Key Concepts of insilicoML

Abstract

Mathematical models, in particular dynamic system models of physiological functions in from molecules and cells to individual organisms play a key role for integration of vast stores of knowledge on physiology since they are capable of describing time evolution of biological system states quantitatively based upon physical and chemical principles or phenomenological logic governing system behavior. The number of mathematical models of biological functions published in peer reviewed journals and complexity of each of those models rapidly increase as computational performance increases. This raises difficulties in reproducing simulated behaviors of the published models and sharing the models by third parties, hindering the promotion of sciences and knowledge integration. InsilicoML (ISML) has been developed to overcome this problem in parallel with other pioneering efforts to define XML languages such as SBML and CellML. In Chap. 4 the focus was on how to use ISIDE to create models written in ISML. In this chapter, specification of ISML is described in rather detail.