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nemo @ 25872

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1	[[tags:egg]]
2
3	== nemo
4
5	An implementation of a description language for computational models of ion channels.
6
7	[[toc:]]
8
9	== Usage
10
11	nemo [options...] [input files ...]
12
13	== Documentation
14
15
16	{{NEMO}} is a program that reads an ion channel description and
17	generates corresponding model simulation code in
18	[[http://www.gnu.org/software/octave/\|GNU Octave]] or the
19	[[http://www.neuron.yale.edu/neuron/docs/help/neuron/nmodl/nmodl.html\|NMODL]]
20	language used by the [[http://www.neuron.yale.edu/neuron/\|NEURON
21	simulator]].
22
23	=== Options
24
25	; {{-i FORMAT}} : specify input format (nemo, xml, sxml, s-exp)
26	; {{--xml[=FILE]}} : write XML output to file (default: <model-name>.xml)
27	; {{--sxml[=FILE]}} : write SXML output to file (default: <model-name>.sxml)
28	; {{--nmodl[=FILE]}} : write NMODL output to file (default: <model-name>.mod)
29	; {{--nmodl-method=METHOD}} : specify NMODL integration method (cnexp, derivimplicit, cvode)
30	; {{--nmodl-kinetic=[STATES]}} : use NMODL kinetic equations for the given reactions
31	; {{--nmodl-depend=VARS}} : specify DEPEND variables for NMODL interpolation tables
32	; {{--octave[=FILE]}} : write Octave output to file (default: <model-name>.m)
33	; {{--matlab[=FILE]}} : write Matlab output to file (default: <model-name>.m)
34	; {{--vclamp-octave[=FILE]}} : write Octave voltage clamp script to file (default: <model-name>_vclamp.m)
35	; {{--vclamp-hoc[=FILE]}} : write HOC voltage clamp script to file (default: <model-name>.ses)
36	; {{-t}} : use interpolation tables in generated code
37	; {{-h, --help}} : print help
38
39
40	=== Model description language
41
42
43	The following constructs comprise the model description language:
44
45
46	; '''{{MODEL}}'''{{ ::= }} ( '''{{INPUT }}''' {''ID''}{{ \| }}( {''ID''} ['''{{AS }}'''{''LOCAL-ID''}] ['''{{FROM }}'''{''NAMESPACE''}] ) ... ) : Declares one or several imported quantities. If the optional '''{{AS}}''' parameter is given, then the quantity is imported as {''LOCAL-ID''}. If the optional '''{{FROM}}''' parameter is given, then the quantity is imported from namespace {''NAMESPACE''}.
47	; {{ \| }}( '''{{OUTPUT}}''' {''ID''} ) : Declares that an existing quantity be exported.
48	; {{ \| }}( '''{{CONST}}''' {''ID''} = {''EXPR''} ) : Declares a constant quantity (its value will be computed at declaration time).
49	; {{ \| }}( '''{{DEFUN}}''' {''ID''} ( {''ARG-ID''} ... ) {''EXPR''} ) : Declares a function (a parameterized expression with no free variables).
50	; {{ \| }}( {''ID''} = {''EXPR''} ) : Declares an assigned quantity (an expression that can refer to other quantities in the system).
51	; {{ \| }}( '''{{REACTION}}''' {''ID''} {''TRANSITIONS''} {''INITIAL-EXPR''} {''OPEN-ID''} ) : Declares a reaction quantity. See below for the syntax of state transition equations. {''INITIAL-EXPR''} is an expression that computes the initial value. {''OPEN-ID''} is the name of the open state. It must be one of the states defined by the transition equations.
52	; {{ \| }}( '''{{COMPONENT}}''' ( '''{{TYPE}}''' {''ID''} ) ( '''{{NAME}}''' {''ID''} ) {''ELEMENTS''} ) : Declares a system component (a quantity that can contain other quantities).
