What is insilicoML

The insilicoML (ISML) is a language that can explicitly describe the hierarchical structures of the physiological functions in the mathematical model.

insilicoML

In ISML, each of elements constructing a model is called a module, and relationships between modules are defined as edges.

Each module is quantitatively characterized by several constant or variable parameters and morphology data which are defined as physical-quantities in the ISML format.

During a simulation, variable physical-quantities change their values according to mathematically defined dynamics. Modules can affect each other quantitatively by transmitting values of physical-quantities.

A value of a physical-quantity goes out through an output port which is placed on a module, and is received by other modules via their input ports. These ports are connected by the edges.

ISML models can be composed, viewed and simulated with insilicoIDE (ISIDE), and are stored in insilicoDB (ISDB) .

insilicoML 1.0

insilicoML (ISML) version 1.0 is partially described in a manuscript Specifications of insilicoML 1.0: A multi-level biophysical model description language (Asai et al.).

Please look at the following Wiki page for more details of ISML 1.0 specifications:

To view all tags defined in ISML 1.0 so far, please look at the following PDF file:

A complete isml-model of Bonhoeffer van der Pol (BVP) model is available as an example of the ISML 1.0 description. (Note that .isml is a suffix for the file of ISML 1.0, thus a XML file.)

  • bvp_pulse.isml -- This is a BVP equation (model) receiving a current pulse stimulus. When the stimulus is on, the BVP shows oscillatory dynamics. Otherwise, it is silent, i.e., the state converges to a fixed point.

Any comments for the specifications are very welcome. Please send email to admin@physiome.jp.
We are willing to discuss on the comments and good ideas will be reflected on the specifications.

insilicoML Developers