Basic Electrophysiology Relacs Plugins  0.9.8
Public Member Functions | Static Public Attributes | Protected Attributes | List of all members
SpikingNeuron Class Referenceabstract

#include <spikingneuron.h>

Inheritance diagram for SpikingNeuron:
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Collaboration diagram for SpikingNeuron:
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Public Member Functions

 SpikingNeuron (void)
 
virtual ~SpikingNeuron (void)
 
virtual string name (void) const
 
virtual int dimension (void) const =0
 
virtual void variables (vector< string > &varnames) const =0
 
virtual void units (vector< string > &u) const =0
 
virtual void operator() (double t, double s, double *x, double *dxdt, int n)=0
 
virtual void init (double *x) const =0
 
virtual void conductances (vector< string > &conductancenames) const
 
virtual void conductances (double *g) const
 
virtual string conductanceUnit (void) const
 
virtual void currents (vector< string > &currentnames) const
 
virtual void currents (double *c) const
 
virtual string currentUnit (void) const
 
virtual string inputUnit (void) const
 
virtual void add (void)
 
virtual void notify (void)
 
double gain (void) const
 
double offset (void) const
 
- Public Member Functions inherited from ConfigClass
 ConfigClass (const string &ident, int group=0, int mode=0xffff, int selectmask=0)
 
 ConfigClass (const ConfigClass &C)
 
virtual ~ConfigClass (void)
 
const string & configIdent (void) const
 
void setConfigIdent (const string &ident)
 
int configGroup (void) const
 
void setConfigGroup (int group)
 
int configMode (void) const
 
void setConfigMode (int mode)
 
void addConfigMode (int mode)
 
void delConfigMode (int mode)
 
int configSelectMask (void) const
 
void setConfigSelectMask (int mask)
 
void addConfig (void)
 
void readConfig (void)
 
virtual void readConfig (StrQueue &sq)
 
virtual void saveConfig (ofstream &str)
 
virtual int configSize (void) const
 
virtual void config (void)
 
virtual void preConfig (void)
 

Static Public Attributes

static const int ScalingFlag = 16
 
static const int ModelFlag = 32
 
static const int DescriptionFlag = 64
 

Protected Attributes

double Gain
 
double Offset
 

Additional Inherited Members

- Public Types inherited from ConfigClass
enum  Action
 
- Static Public Member Functions inherited from ConfigClass
static void setConfigureClasses (ConfigureClasses *cfg)
 

Detailed Description

[ModelLib] Base class for a spiking (point-) neuron

Author
Jan Benda
Alexander Wolf
Version
1.2 (May 7, 2008)
  1. SpikingNeuron inherits Options
  2. Added interface for accessing the values of the ionic currents and conductances
1.1 (Jan 10, 2006)

Each model of a spiking neuron has a name(). The model is implemented as a set of differential equations

\[ \left( \begin{array}{c} \frac{dx_1}{dt} \\ \frac{dx_2}{dt} \\ \vdots \\ \frac{dx_n}{dt} \end{array} \right) = \left( \begin{array}{c} f_1(x_1, x_2, \ldots, x_n, s) \\ f_2(x_1, x_2, \ldots, x_n, s) \\ \vdots \\ f_n(x_1, x_2, \ldots, x_n, s) \end{array} \right) \]

The state of the model is described by the state vector $ \vec x = (x_1, x_2, \ldots, x_n)$ of dimension n = dimension(). operator()() computes the derivatives $ d\vec x/dt$ with respect to time t for the current state x and the stimulus s. The variables() function returns names for each of the state variables x, units() returns the corrsponding units, and init() sets the state variables x to useful initial conditions. The unit of the input s is given by inputUnit().

While integrating the model, the current values of the ionic currents and their corresponding conductances can be retrieved by the currents(double*) const and conductances(double*) const functions. The corresponding names of the currents and conductances are returned by conductances(vector<string>&) const and currents(vector<string>&) const, respectively. The unit of the conductances is conductanceUnit() and the the one of the currents is currentUnit().

Parameter values of the model can be made accessible by adding them to the Options in add(). Changed parameter values are read out from the Options by notify(). The parameter values are classified as either scalingFlag(), modelFlag(), or descriptionFlag().

SpikingNeuron defines two parameters offset() and gain() with default values 0 and 1, respectively, that should be applied to whatever input before it is passed on as the stimulus s for computing the derivatives via operator()().

Constructor & Destructor Documentation

SpikingNeuron ( void  )

Constructs the model, i.e. initializes model parameter with useful default values.

Note
The constructor should not add any new options. This goes into the add() function.

References SpikingNeuron::name(), and ConfigClass::setConfigIdent().

~SpikingNeuron ( void  )
virtual

Member Function Documentation

string name ( void  ) const
virtual
Returns
the name of the model.

Reimplemented in Chacron2007, Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, WangBuzsaki, SimplifiedTraub, TraubErmentrout2001, TraubErmentrout1998, TraubKepler, TraubMiles, TraubHH, FleidervishSI, Awiszus, RushRinzel, Connor, Kepler, Abbott, HodgkinHuxley, MorrisLecarPrescott, MorrisLecar, FitzhughNagumo, PassiveMembrane, and Stimulus.

