Application of ISIDE to Create Models

  • Taishin Nomura
  • Yoshiyuki Asai
Part of the A First Course in “In Silico Medicine” book series (FCISM, volume 1)


In this chapter, usage of the insilico platform is demonstrated. The insilico platform is composed of three blocks, i.e. insilicoML, insilicoIDE and insilicoDB. InsilicoML (ISML) (Asai et al. 2008) is a language specification based on XML to describe mathematical models of physiological functions. InsilicoIDE (ISIDE) (Kawazu et al. 2007; Suzuki et al. 2008, 2009) is a software program on which users can simulate and/or create a model with graphical representations corresponding to the concept of ISML, such as modules and edges. ISIDE also has a command line interface to manipulate large scale models based on Python, which is a powerful script computer language. ISIDE exports ISML models into C\(++\) source codes, CellML format and FreeFEM\(++\) format for further analysis or simulation. InsilicoSim (ISSim) (Heien et al. 2009), which is a part of ISIDE, is a simulator for models written in ISML. InsilicoDB is formed from three databases, i.e. database of ISML models (Model DB), timeseries data (Time-series DB) and morphological data (Morphology DB). These databases are open to the public at the website


Membrane Module System Biology Markup Language Huxley Model Forwarding Edge Persistent Sodium Current 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Copyright information

© Springer 2011

Authors and Affiliations

  1. 1.The Center for Advanced Medical Engineering and InformaticsOsaka UniversityToyonakaJapan

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