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Genomic Object Net: Object Oriented Representation of Biological Systems

One of the most important and interesting topic in the field of bioinformatics is to develop the tool simulating biological phenomenon such as gene expressions and biochemical reactions. The required conditions for realizing the effective simulation tool are 1) Acceptable technical expression of the tool to biologists, 2) Easy to describe biological facts and biological phenomenon on computers, 3) Easy to get the tool through Internet, and 4) Easy to simulate the biological phenomenon on the tool. Our solution to the problems is “exploiting hybrid Petri net (HPN) technique for describing biological systems”. In [1], we showed that, by using HPN, the genetic switch mechanism of λ phage can be realized on computer in a natural manner, and protein and mRNA concentrations of the mechanism can be successfully simulated by using Visual Object Net++ (Figure 1) [2] which is a general purpose system description tool based on HPN technique. The evaluation version of Visual Object Net++ can be downloaded from the site [2]. In this software demonstration, we will show the following examples of biological systems describing and simulating on Visual Object Net++; 1) Circadian rhythms in Drosophila, 2) Delta-Notch lateral inhibitory, and 3) Apoptosis induced by protein Fas. We then introduce our next strategy “Genomic Object Net Project” which may lead us to the development of new efficient bio-simulation tools.