Referenced by NeuronModels::add(), NeuronModels::metaData(), and SpikingNeuron::SpikingNeuron().

virtual int dimension ( void  ) const
pure virtual
Returns
the dimension of the system.
See Also
variables(), operator()()

Implemented in Chacron2007, Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, WangBuzsaki, SimplifiedTraub, TraubErmentrout, TraubMiles, FleidervishSI, RushRinzel, Connor, Abbott, HodgkinHuxley, MorrisLecarPrescott, MorrisLecar, FitzhughNagumo, PassiveMembrane, and Stimulus.

Referenced by NeuronModels::main().

virtual void variables ( vector< string > &  varnames) const
pure virtual
Parameters
[out]varnamesthe names of each of the dimension() variables. Gating variables (ranging between 0 and 1) should be a single lower-case character, potentials and equivalent potentials a single upper-case character, and concentrations should be in brackets (e.g. [Ca]).
See Also
dimension(), units(), operator()()

Implemented in Chacron2007, Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, WangBuzsaki, SimplifiedTraub, TraubErmentrout, TraubMiles, FleidervishSI, RushRinzel, Connor, Abbott, HodgkinHuxley, MorrisLecarPrescott, MorrisLecar, FitzhughNagumo, PassiveMembrane, and Stimulus.

virtual void units ( vector< string > &  u) const
pure virtual
Parameters
[out]uthe units of the variables returned by variables().
See Also
dimension(), operator()()

Implemented in Chacron2007, Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, WangBuzsaki, SimplifiedTraub, TraubErmentrout, TraubMiles, FleidervishSI, RushRinzel, Connor, Abbott, HodgkinHuxley, MorrisLecarPrescott, MorrisLecar, FitzhughNagumo, PassiveMembrane, and Stimulus.

virtual void operator() ( double  t,
double  s,
double *  x,
double *  dxdt,
int  n 
)
pure virtual

Computes the derivative dxdt at time t with stimulus s given the state x. Implement this function with your model.

Parameters
[in]tthe time.
[in]sthe stimulus.
[in,out]xthe state vector.
[out]dxdtthe derivative with respect to time.
[in]nthe number of variables, usually equal to dimension().
See Also
dimension(), init(), variables(), inputUnit()

Implemented in Chacron2007, Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, WangBuzsaki, SimplifiedTraub, TraubErmentrout2001, TraubErmentrout1998, TraubKepler, TraubMiles, TraubHH, FleidervishSI, Awiszus, RushRinzel, Connor, Kepler, Abbott, HodgkinHuxley, MorrisLecarPrescott, MorrisLecar, FitzhughNagumo, PassiveMembrane, and Stimulus.

virtual void init ( double *  x) const
pure virtual

Initialize the state x with useful inital conditions.

Parameters
[out]xthe dimension() state variables of the model.
See Also
dimension(), operator()()

Implemented in Chacron2007, Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, WangBuzsaki, SimplifiedTraub, TraubErmentrout2001, TraubErmentrout1998, TraubKepler, TraubMiles, TraubHH, FleidervishSI, Awiszus, RushRinzel, Connor, Abbott, HodgkinHuxley, MorrisLecarPrescott, MorrisLecar, FitzhughNagumo, PassiveMembrane, and Stimulus.

Referenced by NeuronModels::main().

void conductances ( vector< string > &  conductancenames) const
virtual

Implement this function to return the names of the individual ionic conductances that conductances(double*) const would return. The default implementation returns an empty vector.

Parameters
[out]conductancenamesthe names of the individual ionic conductances.
See Also
currents(double*) const

Reimplemented in Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, TraubErmentrout, TraubMiles, Connor, HodgkinHuxley, MorrisLecarPrescott, and MorrisLecar.

void conductances ( double *  g) const
virtual

Implement this function to return in g the values of the individual ionic conductances. The number of conductances is defined by the size of conductancenames the function conductances(vector<string>&) const returns. The default implementation returns nothing.

Parameters
[out]gthe current values of the individual ionic conductances.
See Also
currents(double*) const

Reimplemented in Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, TraubErmentrout, TraubMiles, Connor, HodgkinHuxley, MorrisLecarPrescott, and MorrisLecar.

string conductanceUnit ( void  ) const
virtual

Returns the unit of the conductances returned by conductances(double*) const. The default implementation returns mS/cm^2.

Reimplemented in Chacron2007, Edman, MilesDai, and MorrisLecar.

Referenced by HodgkinHuxley::add(), Connor::add(), TraubMiles::add(), TraubErmentrout::add(), WangBuzsakiAdapt::add(), Crook::add(), and WangIKNa::add().

void currents ( vector< string > &  currentnames) const
virtual

Implement this function to return in currentnames the names of the individual ionic currents that currents(double*) const would return. The default implementation returns an empty vector.

