5.3 Operating NEURON

Starting and stopping a program

Initiation of a simulation is easily accomplished by going to the directory in which the desired nerve cell program is stored and issuing a command line as below. (Double forward slashes, //, will be used from here on to identify comment lines.)

nrniv nervecell.hoc -

// "nrniv" calls up the InterViews version of NEURON (Ver 3.0). 
          // "nervecell.hoc" is the hoc program which describes 
	   the cell(s) to be simulated and calls the panels
	   desired for control and parameter  manipulation.
                    // "-" tells nrniv to remain in memory

Exit from nrniv with Cntl-D

File & Print Manager Panel

Whenever the nervecell.hoc program calls for a window, this panel, appears in order to provide button control of file printing, saving, and retrieving such a window(s). How a window is brought up is described in Chapter 7. Programming and running simulations with NEURON 3.0.

The panel can be moved on the screen by "clicking" the left mouse button when the cursor is in the panel label area, "dragging", and releasing the button at the desired location. Both printing and file saving are managed by the contents of the boxes displayed. The left box represents the screen and shows the location and size of all open windows; numbered rectangles indicate their position. The right box represents a page of paper where selected (by a left mouse button click) windows may be placed for printing. The rectangles in the page box may be manipulated as follows:

• a. Location on the page is controlled by clicking and holding the left mouse button and dragging to the desired position.
• b. The size of a window on the page is controlled by pressing the middle mouse button on the desired rectangle (or simultaneous pressing both left and right button of a two button mouse) and dragging it downwards to decrease it size or up to increase it.
• c. Deleted a window from the page by clicking on it with the right button.

"Clicking" on the buttons on the left side of the File and Print Manager Panel offer the following options:

• The "Help" button brings up a help system window.
• The "Print" button sends a Postscript image of the page (displayed in the box on the right side) to the assigned printer.
• The "Print to file" button allows pages to be saved as a file in the following formats.
  • Postscript (.ps extension) for later printing and viewing panels and graphs
  • idraw format (.id extension) for editing, polishing for publication, etc. graphs with the idraw program (similar to Macpaint) included in NEURON 3.0.
  • Ascii for saving graphs as columns of Ascii numerbers representing the curves in a graph. This format is useful for importing into plotting and analysis programs.
• The "Session" button saves (with a .ses extension) for recall - for subsequent imulations - of groups of panels & graphs or trays as they appear on the screen. In Sessions, the location of the windows on the screen is important (rather than on the page) because retrieved windows are restored to their position on the screen at the time of saving. Retrieval of saved sessions is readily accomplished by pushing the retrieve button and selecting the desired session from the browser it displays.
• The "Other" button offers a submenu of choices:
  • Select Printer
  • " Land/port" - toggles the page orientation between landscape and portrait. The current mode is indicated by the orientation of the page icon.
  • " Tray" - Arranges a compact collection of panels and graphs: such a tray can be saved under a "Session"
  • Quit

  These functions are shown schematically in a figure.

  Back to: 5.1 Interpreter & Compiled Routines
  Back to: 5.2InterViews Version of NEURON
  Back to: Top of 5.3 Operations
  Forward to: 5.4 NEURON'S Main Menu