Date of Award:

5-2014

Document Type:

Thesis

Degree Name:

Master of Science (MS)

Department:

Computer Science

Committee Chair(s)

Nicholas Flann

Committee

Nicholas Flann

Committee

Kyumin Lee

Committee

Tung Nguyen

Abstract

The number and complexity of genome-scale metabolic networks is increasing as new systems are characterized and existing models are extended. Tools for visualization of network topology and dynamics are not keeping pace and are becoming a bottleneck for advancement. Specifically, visualization tools are not optimized for human comprehension and often produce layouts where important interactions and inherent organization are not apparent. Researchers seek visualizations in which the network is partitioned into functional modules and compartments, arranged in linear, cyclic, or branching schema as appropriate, and most importantly, can be customized to their needs and shared. Challenges include the wide diversity in the biological standards, layout schemas, and network formats. This work introduces a web-based tool that provides this functionality as an extension to the existing web-based tool called Pathway Pioneer (www.pathwaypioneer.org). Pathway Pioneer is a dynamic web-based system built as a front-end graphical user interface to the flux balance analysis tool COBRA-py. Full click-and-drag layout editing capabilities are added allowing each metabolite and reaction to be translated and rotated as connecting edges are automatically redrawn. Initial automated layouts for new models maximize planarity while clustering reactions based on subsystem module and compartment. The users are given maximum flexibility to design specific layouts while details of convention, such as joined in and out of reaction edges, disconnected co-factors, and connected metabolites, are automatically handled. Layouts can be shared among researchers and explored to archival Symphony format, along with pdf and png images. This tool provides the user with a semi automatic layout algorithm along with graphical and interactive tools to fully customize the network layout for optimal comprehension. Export capabilities are compatible with COBRA-py and other visualization tools. It provides a platform for share model development and innovation to the community, sharpening the R&D curve, and improving the turn-around time of model reconstruction at the genome-scale. Pathway Pioneer provides unique capabilities in customization of metabolic networks that complements and overcomes limitations of the growing body of existing tools.

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