ABI Development: Representation, Visualization, and Modeling of Signaling Pathways in Higher Plants

Virginia Polytechnic Institute And State University, Blacksburg VA

Investigators

Abstract

An award is made to Virginia Polytechnic Institute and State University to build the community-based Beacon system to provide computational support for biologists' questions about signaling pathways. Signal transduction pathways hold the key to understanding the early response of higher plants to abiotic stresses, such as drought, flooding, heat, cold, ozone, and salt. For crop plants, the ability to cope with such abiotic stresses can drastically affect productivity. Traditionally, signaling pathways have been difficult to synthesize and impossible to manipulate computationally. Current pathway tools and databases provide only limited support for manipulating pathways as networks. In particular, it is not possible for a biologist to take an existing signaling pathway and ask hypothetical questions that are answered computationally. The project includes the training of recognized authorities by Beacon staff on the system, thereby empowering plant biologists to curate and archive signaling pathways for abiotic stress responses in the Beacon database. Usability of the tool will be addressed via a continual feedback loop between users and developers. The user interface is an editing environment that represents and manipulates a pathway in a standard graphical notation called SBGN Activity Flow language, built on the network visualization tool VANTED and SBGN-ED, an extension of VANTED. Research herein will extend SBGN-ED to create Beacon. The result will be a curation tool that will allow authorities to enter pathways in SBGN Activity Flow language, edit them, annotate them, and save them to an initial Beacon database. The database representation allows the biologist to impose a semantic, such as Boolean semantics, on a pathway. The Beacon simulation engine is then able to computationally implement those semantics and provide results that can be queried and visualized. The Beacon inference engine provides tools to allow biologist to develop testable hypotheses about pathway components. The Beacon system will interest undergraduate students in computational sciences as well as experimental biologists. Well-established outreach programs at Virginia Tech will be used to provide training and educational outreach activities. An experimental component will be implemented in the final years of the project, where Beacon-based predictions concerning phenotype will be tested in the laboratory. At https://bioinformatics.cs.vt.edu/beacon/, users will have access to project outcomes.