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fix typesetting in model docstrings (#1185)
1 parent c5ce3c2 commit e4cb5d6

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models/neurons/aeif_cond_alpha_neuron.nestml

+33-12
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@@ -10,34 +10,34 @@
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#
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# .. math::
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#
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# C_m \frac{dV_m}{dt} =
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# -g_L(V_m-E_L)+g_L\Delta_T\exp\left(\frac{V_m-V_{th}}{\Delta_T}\right) -
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# g_e(t)(V_m-E_e) \\
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# -g_i(t)(V_m-E_i)-w + I_e
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# C_m \frac{dV_m}{dt} =
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# -g_L(V_m-E_L)+g_L\Delta_T\exp\left(\frac{V_m-V_{th}}{\Delta_T}\right) -
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# g_e(t)(V_m-E_e) \\
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# -g_i(t)(V_m-E_i)-w + I_e
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#
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# and
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#
2020
# .. math::
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#
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# \tau_w \frac{dw}{dt} = a(V_m-E_L) - w
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# \tau_w \frac{dw}{dt} = a(V_m-E_L) - w
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#
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# Note that the membrane potential can diverge to positive infinity due to the exponential term. To avoid numerical instabilities, instead of :math:`V_m`, the value :math:`\min(V_m,V_{peak})` is used in the dynamical equations.
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#
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# .. note::
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#
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# The default refractory period for ``aeif`` models is zero, consistent with the model definition in
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# Brette & Gerstner [1]_. Thus, an ``aeif`` neuron with default parameters can fire multiple spikes in a single
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# time step, which can lead to exploding spike numbers and extreme slow-down of simulations.
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# To avoid such unphysiological behavior, you should set a refractory time ``refr_t > 0``.
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# The default refractory period for ``aeif`` models is zero, consistent with the model definition in
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# Brette & Gerstner [1]_. Thus, an ``aeif`` neuron with default parameters can fire multiple spikes in a single
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# time step, which can lead to exploding spike numbers and extreme slow-down of simulations.
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# To avoid such unphysiological behavior, you should set a refractory time ``refr_t > 0``.
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#
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#
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# References
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# ++++++++++
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#
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# .. [1] Brette R and Gerstner W (2005). Adaptive exponential
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# integrate-and-fire model as an effective description of neuronal
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# activity. Journal of Neurophysiology. 943637-3642
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# DOI: https://doi.org/10.1152/jn.00686.2005
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# integrate-and-fire model as an effective description of neuronal
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# activity. Journal of Neurophysiology. 943637-3642
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# DOI: https://doi.org/10.1152/jn.00686.2005
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#
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#
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# See also
@@ -46,6 +46,27 @@
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# iaf_cond_alpha, aeif_cond_exp
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#
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#
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# Copyright statement
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# +++++++++++++++++++
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#
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# This file is part of NEST.
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#
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# Copyright (C) 2004 The NEST Initiative
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#
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# NEST is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 2 of the License, or
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# (at your option) any later version.
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#
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# NEST is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
64+
# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with NEST. If not, see <http://www.gnu.org/licenses/>.
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#
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#
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model aeif_cond_alpha_neuron:
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state:

