===== Readme for Python Scripts ======

This text describes how to run sample Python scripts.

To run the python script, users must make following environment.

** Windows **

1. Install Python 2.5 (available at http://www.python.org/).
Pythonfs version should be 2.5.

2. Install Libxml and Libxslt Python bindings of Python 2.5.
The installer is available at http://users.skynet.be/sbi/libxml-python/.

** Mac OS X **

Install Libxml2 for Mac OS X.


===== About Files =====

** make_bvp_pulse.py **

This script creates bvp pulse model, "bvp_pulse_c.isml".
The model is the same as bvp_pulse.isml at the directory of sample/SimulateWithISSim.
PubMed page of this model's referece is http://www.ncbi.nlm.nih.gov/pubmed/19431309


** make_izhikevich_pulse.py **

This script creates bvp pulse model, "izhikevich_pulse_c.isml".
The model is the same as Izhikevich_2003_neuron_model.isml at the directory of sample/SimulateWithISSim.
PubMed page of this model's referece is http://www.ncbi.nlm.nih.gov/pubmed/18244602


** make_N_coupled_fhn.py **

This script creates coupled FitzHugh-Nagumo model, "N_coupled_FHN_model.isml".
(The single FitzHugh-Nagumo model is single-FHN_model.isml at the directory of sample/SimulateWithISSim)
Variable parameter is  the coupling number N at line 31. 
The default number is "N = 3".


** make_N_coupled_hh.py **

This script creates coupled Hodgkin-Huxley model, "N_coupled_HH_model.isml".
(The single Hodgkin-Huxley model is HodgkinHuxley_1952_neuron_model.isml at the directory of sample/SimulateWithISSim)

Variable parameter is  the coupling number N at line 39. 
The default number is "N = 2".


** adder.isml and gap_junction.isml **

These models are used in make_N_coupled_fhn.py and make_N_coupled_hh.py for coupling models.


===== How to Run Scripts =====

Copy the python file (.py) to the same directory and name it as "initilalize.py".
This directory is different between Windows and Mac OS X.
The default directories are:

  * Windows: C:\Program Files\insilicoPlatform\insilicoIDE
  * Mac OS X: /Applications/insilicoPlatform

Move to the above directry, then type command of "python %file_name%" at your terminal (e.g. Command Prompt, Darwin).
Then,  insilicoML file (.isml) will be cretated.