53
54
55
56	==== Expressions
57
58
59	Expressions in the model description language are defined as:
60
61
62	; '''{{EXPR}}'''{{ ::= }} {''NUM''} : A numeric constant.
63	; {{ \| }}{''ID''} : A variable name.
64	; {{ \| }}( {''ID''} ( {''EXPR''} ... ) ) : A function invocation.
65	; {{ \| }}( {''EXPR''} {''OP''} {''EXPR''} ) : Arithmetic operator invocation. The following operators are supported: {{+ - / * > < <= >= ^}}
66	; {{ \| }}( '''{{LET}}''' ( {''BINDINGS''} ) {''EXPR''} ) : Local variables declaration. Each element in {''BINDINGS''} is of the form: ( {''ID''} {''EXPR''} )
67	; {{ \| }}( '''{{IF}}''' {''CONDITION''} '''{{THEN}}''' {''EXPR''} '''{{ELSE}}''' {''EXPR''} ) : Conditional expression. The expression after '''{{IF}}''' must be a comparison expression.
68
69
70
71	==== State transition equations
72
73
74	State transition equations in the model description language are defined as:
75
76
77	; '''{{TRANSITION}}'''{{ ::= }} ( '''{{->}}''' {''SRC-ID''} {''DEST-ID''} {''EXPR''} ) : Declares that a transition occurs from state {''SRC-ID''} to state {''DEST-ID''} at rate computed by {''EXPR''}.
78	; {{ \| }}( '''{{<->}}''' {''SRC-ID''} {''DEST-ID''} {''EXPR-1''} {''EXPR-2''} ) : Declares that a transition occurs from state {''SRC-ID''} to state {''DEST-ID''} and vice versa, at rates computed by {''EXPR-1''} and {''EXPR-2''}.
79
80
81
82	==== Ion channel definitions
83
84
85	Currently, the {{NMODL}} code generator recognizes and generates code for ion channel components that are defined as follows:
86
87
88	; '''({{COMPONENT (TYPE gate-complex) (NAME {NAME})}}''' ( '''{{COMPONENT}}''' ( '''{{TYPE}}''' gate ) ... ) : One or more gate definitions. Each component of type gate must export the reactions that characterize the gate dynamics.
89	; ( '''{{COMPONENT}}''' ( '''{{TYPE}}''' pore ) ... ) : Conductance law definition. This component must export a constant maximal conductance, or an assigned quantity whose equation represents the conductance law used.
90	; [( '''{{COMPONENT}}''' ( '''{{TYPE}}''' permeating-ion ) ... )]
91	; [( '''{{COMPONENT}}''' ( '''{{TYPE}}''' accumulating-substance ) ... )]
92	; ''')'''
93
94	==== Hodgkin-Huxley ionic conductance extension
95
96
97	The Hodgkin-Huxley ionic conductance extension is a shortcut that declares a reaction corresponding to the Hodgkin-Huxley formulation of ion channel dynamics.
98
99
100	; '''({{HH-IONIC-GATE}}''' : ( {''ION-NAME''} : Ion name: exported variables will be of the form {{{ion}_{id}}}.
101	; ( '''{{M-POWER}}''' {''INTEGER''} ) : Power of state variable {{M}}.
102	; ( '''{{H-POWER}}''' {''INTEGER''} ) : Power of state variable {{H}}. If zero, the initial value and equations for this variable can be omitted.
103	; ( '''{{INITIAL-M}}''' {''EXPR''} ) : Expression that computes initial value for state variable {{M}}.
104	; ( '''{{INITIAL-H}}''' {''EXPR''} ) : Expression that computes initial value for state variable {{H}}.
105	; ( '''{{M-ALPHA}}''' {''EXPR''} ) : Closed state to open state rate expression for state variable {{M}}.
106	; ( '''{{M-BETA}}''' {''EXPR''} ) : Open state to closed state rate expression for state variable {{M}}.
107	; ( '''{{H-ALPHA}}''' {''EXPR''} ) : Closed state to open state rate expression for state variable {{H}}.