models/neurons/aeif_cond_exp_neuron.nestml

+32-11
Original file line numberDiff line numberDiff line change
@@ -12,33 +12,33 @@
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#
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# .. math::
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#
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# C_m \frac{dV_m}{dt} =
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# -g_L(V_m-E_L)+g_L\Delta_T\exp\left(\frac{V_m-V_{th}}{\Delta_T}\right) - g_e(t)(V_m-E_e) \\
17-
# -g_i(t)(V_m-E_i)-w +I_e
15+
# C_m \frac{dV_m}{dt} =
16+
# -g_L(V_m-E_L)+g_L\Delta_T\exp\left(\frac{V_m-V_{th}}{\Delta_T}\right) - g_e(t)(V_m-E_e) \\
17+
# -g_i(t)(V_m-E_i)-w +I_e
1818
#
1919
# and
2020
#
2121
# .. math::
2222
#
23-
# \tau_w \frac{dw}{dt} = a(V_m-E_L) - w
23+
# \tau_w \frac{dw}{dt} = a(V_m-E_L) - w
2424
#
2525
# Note that the membrane potential can diverge to positive infinity due to the exponential term. To avoid numerical instabilities, instead of :math:`V_m`, the value :math:`\min(V_m,V_{peak})` is used in the dynamical equations.
2626
#
2727
# .. note::
2828
#
29-
# The default refractory period for ``aeif`` models is zero, consistent with the model definition in
30-
# Brette & Gerstner [1]_. Thus, an ``aeif`` neuron with default parameters can fire multiple spikes in a single
31-
# time step, which can lead to exploding spike numbers and extreme slow-down of simulations.
32-
# To avoid such unphysiological behavior, you should set a refractory time ``refr_t > 0``.
29+
# The default refractory period for ``aeif`` models is zero, consistent with the model definition in
30+
# Brette & Gerstner [1]_. Thus, an ``aeif`` neuron with default parameters can fire multiple spikes in a single
31+
# time step, which can lead to exploding spike numbers and extreme slow-down of simulations.
32+
# To avoid such unphysiological behavior, you should set a refractory time ``refr_t > 0``.
3333
#
3434
#
3535
# References
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# ++++++++++
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#
3838
# .. [1] Brette R and Gerstner W (2005). Adaptive exponential
39-
# integrate-and-fire model as an effective description of neuronal
40-
# activity. Journal of Neurophysiology. 943637-3642
41-
# DOI: https://doi.org/10.1152/jn.00686.2005
39+
# integrate-and-fire model as an effective description of neuronal
40+
# activity. Journal of Neurophysiology. 943637-3642
41+
# DOI: https://doi.org/10.1152/jn.00686.2005
4242
#
4343
#
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# See also
@@ -47,6 +47,27 @@
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# iaf_cond_exp, aeif_cond_alpha
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#
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#
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# Copyright statement
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# +++++++++++++++++++
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#
53+
# This file is part of NEST.
54+
#
55+
# Copyright (C) 2004 The NEST Initiative
56+
#
57+
# NEST is free software: you can redistribute it and/or modify
58+
# it under the terms of the GNU General Public License as published by
59+
# the Free Software Foundation, either version 2 of the License, or
60+
# (at your option) any later version.
61+
#
62+
# NEST is distributed in the hope that it will be useful,
63+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
64+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
65+
# GNU General Public License for more details.
66+
#
67+
# You should have received a copy of the GNU General Public License
68+
# along with NEST. If not, see <http://www.gnu.org/licenses/>.
69+
#
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#
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model aeif_cond_exp_neuron:
5172

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state:

models/neurons/hh_cond_exp_destexhe_neuron.nestml

+21
Original file line numberDiff line numberDiff line change
@@ -30,6 +30,27 @@
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# hh_cond_exp_traub
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#
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#
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# Copyright statement
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# +++++++++++++++++++
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#
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# This file is part of NEST.
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#
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# Copyright (C) 2004 The NEST Initiative
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#
40+
# NEST is free software: you can redistribute it and/or modify
41+
# it under the terms of the GNU General Public License as published by
42+
# the Free Software Foundation, either version 2 of the License, or
43+
# (at your option) any later version.
44+
#
45+
# NEST is distributed in the hope that it will be useful,
46+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
47+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
48+
# GNU General Public License for more details.
49+
#
50+
# You should have received a copy of the GNU General Public License
51+
# along with NEST. If not, see <http://www.gnu.org/licenses/>.
52+
#
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#
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model hh_cond_exp_destexhe_neuron:
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state:

models/neurons/hh_cond_exp_traub_neuron.nestml

+24-3
Original file line numberDiff line numberDiff line change
@@ -34,10 +34,10 @@
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# ++++++++++
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#
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# .. [1] Brette R et al. (2007). Simulation of networks of spiking neurons: A
37-
# review of tools and strategies. Journal of Computational Neuroscience
38-
# 23:349-98. DOI: https://doi.org/10.1007/s10827-007-0038-6
37+
# review of tools and strategies. Journal of Computational Neuroscience
38+
# 23:349-98. DOI: https://doi.org/10.1007/s10827-007-0038-6
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# .. [2] Traub RD and Miles R (1991). Neuronal networks of the hippocampus.
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# Cambridge University Press, Cambridge UK.
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# Cambridge University Press, Cambridge UK.
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# .. [3] http://modeldb.yale.edu/83319
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#
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#
@@ -47,6 +47,27 @@
4747
# hh_psc_alpha
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#
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#
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# Copyright statement
51+
# +++++++++++++++++++
52+
#
53+
# This file is part of NEST.
54+
#
55+
# Copyright (C) 2004 The NEST Initiative
56+
#
57+
# NEST is free software: you can redistribute it and/or modify
58+
# it under the terms of the GNU General Public License as published by
59+
# the Free Software Foundation, either version 2 of the License, or
60+
# (at your option) any later version.
61+
#
62+
# NEST is distributed in the hope that it will be useful,
63+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
64+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
65+
# GNU General Public License for more details.
66+
#
67+
# You should have received a copy of the GNU General Public License
68+
# along with NEST. If not, see <http://www.gnu.org/licenses/>.
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#
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#
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model hh_cond_exp_traub_neuron:
5172

