StandardRunWidgets

GUI
   Electrode      Grapher        PointProcessGroupManager  ShapeBrowser  
   ExecCommand    ImpedanceTools  PointProcessLocator  ShowMechanism  
   Family         Inserter       PointProcessManager  VecWrap  
   FunctionFitter  MenuExplore   RunControl     VectorPlay     
   GatherVec      NEURONMainPanel  RunFitter    
All standard widgets are available from the NEURONMainPanel. The fastest way to load these widgets is to execute
xopen("$(NEURONDEMO)/lib/hoc/noload.hoc")
nrnmainmenu()
which avoids inefficiencies of the load_proc command on mswindows machines.

Implementations of the standard widgets are in $NEURONHOME/lib/hoc/*.hoc


NEURONMainPanel

StandardRunWidgets
   AxialResistivity  NewGraph    RealTime       
   DistributedMechanisms  PointProcesses  RunControl  
   Miscellaneous  Quiet          celsius        

Main menu for standard control, graphing, menu generation.

To pop up the panel execute:

		load_proc("nrnmainmenu")
		nrnmainmenu()

Serious users should peruse the init and run procedures. The run chain that eventually calls fadvance is

run continuerun step advance fadvance
There is often reason to substitute a new step or advance procedure to do intermediate calculations on the fly. Sometimes it is useful to replace the init() procedure. If so make sure you don't take away functionality which is already there. See $NEURONHOME/lib/hoc/stdrun.hoc for the implementations of these procedures.


Quiet

NEURONMainPanel
When checked, turns off movies and graph flushing during an InitRun Under some circunstances this can speed things up very considerably such as when using the RunFitter in the presence of a Shape Movie plot under MSWINDOWS.


RealTime

NEURONMainPanel
Running display of computation time. Resolution is 1 second.


celsius

NEURONMainPanel
The global temperature, celsius


AxialResistivity

NEURONMainPanel
Assigns uniform value of Ra (ohm-cm) to all sections. Ra used to be a global variable but is now a Section variable that can be different in different sections. This sets Ra forall sections equal to the value displayed in the fieldeditor.


RunControl

NEURONMainPanel
Pops up a RunControl panel for controlling simulation runs.


PointProcesses

NEURONMainPanel
   Managers       Viewers        


DistributedMechanisms

NEURONMainPanel
   Managers       Viewers        


Managers

DistributedMechanisms
   HomogeneousSpec  Inserter     


Inserter

Managers
Starts an Inserter for the currently accessed section that allows one to insert and uninsert density membrane mechanisms. Currently this is most useful for single compartment simulations.


HomogeneousSpec

Managers
Starts a ShowMechanism widget that is useful for specifing constant parameters for membrane mechanisms in all sections of a simulation.


Viewers

DistributedMechanisms
   MechanismsGlobals  NameValues  ShapeName     


ShapeName

Viewers
Starts a MenuExplore widget that allows one to figure out the correspondence between the physical location of a section and a section name. Also allows one to get a parameter menu for the selected section.


NameValues

Viewers
Pops up a panel for displaying values associated with Sections.

Almost completely superceded by the more complete ShapeName except that this widget can make a panel of a single mechanism type.


MechanismsGlobals

Viewers
Menu of possible membrane Mechanism's. Selecting an item pops up a panel showing the global parameters for this type of Mechanism.


NewGraph

NEURONMainPanel
   Currentaxis    PhasePlane     Stateaxis      Voltageaxis    
   Grapher        Shapeplot      VectorMovie    
For creating common kinds of graphs of functions of time. These graphs are connected to the standard run procedure such that at every step (see RunControl) the value of the functions are plotted.


Voltageaxis

NewGraph
Plots values vs t. Suitable for plotting voltage and concentrations, especially when calculations are secondorder correct. v(.5) of currently selected section is always plotted but can be explictly removed with the Delete command in the Graph menu.


Currentaxis

NewGraph
Plots values vs t-.5dt Suitable for plotting ionic currents (when calculations are secondorder correct).


