- Timestamp:
- 12/20/11 12:22:03 (5 months ago)
- Location:
- trunk/src
- Files:
-
- 6 modified
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brian/standardmodels/cells.py (modified) (9 diffs)
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moose/standardmodels/cells.py (modified) (5 diffs)
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nest/standardmodels/cells.py (modified) (12 diffs)
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neuron/standardmodels/cells.py (modified) (11 diffs)
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nineml/cells.py (modified) (4 diffs)
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pcsim/standardmodels/cells.py (modified) (6 diffs)
Legend:
- Unmodified
- Added
- Removed
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trunk/src/brian/standardmodels/cells.py
r957 r1040 19 19 20 20 class IF_curr_alpha(cells.IF_curr_alpha): 21 """Leaky integrate and fire model with fixed threshold and alpha-function- 22 shaped post-synaptic current.""" 21 22 __doc__ = cells.IF_curr_alpha.__doc__ 23 23 24 translations = build_translations( 24 25 ('v_rest', 'v_rest', mV), … … 58 59 59 60 class IF_curr_exp(cells.IF_curr_exp): 60 """Leaky integrate and fire model with fixed threshold and 61 decaying-exponential post-synaptic current. (Separate synaptic currents for 62 excitatory and inhibitory synapses.""" 61 62 __doc__ = cells.IF_curr_exp.__doc__ 63 63 64 64 translations = build_translations( … … 99 99 100 100 class IF_cond_alpha(cells.IF_cond_alpha): 101 102 __doc__ = cells.IF_cond_alpha.__doc__ 103 101 104 translations = build_translations( 102 105 ('v_rest', 'v_rest', mV), … … 141 144 142 145 class IF_cond_exp(cells.IF_cond_exp): 143 """Leaky integrate and fire model with fixed threshold and 144 exponentially-decaying post-synaptic conductance.""" 146 147 __doc__ = cells.IF_cond_exp.__doc__ 148 145 149 translations = build_translations( 146 150 ('v_rest', 'v_rest', mV), … … 192 196 193 197 class SpikeSourcePoisson(cells.SpikeSourcePoisson): 194 """Spike source, generating spikes according to a Poisson process.""" 198 199 __doc__ = cells.SpikeSourcePoisson.__doc__ 200 195 201 translations = build_translations( 196 202 ('rate', 'rate'), … … 220 226 221 227 class SpikeSourceArray(cells.SpikeSourceArray): 222 """Spike source generating spikes at the times given in the spike_times array.""" 228 229 __doc__ = cells.SpikeSourceArray.__doc__ 230 223 231 translations = build_translations( 224 232 ('spike_times', 'spiketimes', ms), … … 236 244 237 245 class EIF_cond_alpha_isfa_ista(cells.EIF_cond_alpha_isfa_ista): 238 """ 239 Exponential integrate and fire neuron with spike triggered and 240 sub-threshold adaptation currents (isfa, ista reps.) according to: 241 242 Brette R and Gerstner W (2005) Adaptive Exponential Integrate-and-Fire Model 243 as an Effective Description of Neuronal Activity. J Neurophysiol 94:3637-3642 244 245 See also: IF_cond_exp_gsfa_grr, EIF_cond_exp_isfa_ista 246 """ 246 247 __doc__ = cells.EIF_cond_alpha_isfa_ista.__doc__ 247 248 248 249 translations = build_translations( … … 302 303 303 304 class EIF_cond_exp_isfa_ista(cells.EIF_cond_exp_isfa_ista): 304 """ 305 Exponential integrate and fire neuron with spike triggered and 306 sub-threshold adaptation currents (isfa, ista reps.) according to: 307 308 Brette R and Gerstner W (2005) Adaptive Exponential Integrate-and-Fire Model 309 as an Effective Description of Neuronal Activity. J Neurophysiol 94:3637-3642 310 311 See also: IF_cond_exp_gsfa_grr, EIF_cond_exp_isfa_ista 312 """ 305 306 __doc__ = cells.EIF_cond_exp_isfa_ista.__doc__ 313 307 314 308 translations = build_translations( … … 367 361 368 362 class HH_cond_exp(cells.HH_cond_exp): 363 364 __doc__ = cells.HH_cond_exp.__doc__ 369 365 370 366 translations = build_translations( -
trunk/src/moose/standardmodels/cells.py
