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nemo
An implementation of a description language for computational models of ion channels.
Usage
nemo [options...] [input files ...]
Documentation
NEMO is a program that reads an ion channel description and generates corresponding model simulation code in GNU Octave, NEST C++ code, or the NMODL language used by the NEURON simulator.
Options
- -i FORMAT
- specify input format (nemo, xml, sxml, s-exp)
- -p
- generate individual files for each current component in the input file
- --xml[=FILE]
- write XML output to file (default: <model-name>.xml)
- --sxml[=FILE]
- write SXML output to file (default: <model-name>.sxml)
- --nest
- write NEST output to files <model-name>.cpp and <model-name>.h
- --nmodl[=FILE]
- write NMODL output to file (default: <model-name>.mod)
- --nmodl-method=METHOD
- specify NMODL integration method (cnexp, derivimplicit, cvode)
- --nmodl-kinetic=[STATES]
- use NMODL kinetic equations for the given reactions
- --nmodl-depend=VARS
- specify DEPEND variables for NMODL interpolation tables
- --octave[=FILE]
- write Octave output to file (default: <model-name>.m)
- --matlab[=FILE]
- write Matlab output to file (default: <model-name>.m)
- --vclamp-octave[=FILE]
- write Octave voltage clamp script to file (default: <model-name>_vclamp.m)
- --vclamp-hoc[=FILE]
- write HOC voltage clamp script to file (default: <model-name>.ses)
- --debug
- print additional debugging information
- -t
- use interpolation tables in generated code
- -h, --help
- print help
Model description language
The following constructs comprise the model description language:
- 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}.
- | OUTPUT {ID}
- Declares that an existing quantity be exported.
- | CONST {ID} = {EXPR}
- Declares a constant quantity (its value will be computed at declaration time).
- | FUN {ID} ( {ARG-ID} ... ) {EXPR}
- Declares a function (a parameterized expression with no free variables).
- | {ID} = {EXPR}
- Declares an assigned quantity (an expression that can refer to other quantities in the system).
- | 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.
- | COMPONENT ( TYPE {ID} ) ( NAME {ID} ) {ELEMENTS} )
- Declares a system component (a quantity that can contain other quantities).
Expressions
Expressions in the model description language are defined as:
- EXPR ::= {NUM}
- A numeric constant.
- | {ID}
- A variable name.
- | {ID} ( {EXPR} ... )
- A function invocation.
- | {EXPR} {OP} {EXPR}
- Arithmetic operator invocation. The following operators are supported: + - / * > < <= >= ^
- | LET ( {BINDINGS} ) {EXPR}
- Local variables declaration. Each element in {BINDINGS} is of the form: ( {ID} {EXPR} )
- | IF {CONDITION} THEN {EXPR} ELSE {EXPR}
- Conditional expression. The expression after IF must be a comparison expression.
State transition equations
State transition equations in the model description language are defined as:
- TRANSITION ::= -> {SRC-ID} {DEST-ID} {EXPR}
- Declares that a transition occurs from state {SRC-ID} to state {DEST-ID} at rate computed by {EXPR}.
- | <-> {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}.
Ionic current definitions
Currently, the NMODL code generator recognizes and generates code for ion channel components that are defined as follows:
- COMPONENT (TYPE ionic-current) (NAME {NAME}) ( COMPONENT ( TYPE gate ) ...
- One or more gate definitions. Each component of type gate must export the reactions that characterize the gate dynamics.
- 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.
- [ COMPONENT ( TYPE permeating-ion ) ... ]
- [ COMPONENT ( TYPE accumulating-substance ) ... ]
Hodgkin-Huxley ionic conductance extension
The Hodgkin-Huxley ionic conductance extension is a shortcut that declares a reaction corresponding to the Hodgkin-Huxley formulation of ion channel dynamics.
- HH-IONIC-GATE
- ( {ION-NAME} : Ion name: exported variables will be of the form {ion}_{id}.
- M-POWER {INTEGER}
- Power of state variable M.
- H-POWER {INTEGER}
- Power of state variable H. If zero, the initial value and equations for this variable can be omitted.
- INITIAL-M {EXPR}
- Expression that computes initial value for state variable M.
- INITIAL-H {EXPR}
- Expression that computes initial value for state variable H.
- M-ALPHA {EXPR}
- Closed state to open state rate expression for state variable M.
- M-BETA {EXPR}
- Open state to closed state rate expression for state variable M.
- H-ALPHA {EXPR}
- Closed state to open state rate expression for state variable H.
- H-BETA {EXPR}
- Open state to closed state rate expression for state variable H.
- M-INF {EXPR}
- Steady state expression for variable M.
