InsilicoIDE and PhysioDesigner received the 2012 Society of Instrument and Control Engineers of Japan (SICE) Award (Technology Award), and the award ceremony was held on August 22, 2012 at the SICEAnnual Conference 2012 held at Akita University.
The “Society of Instrument and Control Engineers (SICE) Award 2012” is based on the paper “Yoshiyuki Asai and Yasunobu Nomura (2010) “Platform Development for Promoting Integrated Biochemistry in Physiome.jp” co-authored by Professor Yasunobu Nomura (Osaka University) and Professor Yoshiyuki Asai (Okinawa Institute of Science and Technology Graduate University) in 2010. (2010) “Platform Development for the Promotion of Integrated Biochemistry in Physiome.jp,” Measurement and Control, 49pp.525-529.

InsilicoIDE and PhysioDesigner are application platforms designed to support modeling and simulation of multilevel biological systems and to promote research in the field of integrated biological sciences. We have been contributing to the development of these programs since 2007, at the request of Okinawa Institute of Science and Technology Graduate University and Osaka University.
When it was first developed, the application name was insilicoIDE, but after its ver. 1.4.4 release, the application name was changed to PhysioDesigner due to a change in the project framework, and at the same time it was upgraded with a major re-engineering. (It will henceforth be referred to as PhysioDesigner in this paper.)

The functions of living organisms, including human beings, are realized as the sum of extremely complex biological, chemical, and physical phenomena at various levels, including the microscopic dynamics at the gene level, the level of interaction between proteins and compounds such as drugs, the cellular level involving metabolism, and the organ level that we can recognize in our daily lives, such as heart beat and respiration. The latest life science is realized as the totality of very complex biological, chemical, and physical phenomena at various levels.
The latest life science aims to understand biological functions as a comprehensive system that includes the interactions of individual elements, based on an understanding of the individual elements that make up biological functions. Perhaps the only way to achieve this is to build physiologically faithful mathematical models based on what is known about the individual elements, and to assemble these models into a model of the whole.

PhysioDesigner is an application platform to support the process of assembling mathematical models of biological systems while explicitly representing the hierarchy of physiological functions in such an integrated life science field.
The graphical interface of PhysioDesigner is designed to simplify the process of building mathematical models of hierarchical physiological functions by eliminating the various processes required for users to build models. PHML is an XML-formatted description language designed to facilitate model sharing. PHML is designed to be able to describe physiological phenomena at various levels, from the intracellular level to the individual level, such as arm movement and circulation, in a generic manner.
In PhysioDesigner, functional units are represented as “modules. The hierarchy of the functional structure is explicitly modeled by treating a set of multiple modules as one module of a higher level concept. For example, as shown in Figure 2, the entire brain or region can be defined as a parent module, neurons can be defined as child modules, and the detailed function of the neural synapses can be defined as lower-level child modules in a hierarchical manner.
With PhysioDesiger, you can not only easily create mathematical models from scratch, but you can also download models from the model database available at physiome.jp and incorporate already created models as part of the model you are currently editing. Simulation of the built model can be done by simulating a simulation of the model. Simulation of the built model can be easily performed by passing the model to the simulator Flint (Figure 1).

Modeling in this area requires simultaneous handling of physiological functions and structures, and PhysioDesigner has already implemented test functions to import medical images and 3D mesh polygon models and incorporate them into the model. We are also currently in the process of further development with Okinawa Institute of Science and Technology Graduate University and Osaka University.
In addition, intracellular biochemical reaction models written in the SBML language, which is particularly good at modeling intracellular phenomena, can be imported and incorporated into PhysioDesigner. This enables the construction of hierarchical models at the cellular network, tissue, and individual levels, including detailed intracellular level models, and simulation of the effects of drugs on the heart when administered, as shown in Figure 3, or conversely, the toxic effects of drugs on the heart.

For example, simulating the effects of a drug on arrhythmia before administering the drug can be useful in reducing the risk of medication and in drug selection. To achieve this, the Okinawa Institute of Science and Technology Graduate University and Osaka University are currently working on a project to build a model on PhysioDesigner that includes pharmacokinetics in the circulatory system, pharmacological effects on cardiomyocytes, and effects on the beating of the heart.
In the future, they have also begun to use PhysioDesigner to construct models that incorporate neural circuits around the basal ganglia and pharmacological effects on neurons, with the aim of building a basic system for predictive medicine for neurological diseases such as Parkinson’s disease.
As described above, PhysioDesigner is contributing to the development of integrated life science by supporting multilevel modeling of physiological functions.

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Figure 1.

 

Figure 2.

 

Figure 3.

Related Links

1. Society of Instrument and Control Engineers
2. SICE Annual conference 2012
3. PhysioDesigner
4 .insilicoIDE
5. Physiome.com