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Tutorial Abstract

Tutorial 2: Pathway analysis

Title: PathCase: Biological Pathways Database System
Presenters: Ali Cakmak, Brendan Elliott and Mustafa Kirac, Department of Electrical Engineering and Computer Science, Case Western Reserve University

Abstract: As the blueprints of cellular actions, biological pathways characterize the roles of genomic entities in various cellular mechanisms, and as such, their availability, manipulation, and queriability over the web is important to facilitate ongoing biological research.

In this tutorial, we showcase PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of genetic, molecular, biochemical and organismal detail. More specifically, this tutorial will walk researchers through  (a) a web-based system with an architecture, containing a server-side and a client-side, and promoting scalability, and flexible and easy adaptation of different pathway databases,  (b) an interactive client-side visualization tool for metabolic pathways, with powerful visualization capabilities, and with integrated gene and organism viewers, (c) two distinct querying capabilities: an advanced querying interface for computer savvy-users, and built-in queries for ease of use, that can be issued directly from pathway visualizations, and (d) a pathway functionality analysis tool. PathCase is now available for three different data sets, namely, KEGG pathways data, sample pathways from the literature, and BioCyc pathways for humans.

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