r957 r1040 14 14 15 15 class IF_cond_exp(cells.IF_cond_exp): 16 """Leaky integrate and fire model with fixed threshold and17 exponentially-decaying post-synaptic conductance."""16 17 __doc__ = cells.IF_cond_exp.__doc__ 18 18 19 19 translations = build_translations( … … 41 41 """Leaky integrate and fire model with fixed threshold and alpha-function- 42 42 shaped post-synaptic conductance.""" 43 43 44 __doc__ = cells.IF_cond_alpha.__doc__ 45 44 46 translations = IF_cond_exp.translations 45 47 model = StandardIF … … 51 53 52 54 class HH_cond_exp(cells.HH_cond_exp): 53 """Single compartment cell with an Na channel and a K channel""" 55 56 __doc__ = cells.HH_cond_exp.__doc__ 57 54 58 translations = build_translations( 55 59 ('gbar_Na', 'GbarNa', 1e-9), … … 72 76 73 77 class SpikeSourcePoisson(cells.SpikeSourcePoisson): 74 """Spike source, generating spikes according to a Poisson process.""" 78 79 __doc__ = cells.SpikeSourcePoisson.__doc__ 75 80 76 81 translations = build_translations( … … 83 88 84 89 class SpikeSourceArray(cells.SpikeSourceArray): 85 """Spike source generating spikes at the times given in the spike_times array.""" 90 91 __doc__ = cells.SpikeSourceArray.__doc__ 86 92 87 93 translations = build_translations( -
trunk/src/nest/standardmodels/cells.py
r957 r1040 11 11 12 12 class IF_curr_alpha(cells.IF_curr_alpha): 13 """ 14 Leaky integrate and fire model with fixed threshold and alpha-function- 15 shaped post-synaptic current. 16 """ 13 14 __doc__ = cells.IF_curr_alpha.__doc__ 17 15 18 16 translations = build_translations( … … 33 31 34 32 class IF_curr_exp(cells.IF_curr_exp): 35 """ 36 Leaky integrate and fire model with fixed threshold and 37 decaying-exponential post-synaptic current. (Separate synaptic currents for 38 excitatory and inhibitory synapses. 39 """ 33 34 __doc__ = cells.IF_curr_exp.__doc__ 40 35 41 36 translations = build_translations( … … 56 51 57 52 class IF_cond_alpha(cells.IF_cond_alpha): 58 """ 59 Leaky integrate and fire model with fixed threshold and alpha-function- 60 shaped post-synaptic conductance. 61 """ 53 54 __doc__ = cells.IF_cond_alpha.__doc__ 62 55 63 56 translations = build_translations( … … 80 73 81 74 class IF_cond_exp(cells.IF_cond_exp): 82 """ 83 Leaky integrate and fire model with fixed threshold and 84 exponentially-decaying post-synaptic conductance. 85 """ 75 76 __doc__ = cells.IF_cond_exp.__doc__ 86 77 87 78 translations = build_translations( … … 104 95 105 96 class IF_cond_exp_gsfa_grr(cells.IF_cond_exp_gsfa_grr): 106 """ 107 Linear leaky integrate and fire model with fixed threshold, 108 decaying-exponential post-synaptic conductance, conductance based 109 spike-frequency adaptation, and a conductance-based relative refractory 110 mechanism. 111 112 See: Muller et al (2007) Spike-frequency adapting neural ensembles: Beyond 113 mean-adaptation and renewal theories. Neural Computation 19: 2958-3010. 114 115 See also: EIF_cond_alpha_isfa_ista 116 """ 97 98 __doc__ = cells.IF_cond_exp_gsfa_grr.__doc__ 99 117 100 translations = build_translations( 118 101 ('v_rest', 'E_L'), … … 140 123 141 124 class IF_facets_hardware1(cells.IF_facets_hardware1): 142 """ 143 Leaky integrate and fire model with conductance-based synapses and fixed 144 threshold as it is resembled by the FACETS Hardware Stage 1. For further 145 details regarding the hardware model see the FACETS-internal Wiki: 146 https://facets.kip.uni-heidelberg.de/private/wiki/index.php/WP7_NNM 147 """ 125 126 __doc__ = cells.IF_facets_hardware1.__doc__ 127 148 128 # in 'iaf_cond_exp', the dimension of C_m is pF, 149 129 # while in the pyNN context, cm is given in nF … … 169 149 170 150 class HH_cond_exp(cells.HH_cond_exp): 171 """Single-compartment Hodgkin-Huxley model.""" 151 152 __doc__ = cells.HH_cond_exp.__doc__ 172 153 173 154 translations = build_translations( … … 192 173 193 174 class EIF_cond_alpha_isfa_ista(cells.EIF_cond_alpha_isfa_ista): 194 """ 195 Exponential integrate and fire neuron with spike triggered and sub-threshold 196 adaptation currents (isfa, ista reps.) according to: 197 198 Brette R and Gerstner W (2005) Adaptive Exponential Integrate-and-Fire Model as 199 an Effective Description of Neuronal Activity. J Neurophysiol 94:3637-3642 200 201 See also: IF_cond_exp_gsfa_grr 202 """ 175 176 __doc__ = cells.EIF_cond_alpha_isfa_ista.