108	; ( '''{{H-BETA}}''' {''EXPR''} ) : Open state to closed state rate expression for state variable {{H}}.
109	; ( '''{{M-INF}}''' {''EXPR''} ) : Steady state expression for variable {{M}}.
110	; ( '''{{M-TAU}}''' {''EXPR''} ) : Time constant expression for variable {{M}}.
111	; ( '''{{H-INF}}''' {''EXPR''} ) : Steady state expression for variable {{H}}.
112	; ( '''{{H-TAU}}''' {''EXPR''} ) : Time constant expression for variable {{H}}.
113	; )
114	; )
115
116	== Examples
117
118
119
120	;; Cerebellar Purkinje Cell: resurgent Na current and high frequency
121	;; firing (Khaliq et al 2003).
122
123	(nemo-model Khaliq03
124
125	((input v
126	(cai from ion-pools)
127	(ica from ion-currents))
128
129	(const ena = 60)
130	(const ek = -88)
131	(const ca0 = 1e-4)
132
133	(component (type gate-complex) (name CaBK)
134	;: BK-type Purkinje calcium-activated potassium current
135
136	(component (type gate)
137
138	;; constants
139	(const CaBK_ztau = 1.0)
140
141
142	;; rate functions
143
144	(CaBK_v = (v + 5))
145
146	(CaBK_minf =
147	(let ((vh -28.9)
148	(k 6.2))
149	(1.0 / (1.0 + exp (neg ((CaBK_v - vh) / k))))))
150
151	(CaBK_mtau =
152	(let
153	((y0 0.000505)
154	(vh1 -33.3)
155	(k1 -10.0)
156	(vh2 86.4)
157	(k2 10.1))
158	((1e3) * (y0 + 1 / (exp ((CaBK_v + vh1) / k1) +
159	exp ((CaBK_v + vh2) / k2))))))
160
161	(CaBK_hinf =
162	(let ((y0 0.085)
163	(vh -32.0)
164	(k 5.8))
165	(y0 + (1 - y0) / (1 + exp ((CaBK_v - vh) / k)))))
166
167
168	(CaBK_htau =
169	(let ((y0 0.0019)
170	(vh1 -54.2)
171	(k1 -12.9)
172	(vh2 48.5)
173	(k2 5.2))
174	((1e3) * (y0 + 1 / (exp ((CaBK_v + vh1) / k1) + exp ((CaBK_v + vh2) / k2))))))
175
176
177	(CaBK_zinf =
178	(let ((k 0.001))
179	(1 / (1 + (k / cai)))))
180
181	(CaBK_z_alpha = (CaBK_zinf / CaBK_ztau))
182	(CaBK_z_beta = ((1 - CaBK_zinf) / CaBK_ztau))
183
184	(reaction
185	(CaBK_z
186	(transitions (<-> O C CaBK_z_alpha CaBK_z_beta))
187	(conserve (1 = (O + C)))
188	(initial (let ((k 0.001))
189	(1 / (1 + k / ca0))))
190	(open O) (power 2)))
191
192	(output CaBK_z )
193
194
195	(hh-ionic-gate
196	(CaBK ;; ion name: exported variables will be of the form {ion}_{id}
197	(initial-m (CaBK_minf))
198	(initial-h (CaBK_hinf))
199	(m-power 3)
200	(h-power 1)
201	(m-inf (CaBK_minf))
202	(m-tau (CaBK_mtau))
203	(h-inf (CaBK_hinf))
204	(h-tau (CaBK_htau))))
205
206	)
207
208	(component (type pore)
209	(const gbar_CaBK = 0.007)
210	(output gbar_CaBK ))
211
212	(component (type permeating-ion) (name k)
213	(const e_CaBK = ek)
214	(output e_CaBK ))
215
216	) ;; end BK current
217
218
219	(component (type gate-complex) (name CaP)
220	;; HH P-type Calcium current
221
222	(component (type gate)
223
224
225	;; rate functions
226	(CaP_inf =
227	(let ((cv -19) (ck 5.5))
228	(1.0 / (1.0 + exp (neg ((v - cv) / ck))))))
