# Standard Run Tools¶↑

All standard tools are available from the NEURONMainMenu. The fastest way to load these tools is to execute:

from neuron import gui


Implementations of the standard tools are in $NEURONHOME/lib/hoc/*.hoc ## NEURON Main Menu¶↑ Main menu for standard control, graphing, menu generation. To pop up the panel execute: from neuron import gui  Warning In HOC code, you may see load_file('nrngui.hoc') instead, but that does not work for Python code as it does not start the thread that monitors for GUI events. Serious users should peruse the init and run procedures. The run chain that eventually calls fadvance() is  h.run --> h.continuerun --> h.step --> h.advance --> h.fadvance  There is often reason to substitute a new step or advance procedure to do intermediate calculations on the fly. Sometimes it is useful to replace the init() procedure. If so make sure you don’t take away functionality which is already there. See$NEURONHOME/lib/hoc/stdrun.hoc for the implementations of these procedures.

A simple example of overriding init:

h('proc init() {finitialize(v_init) nrnpython("myinit()")}')

def myinit():
# new code to happen after initialization here
print('initializing...')
# only need the following if states have been changed
if h.cvode.active():
h.cvode.re_init()
else:
h.fcurrent()
h.frecord_init()


### File¶↑

Pop up a File chooser for loading a previously save graphical interface session (default extension .ses) Session files may be loaded several times.

Pop up a File chooser for loading and executing a hoc file. Selected Hoc files are loaded only once.

Pop up a File chooser for dynamically loading a dll containing compiled and linked model descriptions. This is available only under mac os and mswin.

#### savesession¶↑

Save all the windows, mapped and hidden, in a session file. Greater control over exactly which windows are saved is given by the GroupManager and the Print & File Window Manager.

#### workingdir¶↑

Pops up a Directory chooser for changing to a specified working directory. If a dll file has not already been loaded and if a nrnmech.dll (under mswin) or a nrnmac.dll (under macos) exists in the “changed to” directory then the dll file is loaded.

#### recentdir¶↑

A list of the last 10 directories chosen from the workingdir menu item. On the mac and mswin, if a dll file has not been previously loaded and such a file exists in the directory, then it will be loaded.

Exits NEURON.

### Build¶↑

#### CellBuilder¶↑

Pops up a new instance of a CellBuilder for specifying the topology, shape, and biophysical properties of a neuron.

#### NetworkCell¶↑

##### FromCellBuilder¶↑

Pops up two tools used to specify synapse types and the locations of instances of these synapse types on a cell type defined by the CellBuilder This makes a network ready cell type that can be used by the Note that the only Point Processes used to construct synapse types are those whose model description contains a NET_RECEIVE block. e.g. see ExpSyn and NetworkBuilder.

##### ArtificialCell¶↑

Pops up a tool for constructing artificial network ready cells from PointProcess types containing a NetReceive block that can also act as a NetCon source. e.g. see IntFire1.

#### NetworkBuilder¶↑

Pops up a new instance of a NetBuild class for specifying cells and their NetCon connections. Only network ready cells defined by the NetworkCell tools can be used with this class.

### Tools¶↑

#### Fitting¶↑

##### Parameterized Function¶↑

Starts a FunctionFitter tool 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. The more powerful MulRunFitter is now recommended.

##### Run Fitter¶↑

Starts a RunFitter tool for optimizing simulation parameters to best fit data. The more powerful MulRunFitter is now recommended.

##### Multiple Run Fitter¶↑

Starts a MulRunFitter tool for general optimization problems. This combines and extends dramatically the features of the FunctionFitter and

#### Run Control¶↑

Pops up a RunControl panel for controlling simulation runs.

#### Variable Step Control¶↑

Pops up a VariableTimeStep panel for controlling the CVode variable time step, variable order method.

##### Usevariabledt¶↑

CVode is the integration method. See CVode.active().

##### Localvariabledt¶↑

CVode is the integration method and there is a separate dt for every cell.

##### AbsoluteTolerance¶↑

The absolute tolerance used by CVode when it is active is given by this value times the specific state scale factor. This latter is normally 1, eg, for voltage, but if the state is normally found in a range <<1 or >>1 the scale factor may be explicitly specified in a model description or in the interpreter. See CVode.atol() and CVode.atolscale()

#### PointProcesses¶↑

Several useful tools for managing PointProcesses See Point Processes and Artificial Cells for details about built-in point processes. The corresponding .mod file must in general be examined in order to understand the particulars about a given point process type.

#### Distributed Mechanisms¶↑

Several useful tools for managing density mechanisms such as distributed channels. See Mechanisms for details about built-in density mechanisms. The corresponding .mod file must in general be examined in order to understand the particulars about a given mechanism type.

##### Managers¶↑
###### Inserter¶↑

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.

###### Homogeneous Spec¶↑

Starts a ShowMechanism tool that is useful for specifying constant parameters for membrane mechanisms in all sections of a simulation.

##### Viewers¶↑
###### ShapeName¶↑

Starts a MenuExplore tool 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¶↑

Pops up a panel for displaying values associated with Sections.

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

###### Mechanisms Globals¶↑

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

##### celsius¶↑

Pops up a panel for viewing/setting the global temperature variable celsius .

##### globalRa¶↑

Pops up a panel for assigning a 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. It used to be displayed in the NEURONMainMenu but that location is now administratively incorrect and error prone for models which manage Ra through the CellBuilder.

#### Impedance¶↑

Menu of tools which use the Impedance class to calculate voltage attenuation as a function of position and frequency

##### Frequency¶↑

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¶↑

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¶↑

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¶↑

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

#### Archive And Hardcopy¶↑

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

See project

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 project control.

#### Miscellaneous¶↑

##### Family¶↑
###### Family1¶↑

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

###### Command¶↑

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

##### Builders¶↑
###### Kinetic Scheme Builder¶↑

Starts a KineticBuild tool for simulating a single channel kinetic scheme

### Graph¶↑

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 Run Control) the value of the functions are plotted.

#### Currentaxis¶↑

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

#### Stateaxis¶↑

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¶↑

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

#### VectorMovie¶↑

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¶↑

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¶↑

Starts a Grapher tool 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.

#### Voltageaxis¶↑

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 explicitly removed with the Delete command in the Graph menu.

### Vector¶↑

#### Save to File¶↑

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 vectors and performing simple manipulations on them.

See Save to File

#### GatherValues¶↑

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

#### Play¶↑

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

#### Display¶↑

Starts an VecWrap tool for displaying several vectors and performing simple manipulations on them.

#### Draw¶↑

Starts a tool for drawing a curve.

### Window¶↑

A list of all the ungrouped windows (except the NEURONMainMenu) and window groups. Windows mapped to the screen are indicated by a checkmark; others are hidden. Windows may be hidden by selecting the Hide item on the menubar under the window title. Windows may be hidden or mapped by selecting the item in the ungrouped window list. Selecting a window group will hide or map all the windows in that group.

#### Ungrouped¶↑

A window appears in this list if it is not a member of a window group. All ungrouped windows may be mapped or hidden by selection of the show or hide menu item.

#### GroupManager¶↑

Window group names appear in this list. Selecting this item pops up a window group manager used for creating, renaming, inserting/deleting windows into the group, and saving a selected group to a session file.

The window group manager is a dialog box so it must be closed after use.

When a window group name is defined it may be selected in the WindowGroups list. The windows of the group are indicated in the middle list. Selecting items in this list and the ungrouped windows list removes or inserts the window into the group.