State transition diagram of an enzyme during its life cycle A biological process is visualized as a system of resources periodically changing between one of the following four states based on the underlying resource usage algorithms: (i) ‘used’ (e.g, an enzyme is busy in a reaction), (ii) ‘idle’(e.g, an enzyme is free to enter a new reaction), (iii) ‘created’ (e.g, a molecule is created by a reaction) and (iv) ‘decayed’ (e.g, a molecule is in the process of disintegration at the end of its life-cycle). The state transitions are governed by transition flow rates of the dynamic functions involved in it. The process is initiated by a set of input signal(s) from the external world to the system. These input signals initiate the creation of dynamic events which drive the simulation across in time domain, capturing how the system resources change states.
Ghosh et al. BMC Genomics 2010 11(Suppl 3):S3 doi:10.1186/1471-2164-11-S3-S3