229
230	(CaP_tau =
231	((1e3) *
232	(if (v > -50)
233	then (0.000191 + (0.00376 * exp (neg (((v + 41.9) / 27.8) ^ 2))))
234	else (0.00026367 + (0.1278 * exp (0.10327 * v))))))
235
236
237	(hh-ionic-gate
238	(CaP ;; ion name: exported variables will be of the form {ion}_{id}
239	(initial-m (CaP_inf))
240	(m-power 1)
241	(h-power 0)
242	(m-inf CaP_inf)
243	(m-tau CaP_tau)))
244
245	)
246
247	(component (type permeability)
248
249	(defun ghk (v ci co)
250	(let ((F 9.6485e4)
251	(R 8.3145)
252	(T (22 + 273.19))
253	(Z 2)
254	(E ((1e-3) * v)))
255	(let ((k0 ((Z * F * E) / (R * T))))
256	(let ((k1 (exp (neg(k0))))
257	(k2 (((Z ^ 2) * (E * (F ^ 2))) / (R * T))))
258	(1e-6) * (if (abs (1 - k1) < 1e-6)
259	then (Z * F * (ci - (co * k1)) * (1 - k0))
260	else (k2 * (ci - (co * k1)) / (1 - k1)))))))
261
262	(const pcabar_CaP = 0.00005)
263	(const cao = 2.4)
264	(pca_CaP = (pcabar_CaP * ghk (v cai cao)))
265	(output pca_CaP ))
266
267	(component (type permeating-ion) (name ca) )
268
269
270	) ;; end CaP current
271
272	(component (type gate-complex) (name K1)
273	;; HH TEA-sensitive Purkinje potassium current
274
275	(component (type gate)
276
277	;; constants
278
279	;; rate functions
280
281	(K1_v = (v + 11)) ;; account for junction potential
282
283	(K1_minf =
284	(let ((mivh -24)
285	(mik 15.4))
286	(1 / (1 + exp (neg (K1_v - mivh) / mik)))))
287
288
289	(K1_mtau =
290	(let ((mty0 0.00012851)
291	(mtvh1 100.7)
292	(mtk1 12.9)
293	(mtvh2 -56.0)
294	(mtk2 -23.1))
295	(1e3 * (if (K1_v < -35)
296	then (3.0 * (3.4225e-5 + 0.00498 * exp (neg (K1_v) / -28.29)))
297	else (mty0 + 1.0 / (exp ((K1_v + mtvh1) / mtk1) + exp ((K1_v + mtvh2) / mtk2)))
298	))))
299
300	(K1_hinf =
301	(let ((hiy0 0.31)
302	(hiA 0.78)
303	(hivh -5.802)
304	(hik 11.2))
305	(hiy0 + hiA / (1 + exp ((K1_v - hivh) / hik)))))
306
307
308	(K1_htau =
309	(1e3 * (if ( K1_v > 0 )
310	then (0.0012 + 0.0023 * exp (-0.141 * K1_v))
311	else (1.2202e-05 + 0.012 * exp (neg (((K1_v - (-56.3)) / 49.6) ^ 2))))))
312
313	(hh-ionic-gate
314	(K1 ;; ion name: exported variables will be of the form {ion}_{id}
315	(initial-m (K1_minf))
316	(initial-h (K1_hinf))
317	(m-power 3)
318	(h-power 1)
319	(m-inf (K1_minf))
320	(m-tau (K1_mtau))
321	(h-inf (K1_hinf))
322	(h-tau (K1_htau))))
323
324	)
325
326	(component (type pore)
327	(const gbar_K1 = 0.004)
328	(output gbar_K1 ))
329
330	(component (type permeating-ion) (name k)
331	(const e_K1 = ek)
332	(output e_K1 ))
333
334	) ;; end K1 current
335
336	(component (type gate-complex) (name K2)
337	;; HH Low TEA-sensitive Purkinje potassium current
338
339	(component (type gate)
340
341	;; constants
342
343	;; rate functions
344
345	(K2_v = (v + 11)) ;; account for junction potential
346
347	(K2_minf =
