Theory and simulation of integrate-and-fire neurons driven by shot noise (Droste & Lindner 2017)

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Accession:228604
This archive contains source code for the paper "Exact analytical results for integrate-and-fire neurons driven by excitatory shot noise" by Droste and Lindner, 2017. Specifically, it contains a Python implementation of the analytical formulas derived in that paper (allowing to calculate firing rate, CV and stationary voltage distribution of general integrate-and-fire neurons driven by excitatory shot noise, as well as power spectrum and rate-response of leaky integrate-and-fire neurons with such input) and C++ code implementing a Monte-Carlo simulation to estimate these quantities. A sample Jupyter notebook to play around with the analytics is included, as are scripts to reproduce the figures from the paper.
Reference:
1 . Droste F, Lindner B (2017) Exact analytical results for integrate-and-fire neurons driven by excitatory shot noise J. Comp. Neurosci.
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Model Information (Click on a link to find other models with that property)
Model Type:
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron; Abstract theta neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program; Python;
Model Concept(s):
Implementer(s): Droste, Felix [fedro at posteo.de];
#!/usr/bin/python

import argparse
import os, glob, sys
import json

import param_scan
import param_scan.parameter_sets as ps
import param_scan.simulation_run as si
import param_scan.submitters as su
import param_scan.io as io
import param_scan.dict_comparison as dc
from param_scan.custom_json import json_hook

default_params_name = "parameters"
data_dir_name = "data"
last_run_symlink_name = "last.run"

parser = argparse.ArgumentParser(description='bla')
parser.add_argument('sim', metavar='sim', type=str, help='.sim file describing the simulation')
parser.add_argument('prms', metavar='prms', type=str, nargs="*", help="key=value pairs for overriding default parameters or ~key for deleting keys", default=[])
parser.add_argument('-r', '--revision', dest='rev', type=str, help='git revision', default="HEAD")
parser.add_argument('-j', '--json-prms', dest='json_prms', type=str, default="{}", help='json string of (additional) parameter overrides')
parser.add_argument('-d', '--data-dir', dest='data_dir', type=str, default=data_dir_name)
parser.add_argument('-b', '--base-on', dest='base_on', type=str, help='base on params in given .run or parameters file', default=None)
#parser.add_argument('-s', '--submitter', dest='submitter', type=str, help='submitter ("condor" or "xargs")', default="condor")
parser.add_argument('-s', '--submitter', dest='submitter', type=str, help='submitter ("condor" or "xargs")', default="xargs")


parser.add_argument('--dry-run', action='store_true', dest='dry_run', default=False)
parser.add_argument('--no-wait', action='store_false', dest='wait', default=True)

args = parser.parse_args()

sim_path = os.path.realpath(io.find_in_parents(args.sim))
rev = args.rev
print "Using simulation \n\t%s\nrevision\n\t%s" % (sim_path, rev)

if os.path.exists(args.data_dir) and os.path.isdir(args.data_dir):
    data_dir = args.data_dir
else:
    try:
        data_dir = os.path.realpath(io.find_in_parents(args.data_dir))
    except IOError:
        raise IOError("data dir '%s' not found up to file system boundary" % args.data_dir)
print "Using data dir\n\t%s" % data_dir

prms = {}
if args.base_on is None:
    prmspaths = io.find_all_in_parents(default_params_name)
    if len(prmspaths) > 0:
        relprmspaths = [os.path.relpath(p, os.getcwd()) for p in prmspaths]
        print "Basing on parameters\n\t%s" % " --> ".join(relprmspaths)
        prms = io.load_parameters_incrementally(prmspaths[0])
else:
    fn, x = io.load_run(args.base_on) 
    print "Basing parameters on \n\t%s" % fn
    if x.has_key("parameters"):
        prms = x["parameters"]
    else:
        prms = x

oprms = {}
delkeys = []
for p in args.prms:
    if p.startswith("~"):
        delkeys.append(p[1:])
    else:
        try:
            k, v = p.split("=")
            oprms[k.strip()] = param_scan.ureg.parse_expression(v)
        except ValueError: # too many/few values to unpack
            raise ValueError("parameter overrides need to be given in [key]=[value] pairs (I'm confused by '%s')" % p)
for k in delkeys:
    del prms[k]
if len(delkeys) > 0:
    print "deleting parameters\n\t%s" % ", ".join(delkeys)

oprms.update(json.loads(args.json_prms, object_hook=io.json_hook))
if len(oprms.keys()) > 0:
    print "adding/overriding parameters\n\t%s" % ", ".join(oprms.keys())
prms.update(oprms)

cwd = os.getcwd()
try:
    os.chdir(os.path.dirname(sim_path))
    if args.submitter == "condor":
        submitter = su.condor_submitter
    elif args.submitter == "xargs":
        submitter = su.xargs_submitter
    else:
        raise ValueError("submitter unknown: '%s'" % args.submitter)
    r = si.submit(io.load(sim_path), prms, data_dir, rev=rev, submitter=submitter, dry_run=args.dry_run, unique=False, submitter_args={"wait": args.wait})
    os.chdir(cwd)
    prfx = si.get_prefix(r["sim"], r["parameters"], r["uniqueness"], ignore_underscore=False)
    io.save(r, prfx + ".run")
    if os.path.exists(last_run_symlink_name):
        os.remove(last_run_symlink_name)
    os.symlink(prfx + ".run", last_run_symlink_name)
    print "---> %s" % (prfx + ".run")
finally:
    os.chdir(cwd)