Physiome.jp -toward in silico human

Physiome.jp has been established to provide building blocks useful to develop in silico human. The blocks will include mathematical models and experimental data representing physiological functions.

Physiome.jp is a part of the Worldwide Integrative Biomedical Research Cooperation to promote Physiome and Systems Biology. The building blocks (modules, models, biological data) representing biological functions and structure are databased and served as elements in the catalogue of human knowledge. They can be reused for deeper understanding of human physiology, eventually contributing to establishment of in silico medicine and predictive medicine.

Physiome Project

Platform Overview

Our developing platform directing towards Physiome Project is composed of three pieces: insilicoML, insilicoIDE, and insilicoDB.

insilicoML is a XML-based description language for mathematical models of physiological functions.

insilicoIDE is the integrated development environment that can be used as a composer, viewer and simulator of ISML models.

insilicoDB is a database to store ISML models.

What's New
15 Jan 2010
insilicoIDE 1.0.4 is released.
  • Update Berkeley DB XML to 2.5.16 and Qt to 4.6.
8 Jan 2010
insilicoIDE 1.0.3 is released.
  • insilicoSim (a simulator of ISML) is added.
  • insilico terminal is updated.
  • Model Editor is updated.
  • Several bugs have been fixed.
14 Dec 2009
SBML and ISML Joint Winter School "Winter School on Computational Modeling in Biology"
will be held from 14 December 2009 to 18th December at OIST in Okinawa, Japan.
See http://www.mei.osaka-u.ac.jp/gCOE/school/2009_winter/ for more details.
30 Nov 2009
insilicoIDE 1.0.2 is released.
  • Directory structure is changed (Mac OSX version).
  • Model Editor is updated.
  • Several bugs have been fixed.
13 Oct 2009
insilicoIDE 1.0.0b is released.
10 Jul 2009
About ISDB (the page that explains how to use ISDB) is available.
25 Jun 2009
A trial version of insilico Time-series Database is relaeased.
26 Feb 2009
insilicoIDE 0.3.1 is available.
  • Minor modification enabling insertion of creator information was made on insilicoIDE 0.3.
06 Feb 2009
insilicoIDE 0.3 is available.
  • Vector and matrix operations are supported.
  • Visualization functionality for Morpho-dynamics is enhanced.
  • Several bugs have been fixed.
  • Quick ISIDE installation setup.exe file is available.
  • This may be the finial verion of insilicoIDE 0.X.

News: insilicoIDE 1.0 (ISIDE 1.0) and insilicoML 1.0 (ISML 1.0) will be released in a few months.
28 Jan 2009
A paper on " Specifications of insilicoML 1.0: A Multilevel Biophysical Model Description Language"
by Asai et al. has been published on The Journal of Physiological Sciences.
26 Dec 2008
Summary of A Questionnaire Survey on the Model Sharing
in the Fields of Biosciences and Bioengineering in Japan
performed by Physiome and Systems Biology Initiative Japan
has been published.
22 Dec 2008
The 3rd MEI International Symposium
"Physiome and Systems Biology for Integrated Life Sciences and Predictive Medicine"
Symposium Reports (PPT slides) have been published.
16 Dec 2008
insilicoIDE 0.2.6 is available.
  • Time-Series data can be used for simulation
29 Nov 2008
insilicoDB is updated to XML DB.
A trial version of insilico Morphology Database is relaeased.
20 Oct 2008
insilicoIDE 0.2.5 is available.
  • MPI parallel computation functionality has been improved.
  • Pubmed information can be linked from insilicoIDE.
18 Sep 2008
insilicoIDE 0.2.4 is available.
11 Sep 2008
insilicoIDE 0.2.3 is available.
03 Sep 2008
insilicoIDE 0.2.2 is available.
11 Aug 2008
insilico IDE 0.2.1 is available.
25 Jul 2008
Tutorial is ready.
15 Jul 2008
insilicoIDE 0.2.0 is available.
20 Jun 2008
insilicoIDE 0.1.1 is available.
21 May 2008
insilicoIDE 0.1 is available.
09 Mar 2007
A Windows API generating C++ source code files to simulate dynamics of models in CellML model repository
is available from our downloads services.