Comparative Assessment of Simulation Tools for Biochemical Networks
GökçeTuncer, Vilda Purutçuoğlu

There have recently been many simulation tools developed by researchers for observing the dynamics of biochemical networks. These tools have mainly designed for the stochastic and deterministic simulations and some of them also support the inference of the model parameters under deterministic modellings. Therefore, they are known as the simulation softwares for biochemical systems. Although these tools aim the same purpose in the application, they have their own advantages and disadvantages. Hereby, in this study, to help the users for choosing the most suitable simulation tools for their purposes, we initially present the widely implemented ones, namely, Cellware, COPASI, Dizzy, Dynetica, E-CELL, GENESIS, Jarnac/JDesigner, Systems Biology Toolbox and Virtual Cellsoftwares, and then, compare them according to our selected attributes. For the comparison criteria, we define the theme, user-friendliness, platforms supported, language of the software, capacity in the simulation, inference, visualization and the Systems Biology Markup Language. Finally, we suggest certain tools for academic and non-academic users by taking into account their plausible major attributes for the selection.

Full Text: PDF     DOI: 10.15640/arms.v3n2a9