348	(let ((mivh -24)
349	(mik 20.4))
350	(1 / (1 + exp ((neg(K2_v - mivh)) / mik)))))
351
352
353	(K2_mtau =
354	((1e3) * (if (K2_v < -20)
355	then (0.000688 + 1 / (exp ((K2_v + 64.2) / 6.5) + exp ((K2_v - 141.5) / -34.8)))
356	else (0.00016 + 0.0008 * exp (-0.0267 * K2_v)))))
357
358
359	(hh-ionic-gate
360	(K2 ;; ion name: exported variables will be of the form {ion}_{id}
361	(initial-m (K2_minf))
362	(m-power 4)
363	(h-power 0)
364	(m-inf (K2_minf))
365	(m-tau (K2_mtau))))
366
367	)
368
369	(component (type pore)
370	(const gbar_K2 = 0.002)
371	(output gbar_K2 ))
372
373	(component (type permeating-ion) (name k)
374	(const e_K2 = ek)
375	(output e_K2 ))
376
377	) ;; end K2 current
378
379
380
381
382	(component (type gate-complex) (name K3)
383	;; HH slow TEA-insensitive Purkinje potassium current
384
385	(component (type gate)
386
387	;; constants
388
389	;; rate functions
390
391	(K3_v = (v + 11)) ;; account for junction potential
392
393	(K3_minf =
394	(let ((mivh -16.5)
395	(mik 18.4))
396	(1 / (1 + exp ((neg(K3_v - mivh)) / mik)))))
397
398
399	(K3_mtau =
400	((1e3) * (0.000796 + 1.0 / (exp ((K3_v + 73.2) / 11.7) + exp ((K3_v - 306.7) / -74.2)))))
401
402	(hh-ionic-gate
403	(K3 ;; ion name: exported variables will be of the form {ion}_{id}
404	(initial-m (K3_minf))
405	(m-power 4)
406	(h-power 0)
407	(m-inf (K3_minf))
408	(m-tau (K3_mtau))))
409
410	)
411
412	(component (type pore)
413	(const gbar_K3 = 0.004)
414	(output gbar_K3 ))
415
416	(component (type permeating-ion) (name k)
417	(const e_K3 = ek)
418	(output e_K3 ))
419
420	) ;; end K3 current
421
422	(component (type gate-complex) (name Narsg)
423
424	;; constants
425
426	(component (type gate)
427
428	(const Na_Con = 0.005)
429	(const Na_Coff = 0.5)
430	(const Na_Oon = 0.75)
431	(const Na_Ooff = 0.005)
432
433
434	(const Na_alfac = (pow ((Na_Oon / Na_Con) (1.0 / 4.0))))
435	(const Na_btfac = (pow ((Na_Ooff / Na_Coff) (1.0 / 4.0))))
436
437	(const Na_alpha = 150)
438	(const Na_beta = 3)
439	(const Na_gamma = 150)
440	(const Na_delta = 40)
441	(const Na_epsilon = 1.75)
442	(const Na_zeta = 0.03)
443	(const Na_x1 = 20)
444	(const Na_x2 = -20)
445	(const Na_x3 = 1e12)
446	(const Na_x4 = -1e12)
447	(const Na_x5 = 1e12)
448	(const Na_x6 = -25)
449
450	;; rate functions
451
452	(f01 = (4.0 * Na_alpha * exp (v / Na_x1)))
453	(f02 = (3.0 * Na_alpha * exp (v / Na_x1)))
454	(f03 = (2.0 * Na_alpha * exp (v / Na_x1)))
455	(f04 = (Na_alpha * exp (v / Na_x1)))
456	(f0O = (Na_gamma * exp (v / Na_x3)))
457	(fip = (Na_epsilon * exp (v / Na_x5)))
458	(f11 = (4.0 * Na_alpha * Na_alfac * exp (v / Na_x1)))
459	(f12 = (3.0 * Na_alpha * Na_alfac * exp (v / Na_x1)))
460	(f13 = (2.0 * Na_alpha * Na_alfac * exp (v / Na_x1)))
461	(f14 = (Na_alpha * Na_alfac * exp (v / Na_x1)))
