Date of Award:

8-2014

Document Type:

Thesis

Degree Name:

Master of Science (MS)

Department:

Computer Science

Committee Chair(s)

Nicholas Flann

Committee

Nicholas Flann

Committee

Kyumin Lee

Committee

Xiaojun Qi

Abstract

PathwayPioneer is a website to visualize the biological models. The complex metabolic models are hard to perceive when read through text format. It is even more difficult to understand the flow of network and different subsystem or pathways. PathwayPioneer organizes different subsystems into simple graphical representation. We simplify the complex network based on subsystem and compartment. Users can do computation (flux balance analysis) through the user interface and perceive the changed model visually. Our system is one of its kind to handle large model files with quick response time.

Biologists are often interested in knowing different alternative pathways targeting a particular metabolite. In the Pathway Search using Informed Search project we have developed four different search techniques which consider different properties of the metabolic network and eliminate redundant pathways. We have developed our own SBML parser which parses the SBML file much faster than a commercial libSBML tool. After comparative analysis of the search algorithms we found that the Dynamic Search algorithm performs faster than the other algorithms for finding alternative pathways.

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75262c30fc69b624490238fa9d8f7134

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