pre_mtype_synapselists.o(i)
// Use different color for exc / inh synapses
if (pre_mtypes_excinh.x[i] == 0) {
// Red, excitatory
syn_color = 2
} else {
// Yellow, inhibitory
syn_color = 5
}
// Loop over the synapses.
// enable and plot active synapses,
// disable and remove inactive ones
// only do something if status of a synapse changed since last update
for j=0, pre_mtype_netcons.count()-1 {
if (active_pre_mtypes.x[i] == 1 && \
were_active_pre_mtypes.x[i] == 0) {
// Set weight to correct value
pre_mtype_netcons.o(j).weight = pre_mtype_weights.x[j]
// Draw the synapses
synapse_plot.point_mark(pre_mtype_synapses.o(j), \
syn_color, 4, 6)
} else if (active_pre_mtypes.x[i] == 0 && \
were_active_pre_mtypes.x[i] == 1) {
// Disable synapse by setting weight to 0
pre_mtype_netcons.o(j).weight = 0.0
// Remove synapse from plot
synapse_plot.point_mark_remove(pre_mtype_synapses.o(j))
}
}
// Update the list were_active_pre_mtypes, which is the list of
// mtypes that are active after this update
if (active_pre_mtypes.x[i] == 1 && were_active_pre_mtypes.x[i] == 0) {
were_active_pre_mtypes.x[i] = 1
} else if (active_pre_mtypes.x[i] == 0 && \
were_active_pre_mtypes.x[i] == 1) {
were_active_pre_mtypes.x[i] = 0
}
// Update the netstim frequencies
pre_mtype_netstims = pre_mtype_netstimlists.o(i)
for j=0, pre_mtype_netstims.count()-1 {
pre_mtype_netstims.o(j).interval = 1000.0 / pre_mtype_freqs.x[i]
}
}
}
/** Disable all the synapses */
proc reset_synapses() {
for i=0, n_of_mtypes-1 {
were_active_pre_mtypes.x[i] = 0
}
}
/** Load the synconf file
Arguments:
nsynapses: number of synapses in cell
*/
proc load_synconf() { localobj synconf_file, synconf_gids
strdef synconf_string
nsynapses = $1
synconf_list = new List()
for isynapse=0, nsynapses-1 {
synconf_list.append(new List())
}
synconf_file = new File("synapses/synconf.txt")
{synconf_file.ropen()}
synconf_gids = new Vector()
while (synconf_file.gets(synconf_string) > 0) {
stringtools.left(synconf_string, stringtools.len(synconf_string)-1)
synconf_gids.scantil(synconf_file, -1e15)
for i=0, synconf_gids.size()-1 {
synconf_list.o(synconf_gids.x[i]).append(new String(synconf_string))
}
}
}
/** Load all the synapses
Arguments:
cell_ref: reference to the cell object
*/
proc load_synapses() { local isynapse, nsynapses, ncols, synapse_id, \
pre_cell_id, seg_x, synapse_type, \
dep, fac, use, tau_d, delay, weight, \
base_seed, gid, netstim_id \
localobj synapse_data, synapse_file, cell_ref, \
synapse, section, rng, netcon, netstim
printf("Starting to add synapses\n")
strdef sectionlist_name, synapse_type_name, synconf_string, head_string, \
tail_string
cell_ref = $o1
// Load the file that contains all the information about the synapses
synapse_file = new File("synapses/synapses.tsv")
{synapse_file.ropen()}
// Data structure to store the data in synapses.tsv
synapse_data = new Matrix()
synapse_data.scanf(synapse_file)
synapse_file.close()
nsynapses = synapse_data.nrow
ncols = synapse_data.ncol
// There is only one cell in this simulation, so let's give it gid 1
gid = 4421
// Base seed for the rngs
base_seed = 0
// Load list of hoc commands that have to be execute on every synapse
// to set certain parameters that are not specified in synapse.tsv
load_synconf(nsynapses)
for isynapse=0, nsynapses-1 {
// Read the synapse parameters from the matrix
synapse_id = synapse_data.x[isynapse][0]
pre_cell_id = synapse_data.x[isynapse][1]
pre_mtype = synapse_data.x[isynapse][2]
sectionlist_id = synapse_data.x[isynapse][3]
sectionlist_index = synapse_data.x[isynapse][4]
seg_x = synapse_data.x[isynapse][5]
synapse_type = synapse_data.x[isynapse][6]
dep = synapse_data.x[isynapse][7]
fac = synapse_data.x[isynapse][8]
