This directory includes several sample ISML models. For getting  
started with insilicoIDE (ISIDE), these sample models are prepared  
here. Users can load a model into ISIDE and can give a try to simulate  
it. The simulator provided by physiome.jp is called insilicoSim  
(ISSim) that is included in the package available at www.physiome.jp.  
Or users can convert a model into a C++ code and execute a binary file  
obtained by compiling the code. In this case users need a converter  
such as g++ and Visual C++ (for MS Windows). Models including  
morphology data and partial differential equations are also here. They  
are solved by FreeFEM++ application available at http://www.freefem.org/ff++/index.htm 
. So users need to install it before users try to simulate the models.


Here are the following five subdirectories.
1. SimulateWithISSim
2. SimulateWithFreeFem
3. SimulateWithCpp
4. ShowMorphoDynamics
5. PythonScripts

1. SimulateWithISSim includes models that can be simulated by ISSim.  
The models can be loaded on insilicoIDE (ISIDE) and you can edit them  
as you want. Press Simulation > insilicoSim in the menu bar of ISIDE  
then the simulator is launched. See Readme in the SimulateWithISSim  
directory for more details.

2. SimulateWithFreeFem includes models involving morphology  
information and partial differential equations. The PDEs are solved on  
the morphology with finite element method. The models must be  
converted into FreeFEM++ format form File > Export menu.
Then the converted file must be given to FreeFEM++ application.

3. SimulateWithCpp includes a model using template/instance scheme  
which is one of interesting feature of ISML specification. For  
example, when you want to create a 100 neurons which are basically the  
same with slight difference in static parameter values, then you do  
not need create each of them as an independent neuron. Instead, you  
just create one neuron, and define it as a template. Then you can  
create 100 instances of the template neuron. These 100 instances are  
basically the same with the template, but you can adjust some static  
parameters in each instance.
ISIDE can convert a model including template/instance scheme, so users  
can simulate it by compiling the C++ code. Buy ISSim is not able yet  
to support the template/instance scheme and cannot simulate such  
model. ISIDE also does not yet support template/instance scheme and  
cannot display correctly and edit models including the scheme.

4. ShowMorphoDynamics includes a sample model including morphology  
data, time series data and a directory including morphology data. A  
model can be loaded on ISIDE. Users can see the morphological  
expression of the model by selecting "Show Morphology Data" in a  
context menu appearing by pressing a right mouse button on a module.  
The model also includes a time series data. If users select "Show  
Morpho-Dynamics" in the context menu, a movie will appear on the  
screen which is created using the morphology data and the timeseries  
data.
The model is not for simulation by any means (ISSim, FreeFEM, C++).

5. PythonScripts includes several python scripts to create models.  
These scripts exemplify how to  use python API. Users can execute  
these scripts on a terminal window like as follows:
$ python ./sample/PyhtonScripts/make_N_coupled_hh.py
Notice that the current directly must be the directly that includes  
initialize.py
Then the script generates an ISML model in the current directly.
The model can be loaded in ISIDE and simulated either by ISSim or by  
converting to C++.