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

Explore the representation, visualization, and modeling of signaling pathways in plants using Beacon. This NSF ABI funded project aims to build a database of plant signal transduction pathways, offer simulation and inference engines, and develop phenotypic assays for testing predictions. Get involved in curation workshops to contribute to systems biology notation and interact with a team of experts led by Ruth Grene, Lenny Heath, and Andy Pereira.

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

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  1. 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

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

  3. System Diagram 8/13/2012 Beacon Overview

  4. 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

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

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

  7. 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

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