Date of Award:


Document Type:


Degree Name:

Master of Science (MS)


Computer Science

Committee Chair(s)

Nicholas Flann


Nicholas Flann


Kyumin Lee


Tung Nguyen


The number and complexity of genome-scale metabolic networks have seen a rapid growth in the past 10 years. Today, more than 450 genome-scale metabolic reconstructions of biological systems are characterized and existing models are extended. With the growing influence of these reconstructions on biomedical and biological research, the field has observed a shift from an inward focus on method development to an outward focus on application development.

Static state analysis of metabolic networks in textual format is too cumbersome and time consuming. In addition, visualization and arrangement of these networks to facilitate their analysis is an open research problem. A visually intuitive laid out metabolic network facilitates its analysis for pathway search and metabolic engineering. Currently existing layout algorithms are limited and cannot produce an intuitive layout for a metabolic network. Also, the layouts produced by automatic algorithms suffer from a hair ball layout problem.

Pathway Pioneer Layout extension presents a solution to this problem by providing a graphical user interface-based tool to customize and edit the network according to the user’s choice. Existing layouts can be modified using simple drag and drop functionality resulting in metabolite and reactions to place anywhere on the network. Connecting edges are automatically drawn on these maneuvering of reactions and metabolites.

Pathway Pioneer also allows the user with a versioning system to provide backup and branching of the development work. Sharing of layouts with extensive import and export capabilities provides a rapid development platform for metabolic engineering.

Pathway Pioneer layout extension combined with its analysis tools presents a complete suite for metabolic network visualization and analysis.