462	(f1n = (Na_gamma * exp (v / Na_x3)))
463
464	(fi1 = (Na_Con))
465	(fi2 = (Na_Con * Na_alfac))
466	(fi3 = (Na_Con * Na_alfac * Na_alfac))
467	(fi4 = (Na_Con * Na_alfac * Na_alfac * Na_alfac))
468	(fi5 = (Na_Con * Na_alfac * Na_alfac * Na_alfac * Na_alfac))
469	(fin = (Na_Oon))
470
471	(b01 = (Na_beta * exp (v / Na_x2)))
472	(b02 = (2.0 * Na_beta * exp (v / Na_x2)))
473	(b03 = (3.0 * Na_beta * exp (v / Na_x2)))
474	(b04 = (4.0 * Na_beta * exp (v / Na_x2)))
475	(b0O = (Na_delta * exp (v / Na_x4)))
476	(bip = (Na_zeta * exp (v / Na_x6)))
477
478	(b11 = (Na_beta * Na_btfac * exp (v / Na_x2)))
479	(b12 = (2.0 * Na_beta * Na_btfac * exp (v / Na_x2)))
480	(b13 = (3.0 * Na_beta * Na_btfac * exp (v / Na_x2)))
481	(b14 = (4.0 * Na_beta * Na_btfac * exp (v / Na_x2)))
482	(b1n = (Na_delta * exp (v / Na_x4)))
483
484	(bi1 = (Na_Coff))
485	(bi2 = (Na_Coff * Na_btfac))
486	(bi3 = (Na_Coff * Na_btfac * Na_btfac))
487	(bi4 = (Na_Coff * Na_btfac * Na_btfac * Na_btfac))
488	(bi5 = (Na_Coff * Na_btfac * Na_btfac * Na_btfac * Na_btfac))
489	(bin = (Na_Ooff))
490
491	(reaction
492	(Na_z
493	(transitions
494	(<-> C1 C2 f01 b01)
495	(<-> C2 C3 f02 b02)
496	(<-> C3 C4 f03 b03)
497	(<-> C4 C5 f04 b04)
498	(<-> C5 O f0O b0O)
499	(<-> O B fip bip)
500	(<-> O I6 fin bin)
501	(<-> C1 I1 fi1 bi1)
502	(<-> C2 I2 fi2 bi2)
503	(<-> C3 I3 fi3 bi3)
504	(<-> C4 I4 fi4 bi4)
505	(<-> C5 I5 fi5 bi5)
506	(<-> I1 I2 f11 b11)
507	(<-> I2 I3 f12 b12)
508	(<-> I3 I4 f13 b13)
509	(<-> I4 I5 f14 b14)
510	(<-> I5 I6 f1n b1n)
511	)
512
513	(conserve (1 = (I1 + I2 + I3 + I4 + I5 + I6 + C1 + C2 + C3 + C4 + C5 + O + B)))
514
515	(open O) (power 1)))
516
517	(output Na_z )
518
519	)
520
521	(component (type pore)
522	(const gbar = 0.015)
523	(output gbar ))
524
525	(component (type permeating-ion) (name na)
526	(const e = ena)
527	(output e ))
528
529	) ;; end Narsg component
530
531
532
533
534
535	(component (type gate-complex) (name Ih)
536
537	(component (type gate)
538
539	;; rate functions
540
541	(Ih_inf = (1.0 /(1.0 + exp ((v + 90.1) / 9.9))))
542
543	(Ih_tau = ((1e3) * (0.19 + 0.72 * exp (neg(((v - (-81.5)) / 11.9) ^ 2)))))
544
545	(hh-ionic-gate
546	(Ih ;; ion name: exported variables will be of the form {ion}_{id}
547	(initial-m (Ih_inf))
548	(m-power 1)
549	(h-power 0)
550	(m-inf (Ih_inf))
551	(m-tau (Ih_tau))
552	))
553
554	)
555
556	(component (type pore)
557	(const gbar_Ih = 0.0001)
558	(output gbar_Ih ))
559
560	(component (type permeating-ion) (name non-specific)
561	(const e_Ih = -30)
562	(output e_Ih ))
563
564	) ;; end Ih current
565
566
567	(component (type gate-complex) (name Leak)
568
569	(component (type pore)
570	(const gbar_Leak = 5e-5)
571	(output gbar_Leak ))
572
573	(component (type permeating-ion) (name non-specific)
