1. 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/ 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: Subodh Srivastava
Undergraduate students
Proposal developed in collaboration with iPlant
8/13/ Beacon Overview

3. System Diagram
8/13/ 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/ Beacon Overview

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

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