Parameters
[out]currentnamesthe names of the individual ionic currents.
See Also
conductances(double*) const

Reimplemented in Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, TraubErmentrout, TraubMiles, Connor, HodgkinHuxley, MorrisLecarPrescott, and MorrisLecar.

void currents ( double *  c) const
virtual

Implement this function to return in c the values of the individual ionic currents. The number of currents is defined by the size of currentnames the function currents(vector<string>&) const returns. The default implementation returns nothing.

Parameters
[out]cthe values of the individual ionic currents.
See Also
conductances(double*) const

Reimplemented in Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, TraubErmentrout, TraubMiles, Connor, HodgkinHuxley, MorrisLecarPrescott, and MorrisLecar.

string currentUnit ( void  ) const
virtual

Returns the unit of the currents returned by currents(double*) const. The default implementation returns uA/cm^2.

Reimplemented in Chacron2007, Edman, MilesDai, and MorrisLecar.

string inputUnit ( void  ) const
virtual

Returns the unit of the input (the stimulus). The default implementation returns uA/cm^2.

See Also
operator()()

Reimplemented in Chacron2007, Edman, MilesDai, and MorrisLecar.

void add ( void  )
virtual

Implement this function to add all necessary options. Set the flags of each option to either one of ScalingFlag, ModelFlag, or DescriptionFlag. For example:

addLabel( "Sodium current", ModelFlag );
addNumber( "gna", "Na conductivity", GNa, 0.0, 10000.0, 0.1, "mS/cm^2" ).setFlags( ModelFlag );
addNumber( "ena", "Na reversal potential", ENa, -200.0, 200.0, 1.0, "mV" ).setFlags( ModelFlag );

This implementation adds a label "Input" followed by two numbers "Gain" and "Offset". Call it in your reimplementation via

SpikingNeuron::add();
See Also
notify()

Reimplemented in Chacron2007, Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, SimplifiedTraub, TraubErmentrout1998, TraubErmentrout, TraubMiles, RushRinzel, Connor, HodgkinHuxley, MorrisLecarPrescott, MorrisLecar, FitzhughNagumo, and PassiveMembrane.

References SpikingNeuron::Gain, SpikingNeuron::Offset, and SpikingNeuron::ScalingFlag.

Referenced by NeuronModels::add(), PassiveMembrane::add(), FitzhughNagumo::add(), MorrisLecar::add(), HodgkinHuxley::add(), Crook::add(), MilesDai::add(), WangIKNa::add(), and Edman::add().

void notify ( void  )
virtual

Implement this function to read out the current values from the list of Options. For example:

ENa = number( "ena" );
GNa = number( "gna" );

This implementation reads out the gain() and the offset(). Call it in your reimplementation via

SpikingNeuron::notify();
See Also
add()

Reimplemented in Edman, WangIKNa, MilesDai, Crook, WangBuzsakiAdapt, SimplifiedTraub, TraubErmentrout1998, TraubErmentrout, TraubMiles, RushRinzel, Connor, HodgkinHuxley, MorrisLecarPrescott, MorrisLecar, FitzhughNagumo, and PassiveMembrane.

References SpikingNeuron::Gain, and SpikingNeuron::Offset.

Referenced by PassiveMembrane::notify(), FitzhughNagumo::notify(), MorrisLecar::notify(), MorrisLecarPrescott::notify(), HodgkinHuxley::notify(), Connor::notify(), RushRinzel::notify(), Crook::notify(), MilesDai::notify(), WangIKNa::notify(), Edman::notify(), and NeuronModels::readOptions().

double gain ( void  ) const
Returns
the gain that should be applied to the input.
See Also
offset()

References SpikingNeuron::Gain.

Referenced by NeuronModels::operator()().

double offset ( void  ) const
Returns
the offset that should be applied to the input.
See Also
gain()

References SpikingNeuron::Offset.

Referenced by NeuronModels::operator()().

Member Data Documentation

const int ScalingFlag = 16
static

Flag for selecting input / output gain and offset options.

Referenced by SpikingNeuron::add(), FitzhughNagumo::add(), and MorrisLecar::add().

const int ModelFlag = 32
static

Flag for selecting the model options.

Referenced by PassiveMembrane::add(), FitzhughNagumo::add(), MorrisLecar::add(), MorrisLecarPrescott::add(), HodgkinHuxley::add(), Connor::add(), RushRinzel::add(), TraubMiles::add(), TraubErmentrout::add(), TraubErmentrout1998::add(), SimplifiedTraub::add(), WangBuzsakiAdapt::add(), Crook::add(), MilesDai::add(), WangIKNa::add(), and Edman::add().

const int DescriptionFlag = 64
static

Flag for selecting the model description.

double Gain
protected

The gain that should be applied to the input.

Referenced by SpikingNeuron::add(), SpikingNeuron::gain(), MorrisLecar::MorrisLecar(), MorrisLecarPrescott::MorrisLecarPrescott(), and SpikingNeuron::notify().

double Offset
protected

The offset that should be applied to the input.

Referenced by SpikingNeuron::add(), MorrisLecar::MorrisLecar(), MorrisLecarPrescott::MorrisLecarPrescott(), SpikingNeuron::notify(), and SpikingNeuron::offset().

The documentation for this class was generated from the following files:
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