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 and physiological 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 as well as physiological experimental data (time-series and image-based morphological models).

We will prepare a mailing list to distribute the recent news on insilico platform, such as new release. If you want to subscribe to this mailing list, please send a simple email to admin(at)physiome.jp. Please provide your affiliation in your email to admin(at)physiome.jp. We will provide an automatic signup interface soon.

What's New
27 Feb. 2012
MedMod Tool has been released.
20 Jan. 2012
PhysioDesigner 1.0 α has been released.
See PhysioDesigner.org for details.
18 Nov. 2011
insilicoIDE 1.4.4 has been released.
  • insilicoIDE
    • Converters from ISML to CellML has been improved.
    • Func-expressin and Nominal type physical-quantities can be created now.
    • Several user interfaces have been improved and became more friendly.
    • Several bugs on physical quantity dialog have been fixed.
  • Morphology
    • Metaimage file is added to image file selection of imageviewer and surface model extraction from a meta/raw image file can be done in imageviewer. Mesh decimation function is also built in for FEM mesh.
    • Surface model can be converted to solid model in geometry editor by mesh generator.
    • At the time of geometry definition, this solid model can be used as an external geometry file.
  • insilicoSim
    • Processing speed to load a model has been improved.
    • Time unit can be specified from a combo-box.
21 Oct. 2011
insilicoIDE 1.4.3 has been released.
  • insilicoIDE
    • Now it is possible to create Physical Quantities with func-expression and nominal types.
    • Problem to load and write a models in a path including multibyte characters has been fixed.
    • Interface to link an edge has been improved by shortening a port name to display.
    • Display in a Port table has improved. Physical Quantities associated with in-port are shown now.
  • Morphology
    • Inner region's volume elements can be specified as a segment candidate.
    • Sucessive segment element selection like rubberband->click->rubberband is enabled.
    • External 3D arrow coordinate axis is installed and previous coordinate axis display changes to on and off.
    • Volume and surface selections can't be done simultaneously.
    • Sucessive viewing for selected geometries without closing view window
    • Rearrangement of combination of segment type and format.
    • Add segment name and keyword
    • Segment editor layout is changed
    • Segment list shows only segments belonging to specified geometries
    • Windows bugs are fixed (freeze and down problem)
  • FreeFem++
    • Initial trial of vector-matrix formulization of insilicoML and conversion to FreeFem++. FHN2D fiber sample model is provided.
  • insilicoSim
    • Drag and drop of model file to ISSim window has been supported.
    • Computing speed has been improved a little bit.
12 Sep. 2011
insilicoIDE 1.4.2 has been released.
  • insilicoIDE
    • Improvement of display of Physical-quantities assigned to Ports. Now assignments to both of in-ports and out-ports are indicated in PQ dialog and Port dialog.
    • Improvement of edge connection between a port to a port.
    • Physical-qunatities with vector and matrix type can be defined. Descritization-dependent option is also available to specify the row and col dimension for a vector and matrix.
    • Bugs have been fixed in SBML model import.
    • Miscellaneous interfaces have been improved.
  • Morphology editor
    • Geometry and Segment editors have been unifined and smooth operation of morphology creation has been realized. Check a short note at download site to see the difference between previous and new versions.
    • Following functions have been added or revised.
      • geometry/segment dialog
        • Warning message when switching between geometry and segment dialog
        • Multiple rubberband and click selections
        • Change "Clear" button for segment ID table to "Undo add" button and change "Clear all" button to "Clear" button. Both also clear view selected area.
        • Change "Add" and "Apply" buttons to a single "Apply" button which updates model. Instead, "Update" button to update geometry or segment list is added.
      • View dialog
        • Change "Clear" checkbox to "Clear" button
        • Change View "Apply" button to "Add" and "Delete" buttons and they enable to add or delete segment list items
        • Contents of segment ID table and View becomes consistent
  • Image viewer
    • X-Y, Y-Z, Z-X plane's simaultaneous view have been enabled.
