GUI CellBuilder Grapher NEURONMainPanel ShapeBrowser Electrode ImpedanceTools PointProcessGroupManager ShowMechanism ExecCommand Inserter PointProcessLocator VecWrap Family KineticBuild PointProcessManager VectorPlay FunctionFitter MenuExplore RunControl GatherVec MulRunFitter RunFitterAll standard widgets are available from the NEURONMainPanel. The fastest way to load these widgets is to execute
which avoids inefficiencies of the load_proc command on mswindows machines.xopen("$(NEURONDEMO)/lib/hoc/noload.hoc") nrnmainmenu()
Implementations of the standard widgets are in $NEURONHOME/lib/hoc/*.hoc
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 fadvanceThere 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.
NEURONMainPanelWhen 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.
NEURONMainPanelRunning display of computation time. Resolution is 1 second.
NEURONMainPanelThe global temperature, celsius
NEURONMainPanelAssigns 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.
NEURONMainPanelPops up a RunControl panel for controlling simulation runs.
NEURONMainPanel Managers Viewers
NEURONMainPanel Managers Viewers
DistributedMechanisms HomogeneousSpec Inserter
ManagersStarts 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.
ManagersStarts a ShowMechanism widget that is useful for specifing constant parameters for membrane mechanisms in all sections of a simulation.
DistributedMechanisms MechanismsGlobals NameValues ShapeName
ViewersStarts 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.
ViewersPops 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.
ViewersMenu of possible membrane Mechanism's. Selecting an item pops up a panel showing the global parameters for this type of Mechanism.
NEURONMainPanel Currentaxis PhasePlane Stateaxis Voltageaxis Grapher Shapeplot VectorMovieFor 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.
NewGraphPlots 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.
NewGraphPlots values vs t-.5dt Suitable for plotting ionic currents (when calculations are secondorder correct).
NewGraphPlots values vs t+.5dt Suitable for plotting states such as m_hh, n_hh, etc. These plots may be very accurate when secondorder = 2.
NewGraphStarts a PlotShape . A picture of a neuron suitable for specifying time, space, and shape plots.
NewGraphStarts 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.
NewGraphStarts 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.
NewGraphStarts 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.
NEURONMainPanel ArchiveAndHardcopy Family ParameterizedFunction Clipboard Impedance RunFitterSeveral useful widgets for managing simulations.
Miscellaneous GatherValues VectorPlay VectorWrapperMenu 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:anystring2) 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
ClipboardStarts a GatherVec tool collecting x,y values where x and y come from variables.
ClipboardStarts an VectorPlay tool for playing a vector into a variable.
ClipboardStarts an VecWrap tool for specifying and executing a hoc command.
Miscellaneous Command Family
FamilyStarts a Family widget for controlling a family of simulations. One defines a variable and set of values for looping over an action.
FamilyStarts an ExecCommand tool for specifying and executing a hoc command.
MiscellaneousStarts 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.
MiscellaneousStarts a RunFitter widget for optimizing simulation parameters to best fit data.
Miscellaneous Frequency LogAvsX Path ShapeMenu of tools which use the Impedance class to calculate voltage attenuation as a function of position and frequency
ImpedancePops 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.
ImpedancePops 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.
ImpedancePops 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.
ImpedancePops up an ImpShape template tool for diplaying the morphoelectronic transform of neuron shape in which distance is represented as the negative log of attenuation.
MiscellaneousCheckin this simulation to RCS and print all windows on the printer.
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.