Stateaxis

NewGraph
Plots values vs t+.5dt Suitable for plotting states such as m_hh, n_hh, etc. These plots may be very accurate when secondorder = 2.


Shapeplot

NewGraph
Starts a PlotShape . A picture of a neuron suitable for specifying time, space, and shape plots.


VectorMovie

NewGraph
Starts a Graph that is flushed when above plots are flushed. This is suitable for selecting vectors from the PlotWhat menu and seeing them change every time step.


PhasePlane

NewGraph
Starts a Graph for plotting f(t) vs g(t). When started a dialog box pops up requesting the expression for g(t). As in the PlotWhat browser for graphs you may enter any variable or function, but it should change when the RunControl's InitRun button is pressed.


Grapher

NewGraph
Starts a Grapher widget for plotting any expression vs a specified independent variable. Lines are not drawn on this graph in response to a run. However it can be made to control a family of runs.


Miscellaneous

NEURONMainPanel
   ArchiveAndHardcopy  Family    ParameterizedFunction  
   Clipboard      Impedance      RunFitter      
Several useful widgets for managing simulations.


Clipboard

Miscellaneous
   GatherValues   VectorPlay     VectorWrapper  
Menu for saving/retrieving the last Vector selection to a file. eg. from a PickVector as well as other Vector tools.

The format of the file is: 1) optional first line with the format

label:anystring
2) optional line with one number which is the count of points. 3) a tab separated pair of x, y coordinates each line. If there is no "count" line, there must be no empty lines at the end of the file and the last character must be a newline.

When the file is saved with this menu item, the label and count are always present in the file. For long files retrieval is much more efficient if the count is present.

The implementation of these operations is in $NEURONHOME/lib/hoc/stdlib.hoc


GatherValues

Clipboard
Starts a GatherVec tool collecting x,y values where x and y come from variables.


VectorPlay

Clipboard
Starts an VectorPlay tool for playing a vector into a variable.


VectorWrapper

Clipboard
Starts an VecWrap tool for specifying and executing a hoc command.

SEE ALSO

hoc_obj_


Family

Miscellaneous
   Command        Family         


Family

Family
Starts a Family widget for controlling a family of simulations. One defines a variable and set of values for looping over an action.


Command

Family
Starts an ExecCommand tool for specifying and executing a hoc command.


ParameterizedFunction

Miscellaneous
Starts a FunctionFitter widget for plotting a parameterized function and easily exploring its behaviour while varying the parameters. Also can fit the function to data using either the simplex or principal axis methods.


RunFitter

Miscellaneous
Starts a RunFitter widget for optimizing simulation parameters to best fit data.


Impedance

Miscellaneous
   Frequency      LogAvsX        Path           Shape          
Menu of tools which use the Impedance class to calculate voltage attenuation as a function of position and frequency


Frequency

Impedance
Pops up an ImpedanceRatio template tool for plotting the log of voltage attenuation (and other functions of impedance) between a selected injection and measurement site as a function of frequency.


Path

Impedance
Pops up a Impx template tool for plotting the log of voltage attenuation (and other functions of impedance) at a specific measurement/injection site as a function of a selected path along the neuron in which current is injected/measured.


LogAvsX

Impedance
Pops up a LogAvsX template tool for plotting the log of voltage attenuation (and other functions of impedance) between a specific measurement/injection site as a function of distance to every point on the cell.


Shape

Impedance
Pops up an ImpShape template tool for diplaying the morphoelectronic transform of neuron shape in which distance is represented as the negative log of attenuation.


ArchiveAndHardcopy

Miscellaneous
Checkin this simulation to RCS and print all windows on the printer.

See ProjectManagement

Saves all (saveable) windows in this session to the file start.ses ( save_session ). Prints the entire session to the filter prjnrnpr ( print_session ).

This menu item exists only when nrnmainmenu is executed after the file RCS/nrnversion exists. Ie when the files in the current working directory have been placed under NEURON ProjectManagement control.


neuron/stdrun/0stdrun.hel : Jul 18 10:43