574	(const e_Leak = -60)
575	(output e_Leak ))
576
577	) ;; end leak current
578
579
580	(component (type decaying-pool) (name ca)
581	(const F = 96485.0)
582	(const ca_depth = 0.1)
583	(const ca_beta = 1.0)
584
585	(d (ca) = ((neg (ica) / (2 * ca0 * F * ca_depth)) -
586	((if (ca < ca0) then ca0 else ca) * ca_beta))
587	(initial ca0))
588
589	(cac = (if (ca < ca0) then ca0 else ca))
590
591	(output cac)
592	)
593
594
595	(component (type membrane-capacitance)
596	(const C_m = 1e-3)
597	(output C_m))
598
599	))
600
601
602	== About this egg
603
604	=== Author
605
606	[[/users/ivan-raikov\|Ivan Raikov]]
607
608	=== Version history
609
610	; 5.0-5.1 : Added some flexibility in generating HH rate equations
611	; 4.4 : Voltage clamp script generation
612	; 4.3 : Renamed permeating-substance components to permeating-ion
613	; 4.2 : Using installation-chicken-home to install example files
614	; 4.1 : Documentation converted to wiki format
615	; 4.0 : Introducing the gate-complex element
616	; 3.4 : Documentation update
617	; 3.1-3.3 : Fixes to the examples
618	; 3.0 : Internal restructuring and new examples
619	; 2.5 : Bug fixes in option handling and NMODL backend
620	; 2.4 : Converted to using getopt-long
621	; 2.3 : Added eggdoc as a dependency
622	; 2.2 : Added stx-engine.scm to file manifest
623	; 2.1 : Ported to Chicken 4
624	; 2.0 : Introduced functors
625	; 1.15 : Added nmodl-depend option
626	; 1.14 : Added support for exponential Euler integration
627	; 1.13 : Change in the integration method used for the AKP example
628	; 1.12 : Added support for binary conductances and conservation equations
629	; 1.11 : Bug fixes in the current equations part of NMODL code generator
630	; 1.10 : AKP06 example is now installed in CHICKEN-HOME/nemo/examples
631	; 1.9 : Documentation and example updates
632	; 1.8 : Bug fixes related to kinetic equation processing
633	; 1.6 : Added infix expression parser (nemo format)
634	; 1.0 : Initial release
635
636	=== License
637
638
639	Copyright 2008-2012 Ivan Raikov and the Okinawa Institute of Science and Technology.
640
641	This program is free software: you can redistribute it and/or modify
642	it under the terms of the GNU General Public License as published by
643	the Free Software Foundation, either version 3 of the License, or (at
644	your option) any later version.
645
646	This program is distributed in the hope that it will be useful, but
647	WITHOUT ANY WARRANTY; without even the implied warranty of
648	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
649	General Public License for more details.
650
651	A full copy of the GPL license can be found at
652	<http://www.gnu.org/licenses/>.
653

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