Drs. Heath, Pereria, and Grene Awarded Interdisciplinary NSF Grant

Publish Date: 05/01/2011

Drs. Lenny Heath, Andy Periera (VBI) and Ruth Grene (PPWS) were awarded a new NSG grant entitled “ABI Development: Representation, Visualization, and Modeling of Signaling Pathways in Higher Plants.” Lenny describes the project: “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.  This project builds the, community-based, Beacon system to provide computational support for biologists' questions about signaling pathways, thereby empowering those plant biologists to curate and archive signaling pathways for abiotic stress responses in the Beacon database.  The user interface is an editing environment that represents and manipulates a pathway in a standard graphical notation called SBGN Activity Flow language.  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. Adding or removing relationships in a pathway (adding or removing edges in a network) raises the difficult question of causal inference: Does activity of molecule A cause activity of molecule B? Such questions can be assessed computationally and statistically using such tools as Granger causality, Bayesian networks, and structural equation modeling. The Beacon inference engine provides these tools to allow the biologist to develop testable hypotheses about pathway components.  Well-established outreach programs at Virginia Tech (i.e., NSF-funded projects such as PREP/PREP-U, S-STEM and  the Virginia-North Carolina Louis Stokes Alliance for Minority Participation) 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.