This is the readme file for:

Gomez Gonzalez 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

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 (sh ../experiment/tune-synapses/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/run_ProtocolsFile.hoc