    • Reset button has been added
    • Automatic view after push of operation buttons
  • insilicoSim
    • Support for functions uniform_variate() and gauss_variate(), returning a random variate based on uniform distribution and normal distribution, respectively.
19 Jul. 2011
insilicoIDE 1.4.1 has been released.
  • Improvements on insilicoSim
    • It has supported template / static-instance framework.
    • Now it can run a simulation with a model using dimensionless time.
  • Morphology related improvements
    • Segment selection process was improved for multi selection and target shape formation.
    • Segment file becomes visible.
    • Imageviewer has been improved for easy operation.
  • FreeFem++
    • EEG3D has been updated to get 64ch electrode potential.
  • Miscellaneous improvements on insilicoIDE UI
    • If-then rule interface has been added to Physical-quantity dialog.
    • Initial value is now deletable.
  • A minor revision was made on the insilicoML specification on the definition of the implementation of a physical quantity. Formerly there are types "sde" (stochastic differential equation), "dde" (delay differential equation) for definition of the implementation among others such as "ode", "ae" and "assign". But these two types were abolished. Instead, new attributes "stochastic" and "delay" have been introduced to the definition tag. See specification for more details.
  • Several bugs have been fixed.
10 Jun. 2011
insilicoIDE 1.4.0.2 has been released.
  • Morphology Editor
    • Imageviewer has been installed. Currently, matlab .mat image file can be displayed with gray scale. Image is generated from 3D image data specifying a cut plane. Filtering with a threshold value, typical value's image can be obtained.
    • Segment selection and viewing function has been improved.
  • FreeFem++
    • Electroencephalogram (EEG) analysis has been enabled. Combination with PDE and ODE, and muti timestep control is highlight issues.
  • Physical-quantity editor
    • geometry-id (domain) and segment-id (problem condition) become to be selected from pull down menu.
  • Several bugs have been fixed.
20 May 2011
insilicoIDE 1.4.0.1 has been released.
  • Morphology Editor
    • Bugs in surface/volume segment selection have benn fixed.
    • Bugs in successive selection of rubberband/click and label functions, and segment id list delete operation have been fixed.
  • FreeFem++
    • Surface/volume segment selection has been enabled.
  • Bugs in C++ exporting have been fixed
  • Several bugs have been fixed.
28 Apr. 2011
insilicoIDE 1.4.0 has been released.
  • Morphology related functions have been enhanced.
    • Morphology vierwer
      • Clipping and slicing , color representation and position centering functions have been added.
    • Segment dialog has been updated
      • Nodes, surface and volume elements selection by a rubber band and/or mouse click
      • Segments can be saved to morphology files
    • Physical-quantity dialog
      • Domain for PDE can be specified by geometry of morphology
      • Problem conditions can be assigned to segments of morphology
  • Converter from ISML to FreeFEM format has been enhanced
    • Cardiac electrophysiological excitement propagation simulation, bone elasticity simulation, blood fluid dynamics simulation and brain electrencephalography simulation examples are installed.
  • Delayed Differential Equations (DDEs) has been supported
    • DDEs are described using "Delay" operation in equations
    • InsilicoSim can calculate DDEs
  • InsilicoSim (ISSim) supports the template and static-instance framework
  • ISSim supports extra-implementations with 4th order Runge-Kutta method as well as Euler method
  • Performance of processing XML document by InsilicoAPI has been improved
  • Several bugs have been fixed.
10 Feb. 2011
insilicoIDE 1.3.3 has been released.
  • UI of many dialogs have been improved.
  • Segment specification tool in "Edit segment" dialog has been improved to make it easy to apply boundary conditions.
  • Performance and robustness of insilicoSim has been improved
  • More informative error messages have been shown by insilicoSim.
  • Another CLI version of insilicoSim "isimc" runnable on Mac OS X has beeb included in the package because of a simpler interface. See a supplemental document for details.