- M-TAU {EXPR}
- Time constant expression for variable M.
- H-INF {EXPR}
- Steady state expression for variable H.
- H-TAU {EXPR}
- Time constant expression for variable H.
Examples
;; Cerebellar Purkinje Cell: resurgent Na current and high frequency ;; firing (Khaliq et al 2003).
nemo-model
Khaliq03
input v cai from ion-pools ica from ion-currents
const ena = 60 const ek = -88 const ca0 = 1e-4
component (type ionic-current) (name CaBK) ;: BK-type Purkinje calcium-activated potassium current
component (type gate)
;; constants const ztau = 1.0
;; rate functions
CaBK_v = (v + 5)
minf = (let ((vh -28.9) (k 6.2)) (1.0 / (1.0 + exp (neg ((CaBK_v - vh) / k)))))
mtau = (let ((y0 0.000505) (vh1 -33.3) (k1 -10.0) (vh2 86.4) (k2 10.1)) ((1e3) * (y0 + 1 / (exp ((CaBK_v + vh1) / k1) + exp ((CaBK_v + vh2) / k2)))))
hinf = (let
((y0 0.085)
(vh -32.0)
(k 5.8))
(y0 + (1 - y0) / (1 + exp ((CaBK_v - vh) / k))))
htau = (let
((y0 0.0019)
(vh1 -54.2)
(k1 -12.9)
(vh2 48.5)
(k2 5.2))
((1e3) * (y0 + 1 / (exp ((CaBK_v + vh1) / k1) + exp ((CaBK_v + vh2) / k2)))))
zinf = (let ((k 0.001)) (1 / (1 + (k / cai))))
z_alpha = (zinf / ztau) z_beta = ((1 - zinf) / ztau)
reaction
z
transitions (<-> O C z_alpha z_beta)
conserve (1 = (O + C))
initial (let ((k 0.001)) (1 / (1 + k / ca0)))
open O
power 2
output z
hh-ionic-gate
CaBK ;; ion name: exported variables will be of the form {ion}_{id}
initial-m (minf)
initial-h (hinf)
m-power 3
h-power 1
m-inf (minf)
m-tau (mtau)
h-inf (hinf)
h-tau (htau)
component (type pore)
const gbar_CaBK = 0.007
output gbar_CaBK
component (type permeating-ion) (name k)
const e_CaBK = ek
output e_CaBK
;; end BK current
component (type ionic-current) (name CaP)
;; HH P-type Calcium current
component (type gate)
;; rate functions inf = (let ((cv -19) (ck 5.5)) (1.0 / (1.0 + exp (neg ((v - cv) / ck)))))
tau = ((1e3) * (if (v > -50) then (0.000191 + (0.00376 * exp (neg (((v + 41.9) / 27.8) ^ 2)))) else (0.00026367 + (0.1278 * exp (0.10327 * v)))))
hh-ionic-gate
CaP ;; ion name: exported variables will be of the form {ion}_{id}
initial-m (inf)
m-power 1
h-power 0
m-inf inf
m-tau tau
component (type permeability)
fun ghk (v ci co)
(let ((F 9.6485e4)
(R 8.3145)
(T (22 + 273.19))
(Z 2)
(E ((1e-3) * v)))
(let ((k0 ((Z * (F * E)) / (R * T))))
(let ((k1 (exp (neg (k0))))
(k2 (((Z ^ 2) * (E * (F ^ 2))) / (R * T))))
(1e-6) * (if (abs (1 - k1) < 1e-6)
then (Z * F * (ci - (co * k1)) * (1 - k0))
else (k2 * (ci - (co * k1)) / (1 - k1))))))
const pcabar = 0.00005
const cao = 2.4
pca = (pcabar * ghk (v cai cao))
output pca
component (type permeating-ion) (name ca)
;; end CaP current
component (type ionic-current) (name K1) ;; HH TEA-sensitive Purkinje potassium current
component (type gate)
;; constants
;; rate functions
K1_v = (v + 11) ;; account for junction potential
minf = (let ((mivh -24) (mik 15.4)) (1 / (1 + exp (neg (K1_v - mivh) / mik))))
mtau = (let ((mty0 0.00012851) (mtvh1 100.7) (mtk1 12.9) (mtvh2 -56.0) (mtk2 -23.1)) (1e3 * (if (K1_v < -35) then (3.0 * (3.4225e-5 + 0.00498 * exp (neg (K1_v) / -28.29))) else (mty0 + 1.0 / (exp ((K1_v + mtvh1) / mtk1) + exp ((K1_v + mtvh2) / mtk2))) )))
hinf = (let ((hiy0 0.31) (hiA 0.78) (hivh -5.802) (hik 11.2)) (hiy0 + hiA / (1 + exp ((K1_v - hivh) / hik))))
htau = (1e3 * (if ( K1_v > 0 ) then (0.0012 + 0.0023 * exp (-0.141 * K1_v)) else (1.2202e-05 + 0.012 * exp (neg (((K1_v - (-56.3)) / 49.6) ^ 2)))))
hh-ionic-gate
