Petri net models in computational biology

The paper captures the technical complexity of information exchange in biological systems and proposes a tool, which is a software library recipe in order to facilitate the building of the associated computational models. This software library recipe is based on Differential Petri Net paradigm. The aim of the proposed software was to meet both qualitative and quantitative characteristics of already available software used in modeling biological systems. The proposed software library recipe contains computational Differential Petri Net models, that can be computer simulated, for the following types of chemical reactions: first order irreversible reaction, first order reversible reaction, bimolecular reaction, enzyme - single substrate reaction, for which differential equations solvers were based on proprietary software MATLAB or on open source software Octave and Petri Net analysis was based on proprietary Sirphyco software or on open source software like pneditor or PIPE2 for drawing the Petri Net diagrams of the proposed models. It contains complete example of enzyme with a single substrate kinetics modeling and simulation, by incorporating dynamic information provided by the differential equations system in the descriptive model of interactions modeled with graphs and presents a Differential Petri Net model for this kind of biochemical interactions that occur at molecular level.