Dynamic simulation of biological networks

Abstract

Bioinformatics is an interdiscipline of biology and computer science. It provides useful information in various novel researches such as dynamic simulation of biological networks. GINsim is a Java software for the qualitative simulation of genetic regulatory networks. It has graphical interface that allows manual editing of Logical Regulatory Graphs and the related simulation parameters. The simulation engine will allow generating State Transition Diagram. Identification of stationary states of the network. It also contains various simulation strategies to generate different graphs. In this project, we aim to take advantage of GINsim and implement other supplementary algorithms in order to analyze biological networks and simulation results related to cell fate decisions. More than 30 biological networks, which includes both complete model and reduced models, were constructed in this project. Within reduced models, both wild type model and mutants were involved. Various construction strategies were adopted when running the simulation. Dedicated data preprocessing (file generation, file parsing and storing directed graph with hash map) and path counting algorithms were designed and implemented when analyzing the simulation results. Detailed analysis results were presented with proper explanations.