What is insilicoIDE

insilicoIDE (ISIDE) is an integrated development environment for physiome, i.e. can act as an editor and browser of the multi-level physiological models written in insilicoML (ISML) . ISIDE can import models written in CellML format.

Simulations of the models created by ISIDE can be performed by insilicoSim (ISSim), which is bundled in a ISIDE package available at http://www.physiome.jp/downloads/index.html.

There is another way to run simulations. ISIDE can export C++ and JAVA source codes including numerical integration solvers. Thus users can perform simulations easily by compiling them.

Finite element simulation for partial differential equation based ISML model can be done by exporting FreeFem++ script. Users can perform finite element simulation by running the script.

insilicoIDE ver. 1

The specification of the insilicoML (ISML) is innovated. Now the version of ISML is 1.0. Based upon the upgrade of the ISML specification, we also upgraded the insilicoIDE (ISIDE). There exists a converter from ISML0.1 (previous version) to the ISML1.0, which works with ISIDE ver. 1.

insilicoIDE

Specifications

insilicoIDE (ISIDE) 1.4 can work on Windows 7, Vista, XP and Mac OS X 10.5, 10.6. Unix like operating systems such as FreeBSD and Linux will be supported soon. ISIDE parses an ISML model with using DOM (Document Object Model) by using APIs written in Python 2.5/2.6. The graphical user interface is built with Qt and C++.

The ISIDE package includes insilicoSim (ISSim), which is a simulator parsing models written in ISML and performing numerical calculations. ISSim can also parse and simulate SBML models and SBML-ISML hybrid models. Regarding the hybrid modeling, please refer the specification of ISML and tutorials. ISSim provides a graphical user interface for easy control of simulations. Besides that the package includes a command-line simulator "isim" which has a capability to perform a parallel computation which is useful for large scale simulations. However, the parallel computing works only on Mac OSX because of library related issues. Please have a look at instructions of isim for more detailed explanation.

Morphology based partial differential equation can be solved by FreeFem++, a open source adaptive finite element method codes, i.e. ISIDE exports an ISML model into the FreeFEM++ format. ISIDE equips a morphology viewer and preprocessing tools, and initial and boundary conditions are set by segmentation assignment visually. Strong form equation is automatically converted to weak form equation.

Downloads

Latest File Releases

Change log is here.

Notes
  • Geometry editor and Segment editor are unified in ver. 1.4.2.
    See About_change_of_Morphology_editor.pdf for details.
  • Supplementary Release Note for ver. 1.3 is here.
  • Python APIs are partially sorted out in ver. 1.2. See remark_on_python_apis.txt for details.
  • It is strongly recommended to uninstall the older version of ISIDE before installing the new version.
    To unistall the older version, run "uninstall.exe" (Windows) or delete the "insilicoPlatform" directory (Mac OS X).
Documents

See tutorial for more documents.

File Releases and Memos

insilicoIDE 1.4

Ver.FilenameDatePlatformInstall Memo
1.4.4insilicoIDE1.4.4.exe18 Nov. 2011Windows 7, Vista, XPinstall_memo_windows.txt
1.4.4insilicoIDE1.4.4_osx10.6.dmg18 Nov. 2011Mac OS X 10.6install_memo_osx.txt
1.4.4insilicoIDE1.4.4_osx10.5.dmg18 Nov. 2011Mac OS X 10.5 Intelinstall_memo_osx.txt
1.4.3insilicoIDE1.4.3.exe21 Oct. 2011Windows 7, Vista, XPinstall_memo_windows.txt
1.4.3insilicoIDE1.4.3_osx10.6.dmg21 Oct. 2011Mac OS X 10.6install_memo_osx.txt
1.4.3insilicoIDE1.4.3_osx10.5.dmg21 Oct. 2011Mac OS X 10.5 Intelinstall_memo_osx.txt
1.4.2insilicoIDE1.4.2.exe12 Sep. 2011Windows 7, Vista, XPinstall_memo_windows.txt
1.4.2insilicoIDE1.4.2_osx10.6.dmg12 Sep. 2011Mac OS X 10.6install_memo_osx.txt
1.4.2insilicoIDE1.4.2_osx10.5.dmg12 Sep. 2011Mac OS X 10.5 Intelinstall_memo_osx.txt
1.4.1insilicoIDE1.4.1.exe19 Jul. 2011Windows 7, Vista, XPinstall_memo_windows.txt
1.4.1insilicoIDE1.4.1_osx10.6.dmg19 Jul. 2011Mac OS X 10.6install_memo_osx.txt
1.4.1insilicoIDE1.4.1_osx10.5.dmg19 Jul. 2011Mac OS X 10.5 Intelinstall_memo_osx.txt
1.4.0.2insilicoIDE1.4.0.2.exe10 Jun. 2011Windows 7, Vista, XPinstall_memo_windows.txt
1.4.0.2insilicoIDE1.4.0.2_osx10.6.dmg10 Jun. 2011Mac OS X 10.6install_memo_osx.txt
1.4.0.2insilicoIDE1.4.0.2_osx10.5.dmg10 Jun. 2011Mac OS X 10.5 Intelinstall_memo_osx.txt
1.4.0.1insilicoIDE1.4.0.1.exe20 May 2011Windows 7, Vista, XPinstall_memo_windows.txt
1.4.0.1insilicoIDE1.4.0.1_osx10.6.dmg20 May 2011Mac OS X 10.6install_memo_osx.txt
1.4.0.1insilicoIDE1.4.0.1_osx10.5.dmg20 May 2011Mac OS X 10.5 Intelinstall_memo_osx.txt
1.4.0insilicoIDE1.4.0.exe28 Apr. 2011Windows 7, Vista, XPinstall_memo_windows.txt
1.4.0insilicoIDE1.4.0_osx10.6.dmg28 Apr. 2011Mac OS X 10.6install_memo_osx.txt
1.4.0insilicoIDE1.4.0_osx10.5.dmg28 Apr. 2011Mac OS X 10.5 Intelinstall_memo_osx.txt