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state:

models/neurons/hh_moto_5ht_neuron.nestml

+23-2
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@@ -18,8 +18,8 @@
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# https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=189786
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#
2020
# .. [2] Compartmental model of vertebrate motoneurons for Ca2+-dependent spiking and plateau potentials under pharmacological treatment.
21-
# Booth V, Rinzel J, Kiehn O.
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# http://refhub.elsevier.com/S0896-6273(16)00010-6/sref4
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# Booth V, Rinzel J, Kiehn O.
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# http://refhub.elsevier.com/S0896-6273(16)00010-6/sref4
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#
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# .. [3] Repository: https://github.com/research-team/hh-moto-5ht
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#
@@ -30,6 +30,27 @@
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# hh_psc_alpha
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#
3232
#
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# Copyright statement
34+
# +++++++++++++++++++
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#
36+
# This file is part of NEST.
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#
38+
# Copyright (C) 2004 The NEST Initiative
39+
#
40+
# NEST is free software: you can redistribute it and/or modify
41+
# it under the terms of the GNU General Public License as published by
42+
# the Free Software Foundation, either version 2 of the License, or
43+
# (at your option) any later version.
44+
#
45+
# NEST is distributed in the hope that it will be useful,
46+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
47+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
48+
# GNU General Public License for more details.
49+
#
50+
# You should have received a copy of the GNU General Public License
51+
# along with NEST. If not, see <http://www.gnu.org/licenses/>.
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#
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#
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model hh_moto_5ht_neuron:
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state:
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V_m mV = V_m_init # Membrane potential

models/neurons/hh_psc_alpha_neuron.nestml

+27-6
Original file line numberDiff line numberDiff line change
@@ -27,14 +27,14 @@
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# ++++++++++
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#
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# .. [1] Gerstner W, Kistler W (2002). Spiking neuron models: Single neurons,
30-
# populations, plasticity. New York: Cambridge University Press
30+
# populations, plasticity. New York: Cambridge University Press
3131
# .. [2] Dayan P, Abbott LF (2001). Theoretical neuroscience: Computational and
32-
# mathematical modeling of neural systems. Cambridge, MA: MIT Press.
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# https://pure.mpg.de/pubman/faces/ViewItemOverviewPage.jsp?itemId=item_3006127>
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# mathematical modeling of neural systems. Cambridge, MA: MIT Press.
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# https://pure.mpg.de/pubman/faces/ViewItemOverviewPage.jsp?itemId=item_3006127>
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# .. [3] Hodgkin AL and Huxley A F (1952). A quantitative description of
35-
# membrane current and its application to conduction and excitation in
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# nerve. The Journal of Physiology 117.
37-
# DOI: https://doi.org/10.1113/jphysiol.1952.sp004764
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# membrane current and its application to conduction and excitation in
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# nerve. The Journal of Physiology 117.
37+
# DOI: https://doi.org/10.1113/jphysiol.1952.sp004764
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#
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#
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# See also
@@ -43,6 +43,27 @@
4343
# hh_cond_exp_traub
4444
#
4545
#
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# Copyright statement
47+
# +++++++++++++++++++
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#
49+
# This file is part of NEST.
50+
#
51+
# Copyright (C) 2004 The NEST Initiative
52+
#
53+
# NEST is free software: you can redistribute it and/or modify
54+
# it under the terms of the GNU General Public License as published by
55+
# the Free Software Foundation, either version 2 of the License, or
56+
# (at your option) any later version.
57+
#
58+
# NEST is distributed in the hope that it will be useful,
59+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
60+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
61+
# GNU General Public License for more details.
62+
#
63+
# You should have received a copy of the GNU General Public License
64+
# along with NEST. If not, see <http://www.gnu.org/licenses/>.
65+
#
66+
#
4667
model hh_psc_alpha_neuron:
4768
state:
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V_m mV = V_m_init # Membrane potential

