001: #!/usr/bin/perl -w
002: #!/usr/bin/perl -d:ptkdb -w
003: #
004: ##
005: ## Heccer : a compartmental solver that implements efficient Crank-Nicolson
006: ## integration for neuronal models.
007: ##
008:
009: ##############################################################################
010: ##'
011: ##' Heccer : testbed C implementation
012: ##'
013: ##' Copyright (C) 2006-2007 Hugo Cornelis
014: ##'
015: ##' functional ideas .. Hugo Cornelis, hugo.cornelis@gmail.com
016: ##'
017: ##' coding ............ Hugo Cornelis, hugo.cornelis@gmail.com
018: ##'
019: ##############################################################################
020:
021:
022: use strict;
023:
024:
025: BEGIN
026: {
027: # during tests
028:
029: push @INC, '../glue/swig/perl';
030:
031: # during distcheck
032:
033: push @INC, '../../glue/swig/perl';
034:
035: # after installation
036:
037: push @INC, '/usr/local/glue/swig/perl';
038: }
039:
040:
041: BEGIN
042: {
043: # for main during tests
044:
045: push @INC, './glue/swig/perl';
046:
047: # for main during distcheck
048:
049: push @INC, '../../tests/glue/swig/perl';
050: }
051:
052:
053: use Heccer;
054:
055:
056: # initialize compartments
057:
058: my $compartments
059: = [
060: Heccer::Compartment->new
061: (
062: {
063: dCm => 5.755329373e-12,
064: dEm => -0.08,
065: dInitVm => -0.068,
066: dInject => 0,
067: dRa => 772813.4375,
068: dRm => 8.548598272e9,
069: },
070: ),
071: ];
072:
073: my $channel_cat
074: = Heccer::ChannelActivationInactivation->new
075: (
076: {
077: dReversalPotential => 0.14702148735523224,
078: dMaximalConductance => 1.7546722963501793e-09,
079: iPool => 1,
080: activation => {
081: iPower => 1,
082: gate_concept => {
083: dInitActivation => 0.03891870645,
084: parameters => {
085: forward => {
086: dMultiplier => 2.6e3,
087: dMembraneDependence => 0.0,
088: iNominator => -1.0,
089: dDeNominatorOffset => 1.0,
090: dMembraneOffset => 0.021,
091: dTauDenormalizer => -8e-3,
092: },
093: backward => {
094: dMultiplier => 0.18e3,
095: dMembraneDependence => 0.0,
096: iNominator => -1.0,
097: dDeNominatorOffset => 1.0,
098: dMembraneOffset => 0.04,
099: dTauDenormalizer => 4e-3,
100: },
101: },
102: },
103: },
104: inactivation => {
105: iPower => 1,
106: gate_concept => {
107: dInitActivation => 0.08260212813,
108: parameters => {
109: forward => {
110: dMultiplier => 0.0025e3,
111: dMembraneDependence => 0.0,
112: iNominator => -1.0,
113: dDeNominatorOffset => 1.0,
114: dMembraneOffset => 0.04,
115: dTauDenormalizer => 8e-3,
116: },
117: backward => {
118: dMultiplier => 0.19e3,
119: dMembraneDependence => 0.0,
120: iNominator => -1.0,
121: dDeNominatorOffset => 1.0,
122: dMembraneOffset => 0.05,
123: dTauDenormalizer => -10.0e-3,
124: },
125: },
126: },
127: },
128: },
129: );
130:
131: my $pool
132: = Heccer::ExponentialDecay->new
133: (
134: {
135: dInitValue => 4e-5,
136: dBeta => 7.579027046e+10,
137: dSteadyState => 4e-05,
138: dTau => 0.00010,
139: piExternal => [
140: 2,
141: ],
142: },
143: );
144:
145: my $channel_kc
146: = Heccer::ChannelActivationConcentration->new
147: (
148: {
149: dReversalPotential => 85,
150: dMaximalConductance => 2.80747571e-07,
151: activation => {
152: iPower => 1,
153: gate_concept => {
154: dInitActivation => 0.063531859768213905,
155: parameters => {
156: forward => {
157: dMultiplier => 7.5e3,
158: dMembraneDependence => 0.0,
159: iNominator => -1.0,
160: dDeNominatorOffset => 0.0,
161: dMembraneOffset => 0.0,
162: dTauDenormalizer => 1e12,
163: },
164: backward => {
165: dMultiplier => 0.11e3,
166: dMembraneDependence => 0.0,
167: iNominator => -1.0,
168: dDeNominatorOffset => 0.0,
169: dMembraneOffset => -0.035,
170: dTauDenormalizer => 14.9e-3,
171: },
172: },
173: },
174: },
175: powered_activator => {
176: iPower => 2,
177: activator => {
178: dInitActivation => 0.0099009900989999993,
179: iActivator => 1,
180: parameters => {
181: dBasalLevel => 4.0e-3,
182: dTau => 0.010,
183: },
184: },
185: },
186: },
187: );
188:
189: # initialize the math component array
190:
191: my $math_components
192: = [
193: $channel_kc,
194: $pool,
195: $channel_cat,
196: ];
197:
198: # initialize intermediary
199:
200: our $intermediary
201: = Heccer::Intermediary->new
202: (
203: {
204: comp2mech => [ 3, -1],
205: compartments => $compartments,
206: iCompartments => 1,
207: math_components => $math_components,
208: },
209: );
210:
211:
212: our $config
213: = {
214: settings => {
215: reporting_granularity => 100,
216: steps => 1000,
217: tested_things => (
218: $SwiggableHeccer::HECCER_DUMP_VM_COMPARTMENT_MATRIX
219: | $SwiggableHeccer::HECCER_DUMP_VM_COMPARTMENT_DATA
220: | $SwiggableHeccer::HECCER_DUMP_VM_COMPARTMENT_OPERATIONS
221: | $SwiggableHeccer::HECCER_DUMP_VM_CHANNEL_POOL_FLUXES
222: | $SwiggableHeccer::HECCER_DUMP_VM_MECHANISM_DATA
223: | $SwiggableHeccer::HECCER_DUMP_VM_MECHANISM_OPERATIONS
224: | $SwiggableHeccer::HECCER_DUMP_VM_SUMMARY
225: ),
226: time_step => (1e-6),
227: },
228: };
229:
230:
231: require 'main';
232:
233: