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NEURON NMODL (.mod) Files

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General Information

Named blocks have the general form KEYWORD { statements }
User defined variables can be up to 20 characters.

Variable Declaration Blocks

Users may specify units appropriate for variables, except for those defined by neuron:
- v (millivolts)
- t (milliseconds)
- celsius (C)
- diam (um)
- area (um^2)

Ex:

  PARAMETER {  
    g = 0.001  (siemens/cm2)  < 0, 1e9 >
  }

`PARAMETER`

Variables specified here are assigned by user or changed by hoc
They do not typically change but can throughought but can emulate some external influence on the characteristic properties of the model
- Time-dependent PARAMETER changes - Models with discontinuities
They appear in nrnpointmenu

Ex:

  g = 0.001  (siemens/cm2)  < 0, 1e9 >  : variable = value (units) <minimum, maximum value that can be entered via gui>

Any parameter that doesn’t appear in a NEURON block’s RANGE statement will have a GLOBAL scope, meaning that chaning the value will affect every instance of that mechanism throughout an entire model.

`STATE`

If a model involves differential equations, families of algebraic equations or kinetic reaction schemes, their dependent variables or unknowns are listed in the STATE block.

Variables declared here are called STATE variables or STATES.

`ASSIGNED`

Can be used to declare two kinds of variables:

those given values outside the mod file
those that appear on the left hand side of assignment statements in the mod file The first group includes variables potentially available to every mechanism, like v, celsius, t and ionic variables.

The second group omits variables that are unknons in simmultaneous linear or nonlinear algebraic equations, or that are dependent variables in differential equations, or kinetic reaction schemes

Values are not visible at the hoc level unless it’s declared in a RANGE or GLOBAL statement
The current i isn’t a state variable because the model does not define it in terms of a differential equation, i does not have dynamics of its own, further it is a known set of equations by direct assignment.
In the leak example below v is also similarly declared in the ASSIGNED block. In this case v is a driving force rather than a STATE variable.

Equation Definition Blocks

`NEURON`

The NEURON blockdefines what the model of the mechanism looks like from the outside.

`INITIAL`

Code in the INITIAL block is executed when the run system’s finitialize() method is called.

`BREAKPOINT`

The BREAKPOINT block is the main computation block in NMODL.

Executes simulations by incrementing an independent variable over a sequence of steps or “breakpoints” at which the dependent variables of the model are computed and displayed.
At the end of the BREAKPOINT all variables should be consistent with the independent variable (t)

`DERIVATIVE`

Used to assign values to the derivatives of those STATES that are described by differential equations.

Statements are of the form y' = expr
Can contain higher order derivatives (more apoostrophes)
Equations are integrated using the numerical method specified by the SOLVE statement in the BREAKPOINT block
SOLVE statements should explicity invoke one of the integration methods appropriate for systems in which state variables can vary widely during a time step.

The cnexp method combines second order accuracy with computational efficiency is a good choice for most programs

`KINETIC`

`FUNCTION`

Functions defined by the FUNCTION block are vailable at the hoc level and other mechanisms by adding the suffix to the mechanism that they’re defined in.

Functions that do not reference RANGE varuables can be called from hoc directly (ie: GLOBAL is allowed)
Otherwise, the section will need to be referenced: ```` section_name setdata_suffix(x)

`NET_RECEIVE`

Artificial cell models don’t have BREAKPOINT, KINETTIC or DERIVITIVE. They only act when a new event arrives, these calculations are carried out in the NET_RECIEVE block.

Input is the weight of the connection

Keywords

`SUFFIX`

Two purposes of SUFFIX:

Identifies this to be a distributed mechanism, used by an insert statement
Tells the NEURON interpreter that the names for variables and parameters that belong to this mechanism will include the suffix. Ex:

.mod file

: comment here
NEURON {
  SUFFIX leak
  RANGE i
}

NEURON file

cable{
  nseg = 1 //Number of segments per this section
  insert leak 
}
print cable.i_leak(0.5)

`POINT_PROCESS`

Identifies the mechanism be be a point process, so it will be managed in hoc using an object oriented syntax (synapses).

`NONSPECIFIC_CURRENT`

The NONSPECIFIC_CURRENT has two purposes:

the value i specified after (Ex: NONSPECIFIC_CURRENT i) will be reckonded in charge balance equations
This current will make no contributions to mass balance equations

`RANGE`

Anything denoted by range is accessible by the hoc interpreter
These variables are a function of position and can have different values for each of the segments that make up a section
Each variable mentioned in RANGE should be declared in a PARAMETER or ASSIGNED block.
Alternative to RANGE is GLOBAL

`GLOBAL`

Other

Comments

A single line comment starts with a colon “:”

Multiline comments start with COMMENT and end with ENDCOMMENT

  COMMENT
    This is a
    multiple line
    comment
  ENDCOMMENT

Special Variables

v,celsius,t,diam,area,dt

Examples

LEAK Current

: A passive leak current
NEURON {  : Visible from the NEURON programming environment
  SUFFIX leak  : How the mechanism will be refered to by NEURON code (insert leak) 
  NONSPECIFIC_CURRENT i  : will be reckonded in charge balance equations
  RANGE i, e, g : Values here will need to appear in PARAMETER or ASSIGNED, will be different for each segment/section
}
PARAMETER {  : Variables specified here are assigned by user or changed by hoc 
  g = 0.001  (siemens/cm2)  < 0, 1e9 >  : variable = value (units) <min, max (in hoc/gui)>
  e = -65    (millivolt)
}
ASSIGNED {  : values that will appear on the lefthand side of an assignment statement, or are driving values
  i  (milliamp/cm2)  
  v  (millivolt)
}
BREAKPOINT { 
  i = g*(v - e) 
}

References

This page is part of a collection of pages on various topics of computational neuroscience. Please direct questions and suggestions to the author Tyler Banks [website][github] at tyler@tylerbanks.net.