models/neurons/hill_tononi_neuron.nestml

+26-5
Original file line numberDiff line numberDiff line change
@@ -26,12 +26,33 @@
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# ++++++++++
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#
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# .. [1] Hill S, Tononi G (2005). Modeling sleep and wakefulness in the
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# thalamocortical system. Journal of Neurophysiology. 93:1671-1698.
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# DOI: https://doi.org/10.1152/jn.00915.2004
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# thalamocortical system. Journal of Neurophysiology. 93:1671-1698.
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# DOI: https://doi.org/10.1152/jn.00915.2004
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# .. [2] Vargas-Caballero M, Robinson HPC (2003). A slow fraction of Mg2+
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# unblock of NMDA receptors limits their contribution to spike generation
33-
# in cortical pyramidal neurons. Journal of Neurophysiology 89:2778-2783.
34-
# DOI: https://doi.org/10.1152/jn.01038.2002
32+
# unblock of NMDA receptors limits their contribution to spike generation
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# in cortical pyramidal neurons. Journal of Neurophysiology 89:2778-2783.
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# DOI: https://doi.org/10.1152/jn.01038.2002
35+
#
36+
#
37+
# Copyright statement
38+
# +++++++++++++++++++
39+
#
40+
# This file is part of NEST.
41+
#
42+
# Copyright (C) 2004 The NEST Initiative
43+
#
44+
# NEST is free software: you can redistribute it and/or modify
45+
# it under the terms of the GNU General Public License as published by
46+
# the Free Software Foundation, either version 2 of the License, or
47+
# (at your option) any later version.
48+
#
49+
# NEST is distributed in the hope that it will be useful,
50+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
51+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
52+
# GNU General Public License for more details.
53+
#
54+
# You should have received a copy of the GNU General Public License
55+
# along with NEST. If not, see <http://www.gnu.org/licenses/>.
3556
#
3657
#
3758
model hill_tononi_neuron:

models/neurons/iaf_chxk_2008_neuron.nestml

+27-5
Original file line numberDiff line numberDiff line change
@@ -14,17 +14,18 @@
1414
# follow alpha-function time courses as in the iaf_cond_alpha model.
1515
#
1616
# .. note ::
17-
# In the original Fortran implementation underlying [1]_, all previous AHP activation was discarded when a new spike
18-
# occurred, leading to reduced AHP currents in particular during periods of high spiking activity. Set ``ahp_bug`` to
19-
# ``true`` to obtain this behavior in the model.
17+
#
18+
# In the original Fortran implementation underlying [1]_, all previous AHP activation was discarded when a new spike
19+
# occurred, leading to reduced AHP currents in particular during periods of high spiking activity. Set ``ahp_bug`` to
20+
# ``true`` to obtain this behavior in the model.
2021
#
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#
2223
# References
2324
# ++++++++++
2425
#
2526
# .. [1] Casti A, Hayot F, Xiao Y, Kaplan E (2008) A simple model of retina-LGN
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# transmission. Journal of Computational Neuroscience 24:235-252.
27-
# DOI: https://doi.org/10.1007/s10827-007-0053-7
27+
# transmission. Journal of Computational Neuroscience 24:235-252.
28+
# DOI: https://doi.org/10.1007/s10827-007-0053-7
2829
#
2930
#
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# See also
@@ -33,6 +34,27 @@
3334
# iaf_cond_alpha
3435
#
3536
#
37+
# Copyright statement
38+
# +++++++++++++++++++
39+
#
40+
# This file is part of NEST.
41+
#
42+
# Copyright (C) 2004 The NEST Initiative
43+
#
44+
# NEST is free software: you can redistribute it and/or modify
45+
# it under the terms of the GNU General Public License as published by
46+
# the Free Software Foundation, either version 2 of the License, or
47+
# (at your option) any later version.
48+
#
49+
# NEST is distributed in the hope that it will be useful,
50+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
51+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
52+
# GNU General Public License for more details.
53+
#
54+
# You should have received a copy of the GNU General Public License
55+
# along with NEST. If not, see <http://www.gnu.org/licenses/>.
56+
#
57+
#
3658
model iaf_chxk_2008_neuron:
3759

3860
state:

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