K1 ;; ion name: exported variables will be of the form {ion}_{id}
initial-m (minf)
initial-h (hinf)
m-power 3
h-power 1
m-inf (minf)
m-tau (mtau)
h-inf (hinf)
h-tau (htau)
component (type pore)
const gbar = 0.004
output gbar
component (type permeating-ion) (name k)
const e = ek
output e
;; end K1 current
component (type ionic-current) (name K2) ;; HH Low TEA-sensitive Purkinje potassium current
component (type gate)
;; constants
;; rate functions
K2_v = (v + 11) ;; account for junction potential
minf = (let ((mivh -24) (mik 20.4)) (1 / (1 + exp ((neg (K2_v - mivh)) / mik))))
mtau = ((1e3) * (if (K2_v < -20) then (0.000688 + 1 / (exp ((K2_v + 64.2) / 6.5) + exp ((K2_v - 141.5) / -34.8))) else (0.00016 + 0.0008 * exp (-0.0267 * K2_v))))
hh-ionic-gate
K2 ;; ion name: exported variables will be of the form {ion}_{id}
initial-m (minf)
m-power 4
h-power 0
m-inf (minf)
m-tau (mtau)
component (type pore)
const gbar = 0.002
output gbar
component (type permeating-ion) (name k)
const e = ek
output e
;; end K2 current
component (type ionic-current) (name K3) ;; HH slow TEA-insensitive Purkinje potassium current
component (type gate)
;; constants
;; rate functions
K3_v = (v + 11) ;; account for junction potential
minf = (let ((mivh -16.5) (mik 18.4)) (1 / (1 + exp ((neg (K3_v - mivh)) / mik))))
mtau = ((1e3) * (0.000796 + 1.0 / (exp ((K3_v + 73.2) / 11.7) + exp ((K3_v - 306.7) / -74.2))))
hh-ionic-gate
K3 ;; ion name: exported variables will be of the form {ion}_{id}
initial-m (minf)
m-power 4
h-power 0
m-inf (minf)
m-tau (mtau)
component (type pore)
const gbar = 0.004
output gbar
component (type permeating-ion) (name k)
const e = ek
output e
;; end K3 current
component (type ionic-current) (name Narsg)
component (type gate) const Con = 0.005 const Coff = 0.5 const Oon = 0.75 const Ooff = 0.005
const alfac = (pow ((Oon / Con) (1.0 / 4.0)))
const btfac = (pow ((Ooff / Coff) (1.0 / 4.0)))
const alpha = 150
const beta = 3
const gamma = 150
const delta = 40
const epsilon = 1.75
const zeta = 0.03
const x1 = 20
const x2 = -20
const x3 = 1e12
const x4 = -1e12
const x5 = 1e12
const x6 = -25
;; rate functions
f01 = (4.0 * alpha * exp (v / x1))
f02 = (3.0 * alpha * exp (v / x1))
f03 = (2.0 * alpha * exp (v / x1))
f04 = (alpha * exp (v / x1))
f0O = (gamma * exp (v / x3))
fip = (epsilon * exp (v / x5))
f11 = (4.0 * alpha * alfac * exp (v / x1))
f12 = (3.0 * alpha * alfac * exp (v / x1))
f13 = (2.0 * alpha * alfac * exp (v / x1))
f14 = (alpha * alfac * exp (v / x1))
f1n = (gamma * exp (v / x3))
fi1 = (Con)
fi2 = (Con * alfac)
fi3 = (Con * alfac * alfac)
fi4 = (Con * alfac * alfac * alfac)
fi5 = (Con * alfac * alfac * alfac * alfac)
fin = (Oon)
b01 = (beta * exp (v / x2))
b02 = (2.0 * beta * exp (v / x2))
b03 = (3.0 * beta * exp (v / x2))
b04 = (4.0 * beta * exp (v / x2))
b0O = (delta * exp (v / x4))
bip = (zeta * exp (v / x6))
b11 = (beta * btfac * exp (v / x2))
b12 = (2.0 * beta * btfac * exp (v / x2))
b13 = (3.0 * beta * btfac * exp (v / x2))
b14 = (4.0 * beta * btfac * exp (v / x2))
b1n = (delta * exp (v / x4))
bi1 = (Coff)
bi2 = (Coff * btfac)
bi3 = (Coff * btfac * btfac)
bi4 = (Coff * btfac * btfac * btfac)
bi5 = (Coff * btfac * btfac * btfac * btfac)
bin = (Ooff)
reaction
z
transitions
<-> C1 C2 f01 b01
<-> C2 C3 f02 b02
<-> C3 C4 f03 b03
<-> C4 C5 f04 b04
<-> C5 O f0O b0O
<-> O B fip bip
<-> O I6 fin bin
<-> C1 I1 fi1 bi1
<-> C2 I2 fi2 bi2
<-> C3 I3 fi3 bi3
<-> C4 I4 fi4 bi4
<-> C5 I5 fi5 bi5
