Computer Science and Engineering, Department of


First Advisor

Dr. Juan Cui

Date of this Version

Fall 12-1-2017


Milad Ghiasi Rad, 2017. Design and Implementation of a Stand-Alone Tool for Metabolic Simulations. MS Thesis, University of Nebraska-Lincoln


A Thesis Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science, Major: Computer Science, Under the Supervision of Professor Juan Cui, Lincoln, Nebraska: December, 2017

Copyright 2017 Milad Ghiasi Rad


In this thesis, we present the design and implementation of a stand-alone tool for metabolic simulations. This system is able to integrate custom-built SBML models along with external user’s input information and produces the estimation of any reactants participating in the chain of the reactions in the provided model, e.g., ATP, Glucose, Insulin, for the given duration using numerical analysis and simulations. This tool offers the food intake arguments in the calculations to consider the personalized metabolic characteristics in the simulations. The tool has also been generalized to take into consideration of temporal genomic information and be flexible for simulation of any given biochemical model. After implementation, experimental results have demonstrated the numerical effectiveness of optimization for model selection and the feasibility of the proposed tool for the given metabolic simulation. The proof of concept analysis on the energy metabolism and insulin-glucose metabolism revealed this tool can be promising for a variety of healthcare applications.