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 is composed of three pieces.

insilicoML: an XML-based description language for mathematical models of physiological functions.

insilicoIDE: an Integrated Development Environment which can be used as a viewer, an editor and a simulator of ISML models.

insilicoDB: a database to store ISML models.

What's New
01 Sep. 2010
insilicoIDE 1.3.0 is released.
  • Geometry edit dialog is added. A morphology defined in a module is composed of several geometries.
    Using this dialog, primitive type morphologies such as Cylinder, Triangular-pyramid, Cuboid and so on,
    and external morphology data are set in a module.
    The dialog can show a preview of the morphology data defined in a module.
  • Segment edit dialog is added. Segments are used to define boundary conditions or initial conditions imposed on a morphology data. Users can define several segments for each geometry in this dialog.
  • PDEs and ODEs mixed model can be converted into FreeFEM++ format and simulated by FreeFEM++.
  • A model including static instances can be converted into C++ for numerical simulations.
    In ISML template/instance framework is considered. Please see the specification for more details.
  • APIs for dealing with morphology definitions are sorted out.
  • ISSim can deal with multiple time steps for numerical integration.
  • ISSim interface is improved at the variable selection for drawing graphs.
  • ISIDE interface on zooming out/in is improved.
20 Jul. 2010
Bugs in a sample model (coupled_Luo_Rudy_1991_model.isml) are fixed.
02 Jul. 2010
insilicoIDE 1.2.1 is released.
  • Python API is updated.
  • Model Editor is updated.
  • Several bugs have been fixed.
25 Jun. 2010
insilicoIDE 1.2.0 is released.
  • A SBML model can be included in a module. This allows associations between species/parameters in the SBML model and physical-quantities in ISML for realizing a SBML-ISML hybrid modeling.
  • GUI Appearance of insilico Canvas has been modified. Now it shows physical-quantities and ports list tables and module tree view on the side. Information shown in those tables can be saved into files in CSV format.
  • Graphical representation of modules, ports and edges have been changed.
    • Modules are now represented by round corner squares.
    • Ports are represented by head arrows to show directions of information flow explicitly.
    • Different line types (solid, dashed, dotted) are used to represent the difference of edge types (functional, structural, capsular).
  • A method for editing mathematical expressions has been improved. C-like expression such as "k=3*a/c" can be used.
  • Procedures to make an association between a physical-quantities and a port are simplified.
  • ISIDE can call ISSim directly with passing the model currently opened on ISIDE.
  • ISSim can perform simulations of SBML-ISML hybrid models.
  • Variables to be drawn graphs on ISSim can be selected interactively.
  • During the selection of variables, ISSim shows a provisional graphs.
26 May 2010
Physiome.jp Wiki is opened.
31 Mar. 2010
insilicoIDE 1.1.2 is released.
  • Python API is updated. Improve ISML-FreeFEM converter.
  • Model Editor is updated.
  • insilicoSim is updated.
  • Several bugs have been fixed.
05 Mar. 2010
insilicoIDE 1.1.1 is released.
  • Model Editor is updated. Add view function of conditonal-type physical-quantity implementation.
  • insilicoSim is updated. Add progress bar of the simulation.
  • Several bugs have been fixed.
17 Feb. 2010
insilicoIDE 1.1.0 is released.
  • The library to handle XML document is changed to libxml2 from Oracle Berkeley DB XML,
    which improves the execution speed of the ISIDE.
  • ISIDE can export ISML models into FreeFEM format (with some limitations).
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.