07 Jan. 2011
Harnessing Biological Complexity has been published from Springer.
This textbook introduces many examples of insilicoIDE platform.
Physiome Project
28 Dec. 2010
insilicoIDE 1.3.2 has been released.
  • Model Editor has been updated.
    • Dialog to setup morphologies and segments have been enhanced.
    • Problem conditions can now be configured in the Physical-Quantity dialog.
    • A dialog to edit units has been added.
  • insilicoSim has been updated.
    • isim has been added, which is a command-line version simulator "only" for Mac OSX having a capability to perform a parallel computation on multi-core CPU.
    • Computation performance has been improved.
  • Python API has been updated.
    • Exporting function to FreeFEM++ format has been enhanced.
    • Exporting C++ and JAVA has been improved.
  • Several bugs have been fixed.
  • Documents and Tutorial movies have been added.
06 Oct. 2010
insilicoIDE 1.3.1 has been released.
  • Model Editor is updated.
    • Morphology editor has been updated. Now geometries and segments can be edited.
    • Viewer of Geometries has been updated.
    • insilico Canvas can display template modules and instance modules as well as usual modules such as functional-unit and container.
  • insilicoSim is updated.
    • The interface to select variables to be plotted has been renewed.
    • Simulation results are exported into a CSV file. Now a file describing the correspondence between columns in the CSV file and variable names is also provided additionally.
  • Python API is updated.
    • APIs for manipulating template and instance modules have been updated.
      Some new APIs have been added.
    • APIs for editing morphology information have been updated. Some new APIs have been added.
    • APIs for utilizing morphology information in, such as, initial-value, domain, have been updated.
    • APIs for converting from ISML to C++ and to Java have been updated.
  • Several bugs have been fixed.
01 Sep. 2010
insilicoIDE 1.3.0 has been 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) has been fixed.
02 Jul. 2010
insilicoIDE 1.2.1 has been released.
  • Python API is updated.
  • Model Editor is updated.
  • Several bugs have been fixed.
25 Jun. 2010
insilicoIDE 1.2.0 has been 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 has been opened.
31 Mar. 2010
insilicoIDE 1.1.2 has been 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 has been 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 has been 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 has been released.
  • Update Berkeley DB XML to 2.5.16 and Qt to 4.6.
8 Jan. 2010
insilicoIDE 1.0.3 has been 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 has been released.
  • Directory structure is changed (Mac OS X version).
  • Model Editor is updated.
  • Several bugs have been fixed.
13 Oct. 2009
insilicoIDE 1.0.0b has been released.
10 Jul. 2009
About ISDB (the page that explains how to use ISDB) has been available.
25 Jun. 2009
A trial version of insilico Time-series Database has been relaeased.
26 Feb. 2009
insilicoIDE 0.3.1 has been released.
  • Minor modification enabling insertion of creator information was made on insilicoIDE 0.3.
06 Feb. 2009
insilicoIDE 0.3 has been released.
  • 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 has been released.
  • Time-Series data can be used for simulation
29 Nov. 2008
insilicoDB has been updated to XML DB.
A trial version of insilico Morphology Database has been released.
20 Oct. 2008
insilicoIDE 0.2.5 has been released.
  • MPI parallel computation functionality has been improved.
  • Pubmed information can be linked from insilicoIDE.
18 Sep. 2008
insilicoIDE 0.2.4 has been released.
11 Sep. 2008
insilicoIDE 0.2.3 has been released.
03 Sep. 2008
insilicoIDE 0.2.2 has been released.
11 Aug. 2008
insilico IDE 0.2.1 has been released.
25 Jul. 2008
Tutorial has been ready.
15 Jul. 2008
insilicoIDE 0.2.0 has been released.
20 Jun. 2008
insilicoIDE 0.1.1 has been released.
21 May 2008
insilicoIDE 0.1 has been released.
09 Mar. 2007
A Windows API generating C++ source code files to simulate dynamics of models in CellML model repository
has been available from our downloads services.