Comparison of the simulation tools for the deterministic modeling of biochemical networks

Tuncer, Gökçe
As biochemical networks become more popular, the number of deterministic simulation tools grows rapidly. Although most of the tools have similar functionality, they may differ in their algorithms and capabilities. Therefore, in this thesis, we aim to first present the major simulation tools with their underlying algorithms, and then compare them with respect to some attributes. In the application part, the biochemical networks under different dimensions are simulated and their performances are evaluated. Lastly, we add impulses to the deterministic simulations of the biochemical systems accounting for the external abrupt changes which can be seen in many natural processes. Here we suggest two major scenarios namely, impulses of fixed time and impulses at fixed states. We consider that introducing and comparing the capacities of each tool in terms of the simulation, inference or visualization of the different types of biological networks, their supported algorithms and the features of these algorithms as well as the mathematical background in all these calculations can be helpful for the researchers when they choose the most appropriate tool for their analyses