•The user can observe, through a computer display, dynamic changes in concentrations of proteins, and other chemical compounds in the cell. •The substance list defines all objects which make up the cell and the culture medium. •The rule list defines all of the reactions which can take place within the cell. •The system list defines spatial and/or functional structure of the cell and its environment. •The state of the cell at each time frame is expressed as a list of concentration values of all substances within the cell