insilicoIDE 1.3

Ver.FilenameDatePlatformInstall Memo
1.3.3insilicoIDE1.3.3.exe10 Feb. 2011Windows XP, 2000install_memo_windows.txt
1.3.3insilicoIDE1.3.3_osx10.6.dmg10 Feb. 2011Mac OS X 10.6install_memo_osx.txt
1.3.3insilicoIDE1.3.3_osx10.5.dmg10 Feb. 2011Mac OS X 10.5 Intelinstall_memo_osx.txt
1.3.2insilicoIDE1.3.2.exe28 Dec. 2010Windows XP, 2000install_memo_windows.txt
1.3.2insilicoIDE1.3.2_osx10.6.dmg28 Dec. 2010Mac OS X 10.6install_memo_osx.txt
1.3.2insilicoIDE1.3.2_osx10.5.dmg28 Dec. 2010Mac OS X 10.5 Intelinstall_memo_osx.txt
1.3.1insilicoIDE1.3.1.exe06 Oct. 2010 Windows XP, 2000install_memo_windows.txt
1.3.1insilicoIDE1.3.1_osx10.6.dmg06 Oct. 2010Mac OS X 10.6install_memo_osx.txt
1.3.1insilicoIDE1.3.1_osx10.5.dmg06 Oct. 2010Mac OS X 10.5 Intelinstall_memo_osx.txt
1.3.0insilicoIDE1.3.0.exe01 Sep. 2010Windows XP, 2000install_memo_windows.txt
1.3.0insilicoIDE1.3.0_osx10.6.dmg01 Sep. 2010Mac OS X 10.6install_memo_osx.txt
1.3.0insilicoIDE1.3.0_osx10.5.dmg01 Sep. 2010Mac OS X 10.5 Intelinstall_memo_osx.txt

insilicoIDE 1.2

Ver.FilenameDatePlatformInstall Memo
1.2.1insilicoIDE1.2.1.exe20 Jul. 2010Windows XP, 2000install_memo_windows.txt
1.2.1insilicoIDE1.2.1_osx10.6.dmg20 Jul. 2010Mac OS X 10.6install_memo_osx.txt
1.2.1insilicoIDE1.2.1_osx10.5.dmg20 Jul. 2010Mac OS X 10.5 Intelinstall_memo_osx.txt
1.2.1sample.zip20 Jul. 2010 - only sample models
1.2.0insilicoIDE1.2.0.exe25 Jun. 2010 Windows XP, 2000install_memo_windows.txt
1.2.0insilicoIDE1.2.0_osx10.6.dmg25 Jun. 2010Mac OS X 10.6install_memo_osx.txt
1.2.0insilicoIDE1.2.0_osx10.5.dmg25 Jun. 2010Mac OS X 10.5 Intelinstall_memo_osx.txt

insilicoIDE 1.1

Ver.FilenameDatePlatformInstall Memo
1.1.2insilicoIDE1.1.2.exe31 Mar. 2010Windows XP, 2000-
1.1.2insilicoIDE1.1.2_osx10.6.dmg31 Mar. 2010Mac OS X 10.6install_memo_osx.txt
1.1.2insilicoIDE1.1.2_osx10.5.dmg31 Mar. 2010Mac OS X 10.5 Intelinstall_memo_osx.txt
1.1.1insilicoIDE1.1.1.exe05 Mar. 2010 Windows XP, 2000-
1.1.1insilicoIDE1.1.1_osx10.6.dmg05 Mar. 2010Mac OS X 10.6install_memo_osx.txt
1.1.1insilicoIDE1.1.1_osx10.5.dmg05 Mar. 2010Mac OS X 10.5 Intelinstall_memo_osx.txt
1.1.0insilicoIDE1.1.0.exe16 Feb. 2010Windows XP, 2000-
1.1.0insilicoIDE1.1.0_osx10.6.dmg16 Feb. 2010Mac OS X 10.6install_memo_osx.txt
1.1.0insilicoIDE1.1.0_osx10.5.dmg16 Feb. 2010Mac OS X 10.5 Intelinstall_memo_osx.txt

