ModelDB/showModel.cshtml

* simulation from:
Lytton WW; Contreras D; Destexhe A; Steriade M. Dynamic interactions
determine partial thalamic quiescence in a computer network model of
spike-and-wave seizures. J Neurophysiol, 77:1679-1696, 1997.
Fig 7 on p 1688  (jnphys77:1679.pdf)

Simulation of figure 7 may take several minutes. fig7.gif shows the output of
the simulation.

A phase plane analysis of a two cell interaction between a
thalamocortical neuron (TC) and a thalamic reticularis neuron (RE).
Figure legend : Analysis of spontaneous transition from mutual to
quiescent mode with bursting viewed in the RE T-channel m/h plane.
  A. RE neuron voltage trace (A1) and TC voltage trace (A2) shows 8
bursts of mutual activity followed by switch into the quiescent
state.  Color for each cycle give the key for the phase planes
below.  Interburst intervals are depicted in panel Ba.  Alternating
bursts are shown in panels Bb and Bc.  Initial oscillation appears
to be approximately period-2 with burst alternating with an
interburst depolarization.
  B. Apparent approximate period-2 oscillation illustrated to be
period-4: four cycles occur before the cycle repeats.  In each phase
plane, abscissa gives the value of mT (T channel activation),
ordinate the value of hT (T channel inactivation).
Trajectories run counterclockwise.  Interbursts alternated
between large cycles (solid line type) and small cycles (dashed line type)
  Burst Bb
showed a progression of gradually increasing hT, while burst Bc
was more coherent and showed no regular shift.  The inner loop in Ba
gradually collapsed to terminate the oscillation.  The subsequent
interburst (grey dashed) was similar in extent to large cycle.
  C. Inner and outer interburst cycles seen in the voltage-calcium plane
corresponded to Ba-inner and Ba-outer respectively.  The collapse of the inner
cycle is not as clear as in Ba, however.  Trajectories run clockwise.

* COMPILE and RUN:
  nrnivmodl
RUN:
  $CPU/special init.hoc -
RE-RUN:
  simsim() allows you to simulate a simulation by graphing out the
    saved data slowly so that you can see the phase planes unfold in time
    (can be slowed down by setting disp_delay to a large number)

* notes
1) graphics box comes up with graphs set to "New View" to allow closer
inspection of phase planes
2) use 'vecpanel()' call to bring up interactive tool for generating
other graphics
3) original figure only showed data from about t=600 rather than from beginning

* hoc list: from ~/nrniv/tcre2 geom.hoc v5, network.hoc v39, params.hoc v108
 run.hoc v105

init.hoc    master hoc file
geom.hoc    defines single compartment cells and column
network.hoc creates cells, connectivity and stimulation
params.hoc  sets parameters
run.hoc     additional initialization routines, graphing

boxes.hoc   make large arrays of graphs. not used here due to
specialized layout
declist.hoc list handling routines
decvec.hoc  vector handling routines
default.hoc flags and values
grvec.hoc   main vector graphic routines
local.hoc   additional initialization routines
nrnoc.hoc   main initialization routines
simctrl.hoc simulation control package using RCS

* mod list
HH_traub.mod            SUFFIX hh2
IAHP_destexhe.mod:      SUFFIX iahp
ICAN_destexhe.mod:      SUFFIX ican
IT2_huguenard.mod:      SUFFIX it2
IT_wang.mod             SUFFIX it
Ih_old.mod:             SUFFIX iar
calciumpump_destexhe.mod SUFFIX cad
gen.mod:                POINT_PROCESS gen
nmda.mod:               POINT_PROCESS NMDA
passiv.mod:             SUFFIX Pass
presyn.mod:             POINT_PROCESS PRESYN
pulse.mod:              POINT_PROCESS PULSE
AMPA.mod                POINT_PROCESS AMPA
NMDA.mod                POINT_PROCESS NMDA
GABAB1.mod              POINT_PROCESS GABAB1
GABALOW.mo              POINT_PROCESS GABALOW
rand.mod:               SUFFIX nothing

* mechanisms and processes used
Pass     leak current
hh2      Hodgin-Huxley INa and IK
it       TC IT current
iar      Ih current
it2      reticular IT current
iahp     slow IAHP
ican     slow ICAN
cad      calcium pump

gen      random spike generator
AMPA
NMDA
IClamp