5.4 NEURON's Main Menu Panel
When NEURON 3.0 reads a hoc file and executes a call for the
procedure "nrnmainmenu()",
it brings us the
panel with buttons as shown below.
The buttons on this panel provide access to all the major
operations necessary for simulation control up to what might be called the
"oscilloscope" level of complexity. An example would be stimulation of the cell, recording the
time course of a few variables, and managing changes in a few parameters.
This level of complexity is sufficient for a large variety of problems such as
- Monitoring all assignments of morphology, distributed mechanisms,
point processes, ion concentrations, etc. when starting a new simulation.
- Exploring the range of behaviors associated with parameter changes.
- Manual fitting of parameters to experimental data, for example as described
in Chapter 3. under Manual Iterative Searches for
"best fit"
The extraction of summary information from a large series of sumulation runs
will usually "problem specific" and will probably require a hoc program to
capture and plot the desired information. Examples of this will be available in
Chapter 15 of
the Reference Manual.
The computation time (CPU time) is
shown on the top line. The temperature for the simulation is shown in degrees Celsius.
The default value for the axial resistivity is the choice made by Hodgkin & Huxley (1952d)
35.4 ohm-cm
for calculation of the velocity of their propagating action potential. For land based animals,
this resistivity should be increased about 5-fold to 150ohm-cm.
The numbers in the boxes next to the "celsius" and "Axial Resistivity"
buttons can be changed by the
Field editor . This editor functions in all of the
value fields associated with panel buttons.
Graphic programming and simulation control are made available
by "clicking" on the last four buttons
in the main panel:
"Run Control" brings up another
major panel; this one is most useful for control of simulation runs. It's
use and functions are described in some detail in Chapter 8.
"New Graph" brings us a browser from which to choose a variety of graph types such as voltage or current vs time.
Its functions are described in more detail in Chapter 8 under
Graphs
"Point Processes" offers a sub-menu choice of Managing or
Viewing .
"Managing" provides for
the creation and placement of a
point process or an electrode.
The "Electrode" itself is also a point
process but includes the capability of not only toggling between a
current clamp
and a voltage clamp but also to run through a family of voltage clamp levels.
Viewing. The parameters of existing processses may be viewed by sequential selection of the Point Process "Viewers" button, "Point Processes", the process
desired. The screen will display panels as in this figure.
"Distributed Mechanisms" offers a
sub-menu choice of Managing or Viewing these mechanisms.
"Managing" allows the insertion of channels,
mechanisms, etc., in particular sections or homogeneously throughout the structure.
" "Miscellaneous" brings up a panel of global
assignments 
Details on the use of these sub-menus will be presented
as we work through a simple sample application program.