insilicoIDE 1.0

Ver.FilenameDatePlatformInstall Memo
1.0.4 insilicoIDE1.0.4.exe15 Jan. 2010Windows XP, 2000install_memo_windows.txt
1.0.4 insilicoIDE1.0.4_osx10.6.dmg15 Jan. 2010Mac OS X 10.6 install_memo_osx.txt
1.0.4 insilicoIDE1.0.4_osx10.5.dmg 15 Jan. 2010Mac OS X 10.5 Intel install_memo_osx.txt
1.0.3insilicoIDE1.0.3.exe8 Jan. 2010 Windows XP, 2000install_memo_windows.txt
1.0.3insilicoIDE1.0.3_osx10.6.dmg13 Jan. 2010 Mac OS X 10.6install_memo_osx.txt
1.0.3 insilicoIDE1.0.3_osx10.5.dmg 13 Jan. 2010 Mac OS X 10.5 Intelinstall_memo_osx.txt
1.0.2 insilicoIDE1.0.2.zip 30 Nov. 2009 Windows XP, 2000 install_memo_windows.txt
1.0.2 insilicoIDE1.0.2.tar.gz 30 Nov. 2009 Mac OS X 10.5 Intel-
1.0.0b insilicoIDE1.0.0b_win.zip 13 Oct. 2009 Windows XP, 2000 install_memo_windows.txt
1.0.0b insilicoIDE1.0.0b.pkg 13 Oct. 2009 Mac OS X 10.5 Intel-

insilicoIDE 0.3

Ver.FilenameDatePlatformHow to InstallUser Manual
0.3.1 insilicoIDEsetup.exe 26 Feb. 2009 Windows XP, 2000 howtoinstall_0.3.1.html readme_getting_started.pdf
0.3.1 insilicoIDE0.3.1.zip 26 Feb. 2009 Windows XP, 2000 howtoinstall_0.3.1.html readme_getting_started.pdf
0.3.0 insilicoIDEsetup.exe 06 Feb. 2009 Windows XP, 2000 howtoinstall_0.3.html readme_getting_started.pdf

insilicoIDE 0.2

Ver.FilenameDatePlatformHow to InstallUser Manual
0.2.6 insilicoIDE0.2.6.zip 16 Dec. 2008 Windows XP, 2000 howtoinstall_0.2.html gettingstarted_0.2.5-1.html
0.2.5 insilicoIDE0.2.5.zip 20 Oct. 2008 Windows XP, 2000 howtoinstall_0.2.html gettingstarted_0.2.5-1.html
0.2.4 insilicoIDE0.2.4.zip 18 Sep. 2008 Windows XP, 2000 howtoinstall_0.2.html gettingstarted_0.2-1.html
0.2.3 insilicoIDE0.2.3.zip 11 Sep. 2008 Windows XP, 2000 howtoinstall_0.2.html gettingstarted_0.2-1.html
0.2.2 insilicoIDE0.2.2.zip 03 Sep. 2008 Windows XP, 2000 howtoinstall_0.2.html gettingstarted_0.2-1.html
0.2.1 insilicoIDE0.2.1.zip 11 Aug. 2008 Windows XP, 2000 howtoinstall_0.2.html gettingstarted_0.2-1.html
0.2.0 insilicoIDE0.2.zip 15 Jul. 2008 Windows XP, 2000 howtoinstall_0.2.html gettingstarted_0.2-1.html

insilicoIDE 0.1

Ver.FilenameDatePlatformHow to InstallUser Manual
0.1.1 insilicoIDE0.1.1.zip 20 Jun. 2008 Windows XP, 2000 howtoinstall_0.1.1.html gettingstarted_0.1.1-1.html
0.1.1 insilicoIDE 0.1.1pg.zip 20 Jun. 2008 Windows XP, 2000 howtoinstall_0.1.1.html gettingstarted_0.1.1-1.html
0.1.0 insilicoIDE0.1.zip 21 May 2008 Windows XP, 2000 howtoinstall_0.1.0.html gettingstarted_0.1.0-1.html
0.1.0 insilicoIDE 0.1.0.pg.zip 21 May 2008 Windows XP, 2000 howtoinstall_0.1.0.html gettingstarted_0.1.0-1.html