A.1
A.2
A.3

B.1
B.2

C.1
C.2
C.3

D.1

E.1
E.2
E.3
E.4
E.5
E.6

Basic
Commands

Manual

Terminology:

Sections - somas, dendritic segments

Segments

Mechanisms have properties

associated with a specific point - electordes & synapses (handled as objects);

associated with whole section - channels

 

 

 

LIBRARY

load_file("name of file")

• Standard files include
  • nrngui.hoc - this file initializes the graphical user interface and will open a window with commands for accessing variables through a GUI.

GENERAL FUNCTIONS

• pt3dclear()
• pt3dadd()

SECTIONS

• Create name of section
• Access name of section

Sections have default properties Properties

• Length (L)
• Number of segments (nseg)
• Diameter (diam)
• Axial Resistance (Ra)

MEMBRANE MECHANISMS

• Insert (adding a membrane mechanism to a section)
  • pas
    • Properties
      • specific membrane conductance [S/cm²] (g_pas)
      • reversal potential [mV] (e_pas)
    • State Variables
  • hh
    • Properties - are used for calculation and can be changed
      • The maximum specific sodium channel conductance [Default value = 0.120 S/cm²] (gnabar_hh:)
      • gkbar_hh: The maximum specific potassium channel conductance [Default value = 0.036 S/cm²]
      • gl_hh: The maximum specific leakage conductance [Default value = 0.0003 S/cm²]
      • ena: The reversal potential for the sodium channel [Default value = 50 mV]
      • ek: The reversal potential for the potassium channel [Default value = -77 mV]
      • el_hh: The reversal potential for the leakage channel [Default value = -54.3 mV]
    • State Variables - can be printed
      • m_hh: The sodium activation state variable
      • h_hh: The sodium inactivation state variable
      • n_hh: The potassium activation state variable
      • ina: The sodium current
      • ik: The potassium current

POINT PROCESSES

• objectvar name of point process (e.g. objectvar stim)- Used to name a point process
  • Object
• Current Clamp - IClamp(position along segment 0-1)
  • Properties
    • Delay from onset of recording to start of current pulse (del)
    • Duration of the pulse/stimulus (dur)
    • Ampolitude of the pulse/stimulus (amp)
• Voltage Clamp - VClamp(position along segment 0-1)
• Standard Synapse - ExpSyn(position along segment 0-1)

 

Acknowledgements

Last modified on 10/29/04 by
Albert Borroni, CS/Neuoriscience Oberlin College (aborroni@oberlin.edu)

based on tutorial written by
Andrew Gillies (andrew@anc.ed.ac.uk)
David Sterratt (dcs@anc.ed.ac.uk)
which is originally based on the tutorials by Kevin E. Martin
with the assistance of Ted Carnevale and Michael Hines