Instructions:

1- Copy all the folders in your computer.

2- Compile the mechanisms (in folder ../mechanism) with command
"nrnivmodl" (model is currently linux/unix only)

3- This step is necesary only if some mechanism is changed by the
user. In this version, the neurons are tuned with the current
mechanisms.(Gómez et al,Front Comput Neurosci 2011)

   For tunning the neuron:
     a) Select the cell that you want to tune in file
     "../experiment/tune-synapses/Simulation_gradient.hoc" in the
     variable ID_cell=1,2... (1=n123, 2=n125, 3=n128, 4=n129, 5=n130)
     b) Execute the tunning (../experiment/tune-synapses/sh
     run_simulation_gradient) and to copy output file in
     ../junio/tuned-nXXX-trunk/


4- Run simulation:

    a) Select the cell that you want to study in file
      "proximalCA1_1.hoc" in the variable ID_cell=1,2... (1=n123,
      2=n125, 3=n128, 4=n129, 5=n130)
    b) Select the Parameters inside
      "../experiment/junio/ParameterFile.hoc"
    c) Design the protocols inside
      "../experiment/junio/ProtocolsFile.hoc"
    d) Execute "../experiment/junio/ sh run_ProtocolsFile.hoc"
 

Gómez González JF, Mel BW, Poirazi P. Distinguishing Linear
vs. Non-Linear Integration in CA1 Radial Oblique Dendrites: It's about
Time. Front Comput Neurosci. 2011;5:44.
doi: 10.3389/fncom.2011.00044