README file for genesis code used to run simulations in

"Using potassium currents to solve signal-to-noise problems in
inhibitory feedforward networks of the striatum", by Kotaleski JH,
Plenz D, Blackwell KT. in J Neurophysiol. 2006 Jan;95(1):331-41

Main scripts are:

rect-isi05-g3c7fast-A100corr.g, which uses different correlation
values and the following use different values of A current:
rect-isi05-g3c7fast-A60.g
rect-isi05-g3c7fast-A100.g
rect-isi05-g3c7fast-A80.g
rect-isi05-g3c7fast-A120.g

In addition, the following main scripts evalutes effect of dopamine:

dopa-g3c7fast-A100.g
dopa-g3c7fast-A120.g
dopa-g3c7fast-A80.g

to run them, just type genesis {filename}

Note that the paramter corr is actually square root of the
correlation.

Before running the simulations, first it is necessary to create spike
trains.

E.g. one set of spike trains is the signal:
rect400-isi05-0
rect400-isi05-1, ...
rect400-isi05-308

is for a 400 ms long upstate repeated once every 700 msec up to 10
sec.  These files contain the spike times, and were created using an
exponential distribution with mean interspike interval of 0.5 sec.
The file rect200-isi05.log shows the parameters used with the C
program fs-sine to make these files.

another set of spike trains is the "noise" or down-state signal:
noise-isi"@{noiseisi}@"-" These files also contain spike times, and
were created using an exponential distribution with mean interspike
interval of {noiseisi}.  The script Poisson_train.g (which uses the
genesis object timetable) was used to make the noise spike trains.

To run the simulation in voltage clamp:
1. simdt=1e-6 (instead of 1e-5)

2. add the line
include vclamp.g (before or after the readcell command)

3. After the readcell command, add the following lines:
make_vclamp /fs/soma
setfield /vclamp/pulsegen level1 {vh} width1 0.00 delay1 1000.0
baselevel {vh} trig_mode 0 trig_time 0.0

where {vh} is the value of the voltage clamp

4. To look at the data, either use the make_vcgraph function, or add
the line: addmsg /vclamp/rev_sign /output/plot SAVE output

after the command: create asc_file /output/plot

See the file vclamp5-sim.g for an example (this was used to traces for 
figure 3).