__doc__ 203 177 204 178 translations = build_translations( … … 226 200 227 201 class SpikeSourcePoisson(cells.SpikeSourcePoisson): 228 """Spike source, generating spikes according to a Poisson process.""" 202 203 __doc__ = cells.SpikeSourcePoisson.__doc__ 229 204 230 205 translations = build_translations( … … 244 219 245 220 class SpikeSourceInhGamma(cells.SpikeSourceInhGamma): 246 """ 247 Spike source, generating realizations of an inhomogeneous gamma process, 248 employing the thinning method. 249 250 See: Muller et al (2007) Spike-frequency adapting neural ensembles: Beyond 251 mean-adaptation and renewal theories. Neural Computation 19: 2958-3010. 252 """ 221 222 __doc__ = cells.SpikeSourceInhGamma.__doc__ 253 223 254 224 translations = build_translations( … … 269 239 270 240 class SpikeSourceArray(cells.SpikeSourceArray): 271 """Spike source generating spikes at the times given in the spike_times array.""" 241 242 __doc__ = cells.SpikeSourceArray.__doc__ 272 243 273 244 translations = build_translations( … … 279 250 280 251 class EIF_cond_exp_isfa_ista(cells.EIF_cond_exp_isfa_ista): 281 """ 282 Exponential integrate and fire neuron with spike triggered and sub-threshold 283 adaptation currents (isfa, ista reps.) according to: 284 285 Brette R and Gerstner W (2005) Adaptive Exponential Integrate-and-Fire Model as 286 an Effective Description of Neuronal Activity. J Neurophysiol 94:3637-3642 287 288 See also: IF_cond_exp_gsfa_grr 289 """ 252 253 __doc__ = cells.EIF_cond_exp_isfa_ista.__doc__ 290 254 291 255 translations = build_translations( -
trunk/src/neuron/standardmodels/cells.py
r957 r1040 19 19 20 20 class IF_curr_alpha(cells.IF_curr_alpha): 21 """Leaky integrate and fire model with fixed threshold and alpha-function-22 shaped post-synaptic current."""21 22 __doc__ = cells.IF_curr_alpha.__doc__ 23 23 24 24 translations = build_translations( … … 42 42 43 43 class IF_curr_exp(cells.IF_curr_exp): 44 """Leaky integrate and fire model with fixed threshold and 45 decaying-exponential post-synaptic current. (Separate synaptic currents for 46 excitatory and inhibitory synapses.""" 44 45 __doc__ = cells.IF_curr_exp.__doc__ 47 46 48 47 translations = build_translations( … … 66 65 67 66 class IF_cond_alpha(cells.IF_cond_alpha): 68 """Leaky integrate and fire model with fixed threshold and alpha-function-69 shaped post-synaptic conductance."""67 68 __doc__ = cells.IF_cond_alpha.__doc__ 70 69 71 70 translations = build_translations( … … 92 91 93 92 class IF_cond_exp(cells.IF_cond_exp): 94 """Leaky integrate and fire model with fixed threshold and95 exponentially-decaying post-synaptic conductance."""93 94 __doc__ = cells.IF_cond_exp.__doc__ 96 95 97 96 translations = build_translations( … … 118 117 119 118 class IF_facets_hardware1(cells.IF_facets_hardware1): 120 """Leaky integrate and fire model with conductance-based synapses and fixed 121 threshold as it is resembled by the FACETS Hardware Stage 1. For further 122 details regarding the hardware model see the FACETS-internal Wiki: 123 https://facets.kip.uni-heidelberg.de/private/wiki/index.php/WP7_NNM 124 """ 119 120 __doc__ = cells.IF_facets_hardware1.__doc__ 125 121 126 122 translations = build_translations( … … 147 143 class HH_cond_exp(cells.HH_cond_exp): 148 144 145 __doc__ = cells.HH_cond_exp.__doc__ 146 149 147 translations = build_translations( 150 148 ('gbar_Na', 'gbar_Na', 1e-3), # uS -> mS … … 172 170 173 171 class IF_cond_exp_gsfa_grr(cells.IF_cond_exp_gsfa_grr): 174 """ 175 Linear leaky integrate and fire model with fixed threshold, 176 decaying-exponential post-synaptic conductance, conductance based 177 spike-frequency adaptation, and a conductance-based relative refractory 178 mechanism. 179 180 See: Muller et al (2007) Spike-frequency adapting neural ensembles: Beyond 181 mean-adaptation and renewal theories. Neural Computation 19: 2958-3010. 182 183 See also: EIF_cond_alpha_isfa_ista 184 """ 172 173 __doc__ = cells.IF_cond_exp_gsfa_grr.