Date of Award:


Document Type:


Degree Name:

Master of Science (MS)


Computer Science

Committee Chair(s)

Nicholas S. Flann


Nicholas S. Flann


Xiaojun Qi


Tung Thanh Nguyen


As stoichiometric metabolic models increase in complexity and fidelity, design and reconstruction tools are urgently needed to increase the productivity of this time-consuming process. Engineers require software for the exploration, evaluation, and rapid analysis of model alternatives within an intuitive visualization and data management framework. This thesis introduces such a tool: Pathway Pioneer (, a web based system built as a front-end graphical user interface to the flux balance analysis tool COBRA. Pathway Pioneer adds additional functionality for customized network layout and model-engineering collaboration through shared models and model version control. Pathway Pioneer is a dynamic, clickable, browser-based visualization system for metabolic network models retrieved from databases such as BiGG or developed in-house as SBML or XLS compliant files. The user can customize the network layout to visually organize the metabolites and reactions into functional modules. The tool supports zooming and panning, level-of-detail control, flux visualization, keyword searching, and hierarchical subsystem organization. A reaction may be knocked out, set as an objective, looked up in a database or many other operations by a single click on the visualized network. Following each operation the visualization is refreshed with the new flux values. The system supports model revision control to manage alternative network configurations and supports sharing of models and layouts to the broader community. By moving the computationally intensive model analysis from the user computer to remote servers, Pathway Pioneer enables the application of high performance cloud-based resources for greater efficiency and scalability. I demonstrate the utility of Pathway Pioneer through application in model reconstruction and analysis of many standard models and also two new models under development: Eukaryotic multicompartment Chinese Hamster Ovary (Cho) cells and in a large-scale Escherichia coli system for bio-manufacturing.