insilicoIDE 0.3 How to Install

This tutorial provides step-by-step instructions on how to install insilicoIDE 0.3.

For the moment, insilicoIDE does not support Windows Vista.
Windows XP is highly recommended as working platform for insilicoIDE 0.3.

1. Download insilicoIDE 0.3 (Download insilicoIDEsetup.exe).

The latest insilicoIDE is available at http://www.physiome.jp/downloads/index.html .

2. Install

Execute insilicoIDEsetup.exe, then an install wizard starts.

At the first stage, users can select components to install. Then at the second stage, users select the location path to install.

The wizard offers four check boxes to select the components to install.

  1. insilicoIDE: insilcoIDE executable file and several files which are necessary for simulating models and drawing graphs.
  2. Visual C++ 2005 Express Edition: This is used as default compiler for simulating models.
  3. Libraries: Visualization on insilicoIDE and compiling models for simulations depends on
  4. Model samples: Several sample models written in insilicooML are included in the package so that users can immediately test insilicoIDE. See readme_getting_started.pdf for quick guide.

If users have already installed Visual C++ 2005 or 2008 in the default directory in the Windows system, the second choice (Visual C++ 2005 Express Edition) is not necessary and may be checked off. In case that users want to install Visual C++ 2005 Express Edition manually, users uncheck the second check box (Visual C++ 2005 Express Edition) and see section 3.1 below.

The details of libraries installed by the wizard are described below in section 3.2. If users prefer installing them manually, uncheck the chek box "Libraries", and proceed as explained in section 3.2. Notice that these libraries are used for visualizing morphological information on insilicoIDE, drawing graphs of dynamical variables, performing simulations with vector, matrix calculations, and parallel computation.

If users fully installed insilicoIDE 0.3, the following files and directories are located in the place that users selected to install at the wizard. If users install sample insilicoML models, several morphology data and time series data are also installed as well as inslicoML files. The morphology data are used in models DoublePendulum.xml model and Strove_1999_neuromusculoskeletalSystem.xml. The time series data is used in Hodgkin_Huxley_1952_model_forAPClamp.xml. As explained in tutorial documentation, users can try out these modes immediately after installing insilicoIDE.

  • InsilicoIDE.exe
  • glut32.dll
  • ISIDEResultViewer.py
  • showgraph.py
  • lapackpp.dll
  • lapackpp.lib
  • readme_getting_started.pdf
  • readme_how_to_install.pdf
  • samples/
    • ActionPotentialGenerator.xml
    • DoublePendulum.xml
    • Hodgkin_Huxley_1952_model.xml
    • Hodgkin_Huxley_1952_model_forAPClamp.xml
    • Sinusoidal_current_generator.xml
    • Stroeve_1999_neuromusculoskeletalSystem.xml
    • VisualModel/
      • bar.wrl
      • Forearm.wrl
      • Head.wrl
      • Trunk.wrl
      • Upperarm_r.wrl
    • TimeSeriesData/
      • HHmodel_voltage.csv
  • library/
    • gtk-dev-2.12.9-win32-2.exe
    • lapackpp-2.5.1-setup.exe
    • library_setup.bat
    • matplotlib-0.98.1.win32-py2.5.exe
    • numpy-1.1.0-win32-superpack-python2.5.exe
    • pycairo-1.4.12-1.win32-py2.5.exe
    • pygobject-2.14.1-1.win32-py2.5.exe
    • pygtk-2.12.1-2.win32-py2.5.exe
    • python-2.5.2.msi
    • vcsetup.exe
  • inSilicoSim/
    • ...

After successful installation, a white canvas of insilicoIDE will appear by double clicking InsilicoIDE.exe.

3. Instructions for manual installation

The following instructions are for users who prefer installing relevant libraries manually instead of using above install wizard.

3.1. Install Visual C++ 2005 or 2008 (Express Edition for free).

If users have already installed Visual C++ 2005 or 2008 to the default directory or will not use a functionality to draw a graph of simulated waveforms on insilicoIDE (i.e., if users only use insilicoIDE to generate C++ source codes) or skip this step.

When users try to draw a graph of simulated waveforms, the insilicoIDE package generates C++ source codes, compiles the codes and runs the simulation behind. In this process, the insilicoIDE uses Visual C++ compiler located at "C:\Program Files\Microsoft Visual Studio 8\VC\bin\cl.exe" or "C:\Program Files\Microsoft Visual Studio 9.0\VC\bin\cl.exe". For this compilation, users need to install Visual C++ 2005 or 2008.

Install Visual C++ 2005 or 2008 to the default directory.
If users do not have Visual C++ 2005 or 2008, users can download them for free.

3.2. Installing libraries manually, follow the steps below.

The insilicoIDE requires the following libraries which are freely available in the internet. To install those libraries, please follow the instruction of each library. In most cases, chek the box "Install Library".

GLUT for OpenGL

glut32.dll should be in the same directory with InsilicoIDE.exe, or in the directory
C:\WINDOWS\system32. Detailed information can be found inhttp://www.opengl.org/resources/libraries/glut/.

METIS for parallel simulation

For the prallel simulation, insilicoIDE can generate C++ source codes with MPI (Message Passing Interface). The METIS library is required to compile parallel simulations, available at http://glaros.dtc.umn.edu/gkhome/metis/metis/download. Please install the METIS library, too, if users are interested in the parallel computation.

insilicoIDE includes METIS library in the "inSilicoSim" directory.

Python and GTK for drawing graph

Users need to install libraries related to python and GTK for drawing graphs. The relevant libraries are the following.

Library File Name
1   Gtk+ Development Environment for windows   gtk-dev-2.12.9-win32-2.exe
2   Python 2.5.2   python-2.5.2.msi
3   Numerical Python 1.1.0   numpy-1.1.0-win32-superpack-python2.5.exe
4   Python bindings for the cairo graphics library 1.4.12   pycairo-1.4.12-1.win32-py2.5.exe
5   the Python bindings for GObject   pygobject-2.14.1-1.win32-py2.5.exe
6   GTK+ for Python   pygtk-2.12.1-2.win32-py2.5.exe
7   A pure python plotting library   matplotlib-0.98.1-win32-py2.5.exe

Please follow each installation indication for each library. Almost all cases, what users need to do is to download them and double click them.
Since some of above libraries depend to other libraries, the order of the installation is important. Keep the above order indicated in the table.

It is required to locate ISIDEResultViewer.py which is included in the package at the same folder as InsilicoIDE.exe for drawing graphs.

Lapack++

Users need to install and compile following files to use matrix operation library " Lapack++".

File Name
1   lapackpp-2.5.1-setup.exe
2   lapackpp-2.5.2.tar.gz

  1. Install the lapackpp-2.5.1-setup.exe by double clicking it.
  2. Unpack the lapackpp-2.5.2.tar.gz and compile the source code.
  3. After compiling the codes, a library " lapackpp.lib" is needed to be copied to the same directory with InsilicoIDE.exe.
See http://lapackpp.sourceforge.net/ for more details.