Date of Award:

5-2014

Document Type:

Thesis

Degree Name:

Master of Science (MS)

Department:

Computer Science

Committee Chair(s)

Nicholas S. Flann

Committee

Nicholas S. Flann

Committee

Xiaojun Qi

Committee

Tung Thanh Nguyen

Abstract

Every so often the field of genome-scale metabolic networks undergoes radical changes, each bringing its own complexity and challenges. The existing visualization tools, owing to their inability to assist in generating layouts suitable for easy readability and conceptualization, hinder further advancement. The lack of in-depth comprehensible representation of the intricacies of interaction and arrangements within the network topology prevents researchers from being able to advance at a faster speed despite the growing number of networks and systems. The far and wide diverse standards, layout schemas and network formats of the biological realm contribute to the existing challenges of developing visualization tools that can render user-friendly, dynamic, and all-encompassing visualizations of the metabolite reactions. I aim to provide a front-end graphical user-interface to the existing flux balance analysis tool Cobra-Py, which incorporates most of the above mentioned desired functionalities. Pathway Pioneer is a dynamic web-based tool based on Web 2.0 technologies, built to provide a complete suite to help researchers analyze, engineer, and customize metabolic network layouts suitably for optimal comprehension. Its graphical user interface makes it user friendly and interactive. The user has maximum flexibility to design layouts per requirements without worrying about details of convention such as joined in and outflow of reactions, disconnected co-factors, and connected metabolites. Furthermore, all layouts can be shared with co-researchers, which makes Pathway Pioneer a collaboration platform for Model Developments and Innovations. The R&D curve for model reconstruction at the genome scale would see positive growth with the aid of this tool. This tool aims to overcome the limitations of existing visualization tools while simultaneously complementing them.

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26a3177e401c033c650770514a4ca842

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