<-> I1 I2 f11 b11
<-> I2 I3 f12 b12
<-> I3 I4 f13 b13
<-> I4 I5 f14 b14
<-> I5 I6 f1n b1n
conserve (1 = (I1 + I2 + I3 + I4 + I5 + I6 + C1 + C2 + C3 + C4 + C5 + O + B))
open O
power 1
output z
component (type pore)
const gbar = 0.015
output gbar
component (type permeating-ion) (name na)
const e = ena
output e
;; end Narsg component
component (type ionic-current) (name Ih)
component (type gate)
;; rate functions
inf = (1.0 / (1.0 + exp ((v + 90.1) / 9.9)))
tau = ((1e3) * (0.19 + 0.72 * exp (neg (((v - (-81.5)) / 11.9) ^ 2))))
hh-ionic-gate
Ih ;; ion name: exported variables will be of the form {ion}_{id}
initial-m (inf)
m-power 1
h-power 0
m-inf (inf)
m-tau (tau)
component (type pore)
const gbar = 0.0001
output gbar
component (type permeating-ion) (name non-specific)
const e = -30
output e
;; end Ih current
component (type ionic-current) (name Leak)
component (type pore)
const gbar = 5e-5
output gbar
component (type permeating-ion) (name non-specific)
const e = -60
output e
;; end leak current
component (type decaying-pool) (name ca)
const F = 96485.0
const ca_depth = 0.1
const ca_beta = 1.0
d (ca) = ((neg (ica) / (2 * ca0 * F * ca_depth)) -
((if (ca < ca0) then ca0 else ca) * ca_beta))
initial ca0
cac = (if (ca < ca0) then ca0 else ca)
output cac
component (type membrane-capacitance)
const C_m = (1e-3)
output C_m
component (type voltage-clamp) (name K1)
const vchold = -71
const vcbase = -69
const vcinc = 10
const vcsteps = 8
const vchdur = 30
const vcbdur = 100
output vchold vcbase vcinc vcsteps vchdur vcbdur
About this egg
Author
Version history
- 9.0
- transitioning to ersatz templates for code generation
- 7.0-8.x
- support for the NEST simulator and CVODE solver, discrete events, synaptic components
- 6.11
- bug fix in surface XML generation
- 6.9
- added -p and --surface-xml option
- 6.4-6.8
- bug fixes and enhancements to NMODL code generator
- 6.3
- bug fixes in XML parsing
- 6.2
- supported for deployment as a self-contained package
- 6.0-6.1
- introduced indentation-based syntax
- 5.0-5.1
- Added some flexibility in generating HH rate equations
- 4.4
- Voltage clamp script generation
- 4.3
- Renamed permeating-substance components to permeating-ion
- 4.2
- Using installation-chicken-home to install example files
- 4.1
- Documentation converted to wiki format
- 4.0
- Introducing the gate-complex element
- 3.4
- Documentation update
- 3.1-3.3
- Fixes to the examples
- 3.0
- Internal restructuring and new examples
- 2.5
- Bug fixes in option handling and NMODL backend
- 2.4
- Converted to using getopt-long
- 2.3
- Added eggdoc as a dependency
- 2.2
- Added stx-engine.scm to file manifest
- 2.1
- Ported to Chicken 4
- 2.0
- Introduced functors
- 1.15
- Added nmodl-depend option
- 1.14
- Added support for exponential Euler integration
- 1.13
- Change in the integration method used for the AKP example
- 1.12
- Added support for binary conductances and conservation equations
- 1.11
- Bug fixes in the current equations part of NMODL code generator
- 1.10
- AKP06 example is now installed in CHICKEN-HOME/nemo/examples
- 1.9
- Documentation and example updates
- 1.8
- Bug fixes related to kinetic equation processing
- 1.6
- Added infix expression parser (nemo format)
- 1.0
- Initial release
License
Copyright 2008-2014 Ivan Raikov This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. A full copy of the GPL license can be found at <http://www.gnu.org/licenses/>.