__doc__ 174 185 175 translations = build_translations( 186 176 ('v_rest', 'v_reset'), … … 213 203 214 204 class SpikeSourcePoisson(cells.SpikeSourcePoisson): 215 """Spike source, generating spikes according to a Poisson process.""" 205 206 __doc__ = cells.SpikeSourcePoisson.__doc__ 216 207 217 208 translations = build_translations( … … 224 215 225 216 class SpikeSourceArray(cells.SpikeSourceArray): 226 """Spike source generating spikes at the times given in the spike_times array.""" 217 218 __doc__ = cells.SpikeSourceArray.__doc__ 227 219 228 220 translations = build_translations( … … 233 225 234 226 class EIF_cond_alpha_isfa_ista(cells.EIF_cond_alpha_isfa_ista): 235 """ 236 Exponential integrate and fire neuron with spike triggered and sub-threshold 237 adaptation currents (isfa, ista reps.) according to: 238 239 Brette R and Gerstner W (2005) Adaptive Exponential Integrate-and-Fire Model as 240 an Effective Description of Neuronal Activity. J Neurophysiol 94:3637-3642 241 242 See also: IF_cond_exp_gsfa_grr 243 """ 227 228 __doc__ = cells.EIF_cond_alpha_isfa_ista.__doc__ 244 229 245 230 translations = build_translations( … … 269 254 270 255 class EIF_cond_exp_isfa_ista(cells.EIF_cond_exp_isfa_ista): 271 """Like EIF_cond_alpha_isfa_ista, but with single-exponential synapses.""" 256 257 __doc__ = cells.EIF_cond_exp_isfa_ista.__doc__ 272 258 273 259 translations = EIF_cond_alpha_isfa_ista.translations -
trunk/src/nineml/cells.py
r1010 r1040 59 59 60 60 class IF_curr_exp(cells.IF_curr_exp, CellTypeMixin): 61 """Leaky integrate and fire model with fixed threshold and 62 decaying-exponential post-synaptic current. (Separate synaptic currents for 63 excitatory and inhibitory synapses.""" 61 62 __doc__ = cells.IF_curr_exp.__doc__ 64 63 65 64 translations = standardmodels.build_translations( … … 90 89 class IF_cond_exp(cells.IF_cond_exp, CellTypeMixin): 91 90 91 __doc__ = cells.IF_cond_exp.__doc__ 92 92 93 translations = standardmodels.build_translations( 93 94 ('tau_m', 'membraneTimeConstant'), … … 118 119 119 120 class IF_cond_alpha(cells.IF_cond_exp, CellTypeMixin): 121 122 __doc__ = cells.IF_cond_alpha.__doc__ 120 123 121 124 translations = standardmodels.build_translations( … … 147 150 148 151 class SpikeSourcePoisson(cells.SpikeSourcePoisson, CellTypeMixin): 152 153 __doc__ = cells.SpikeSourcePoisson.__doc__ 149 154 150 155 translations = standardmodels.build_translations( -
trunk/src/pcsim/standardmodels/cells.py
r957 r1040 17 17 18 18 class IF_curr_alpha(cells.IF_curr_alpha): 19 """Leaky integrate and fire model with fixed threshold and alpha-function-20 shaped post-synaptic current."""19 20 __doc__ = cells.IF_curr_alpha.__doc__ 21 21 22 22 translations = build_translations( … … 42 42 43 43 class IF_curr_exp(cells.IF_curr_exp): 44 """Leaky integrate and fire model with fixed threshold and 45 decaying-exponential post-synaptic current. (Separate synaptic currents for 46 excitatory and inhibitory synapses.""" 44 45 __doc__ = cells.IF_curr_exp.__doc__ 47 46 48 47 translations = build_translations( … … 68 67 69 68 class IF_cond_alpha(cells.IF_cond_alpha): 70 """Leaky integrate and fire model with fixed threshold and alpha-function-71 shaped post-synaptic conductance."""69 70 __doc__ = cells.IF_cond_alpha.__doc__ 72 71 73 72 translations = build_translations( … … 96 95 97 96 class IF_cond_exp(cells.IF_cond_exp): 98 """Leaky integrate and fire model with fixed threshold and99 exponentially-decaying post-synaptic conductance."""97 98 __doc__ = cells.IF_cond_exp.__doc__ 100 99 101 100 translations = build_translations( … … 125 124 """ Implemented not tested """ 126 125 class SpikeSourcePoisson(cells.SpikeSourcePoisson): 127 """Spike source, generating spikes according to a Poisson process.""" 126 127 __doc__ = cells.SpikeSourcePoisson.__doc__ 128 128 129 129 translations = build_translations( … … 164 164 165 165 class SpikeSourceArray(cells.SpikeSourceArray): 166 """Spike source generating spikes at the times given in the spike_times array.""" 166 167 __doc__ = cells.SpikeSourceArray.__doc__ 168 167 169 translations = build_translations( 168 170 ('spike_times', 'spikeTimes'), # 1e-3),