use = synapse_data.x[isynapse][9]
tau_d = synapse_data.x[isynapse][10]
delay = synapse_data.x[isynapse][11]
weight = synapse_data.x[isynapse][12]
// Create sectionref to the section the synapse will be placed on
if ( sectionlist_id == 0 ) {
cell_ref.soma[sectionlist_index] section = new SectionRef()
sectionlist_name = "somatic"
} else if ( sectionlist_id == 1 ) {
cell_ref.dend[sectionlist_index] section = new SectionRef()
sectionlist_name = "basal"
} else if ( sectionlist_id == 2 ) {
cell_ref.apic[sectionlist_index] section = new SectionRef()
sectionlist_name = "apical"
} else if ( sectionlist_id == 3 ) {
cell_ref.axon[sectionlist_index] section = new SectionRef()
sectionlist_name = "axonal"
} else {
printf("Sectionlist_id %d not support\n", sectionlist_id)
exit(1)
}
// If synapse_type < 100 the synapse is inhibitory, otherwise
// excitatory
if ( synapse_type < 100 ) {
synapse_type_name = "inhibitory"
section.sec synapse = new ProbGABAAB_EMS(seg_x)
synapse.tau_d_GABAA = tau_d
rng = new Random()
rng.MCellRan4( isynapse*100000+100, gid+250+base_seed )
rng.lognormal(0.2, 0.1)
synapse.tau_r_GABAA = rng.repick()
pre_mtypes_excinh.x[pre_mtype] = 1
} else {
synapse_type_name = "excitatory"
section.sec synapse = new ProbAMPANMDA_EMS(seg_x)
synapse.tau_d_AMPA = tau_d
pre_mtypes_excinh.x[pre_mtype] = 0
}
synapse.Use = abs( use )
synapse.Dep = abs( dep )
synapse.Fac = abs( fac )
// Execute all the extra synaptic configuration lines from synconf.txt
tmp_synapse = synapse
for isynconf=0,synconf_list.o(isynapse).count()-1 {
synconf_string = synconf_list.o(isynapse).o(isynconf).s
// Replacing all occurrences of %s with the temporary synapse name
while( stringtools.substr( synconf_string, "%s" ) != -1 ) {
stringtools.head(synconf_string, "%s", head_string)
stringtools.tail(synconf_string, "%s", synconf_string)
sprint(synconf_string, "%s%s%s", head_string, "tmp_synapse", synconf_string)
}
// Add {} around the string
sprint(synconf_string, "{%s}", synconf_string)
// Execute the statement
execute1(synconf_string, this)
}
// Create the random number generator for the synapse
rng = new Random()
rng.MCellRan4( isynapse*100000+100, gid+250+base_seed )
rng.uniform(0,1)
synapse.setRNG( rng )
rng_list.append(rng)
synapse_list.append(synapse)
// Check if there is already a netstim (spike generator)
// for the presynaptic cell
// If it exists, use that one
// Otherwise create a new one
if (pre_cell_ids.contains(pre_cell_id)) {
netstim_id = pre_cell_ids.indwhere("==", pre_cell_id)
netstim = netstim_list.o(netstim_id)
} else {
section.sec netstim = new NetStim(seg_x)
netstim.start = 0
netstim.interval = 100
netstim.number = 1e20
netstim.noise = 1
netstim_list.append(netstim)
pre_mtype_netstimlists.o(pre_mtype).append(netstim)
pre_cell_ids.append(pre_cell_id)
}
// Create a connection between the netstim and the synapse
netcon = new NetCon(netstim, synapse)
netcon.delay = delay
netcon.weight = 0.0
netcon_list.append(netcon)
// Save all the objects we made to make them persistent
pre_mtype_netconlists.o(pre_mtype).append(netcon)
pre_mtype_weightlists.o(pre_mtype).append(weight)
weights.append(weight)
delays.append(delay)
pre_mtype_synapselists.o(pre_mtype).append(synapse)
pre_mtypes_bitmap.x[pre_mtype] = 1
printf("Added %s synapse %d originating from cell %d of m-type %s on %s section %d(%f) and dep %f\n", \
synapse_type_name, synapse_id, pre_cell_id, id_mtype_map.o(pre_mtype).s, sectionlist_name, \
sectionlist_index, seg_x, dep)
}
// Make a list of all the m-types presynaptic to this cell, used by the GUI
for i=0, n_of_mtypes-1 {
if (pre_mtypes_bitmap.x[i] == 1) {
pre_mtypes.append(i)
}
}
}
endtemplate synapses_863902f300