What is 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.