Department of Computer Science

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Department of Computer Science Beacon: Representation, Visualization, and Modeling of Signaling Pathways in Higher Plants Lenwood S. Heath Department of Computer Science Blacksburg, VA 24061 Beacon Workshop Virginia Tech August 13, 2012 8/13/2012 Beacon Overview

History and People NSF ABI funded project, 2011-2015 Investigators: Ruth Grene, Lenny Heath, Andy Pereira Graduate students: Elijah, Curtis, and Delasa Postdoc: Subodh Srivastava Undergraduate students Proposal developed in collaboration with iPlant 8/13/2012 Beacon Overview

System Diagram 8/13/2012 Beacon Overview

Beacon Objectives Systems Biology Graphical Notation (SBGN) Activity Flow curation tool Curation workshop to build signaling networks Beacon database Several import/export formats Simulation engine Inference engine using omics data 8/13/2012 Beacon Overview

ABA Pathway — SBGN-ED 8/13/2012 Beacon Overview

ABA Pathway — Beacon Editor 8/13/2012 Beacon Overview

Beacon Benefits Database of plant signal transduction pathways Compatibility with various standards Simulation — asking “What if?” questions Inference using omics data Development of phenotypic assays to test predictions from simulations and inferences 8/13/2012 Beacon Overview