Plant Metabolic Network Resources and Applications

We will introduce researchers to the data, resources, and analyses tools available in the eighteen metabolic pathway databases present at the Plant Metabolic Network (www.plantcyc.org), including AraCyc, CornCyc, OrzyaCyc, BrachypodiumCyc, ChlamyCyc, SoyCyc, and MossCyc, as well as the related MetaCyc (www.metacyc.org) and SolCyc databases (http://solgenomics.net/tools/solcyc). We will explain how the underlying data about enzymes, pathways, compounds, and reactions are annotated and added to the Pathway Tools-based databases and highlight the different tools that the software offers for data analysis and hypothesis generation. Additional speakers will then provide examples of how these resources can be used and extended by researchers to enhance their lab-based and/or bioinformatic investigations. Although no computer is required, attendees are encouraged to bring their own electronic devices to follow along during the tool demonstration. During the final portion of the workshop the organizers will provide individual help to attendees who want to explore the resources or submit data for entry into the databases. This workshop will include a number of different species including Arabidopsis thaliana, Zea mays (maize), Glycine max (soybean), Manihot esculenta (cassava), Oryza sativa japonica group (rice), Vitis vinifera (wine grape), Physcomitrella patens (moss), Chlamydomonas reinhardtii, Selaginella moellendorffii, Carica papaya, Populus trichocarpa (poplar), Hordeum vulgare (barley), Brachypodium distachyon, Brassica rapa ssp. pekinensis (Chinese cabbage), Setaria italica, Sorghum bicolor, Panicum virgatum(switchgrass), and Solanum lycopersicum (tomato).
Date: Saturday, January 11, 2014
Time: 4:00 PM-6:10 PM
Room: Pacific Salon 4-5 (2nd Floor)
Kate A. Dreher
4:00 PM
Curation in Metabolic Databases: Implementing Tools and Rules Across the Universal Metabolic Database MetaCyc to Species-Specific Plant/Genome Databases
Hartmut Foerster, Boyce Thompson Institute for Plant Research; Lukas Mueller, Boyce Thompson Institute for Plant Research

4:25 PM
Introduction to the Plant Metabolic Network: 18 Databases and Omics-Level Tools for Analysis and Discovery
Kate A. Dreher, Carnegie Institution for Science; Peifen Zhang, Carnegie Institution for Science; Lee Chae, Carnegie Institution for Science; Sue Y. Rhee, Carnegie Institution for Science; Ricardo Nilo-Poyanco, Carnegie Institution for Science; Chuan Wang, Carnegie Institution for Science; Taehyong Kim, Carnegie Institution for Science

4:40 PM
CornCyc at MaizeGDB: Curation and Use Cases
Mary Schaeffer, USDA ARS and University of Missouri; Taner Z. Sen, USDA -ARS /Iowa State University; Jack Gardiner, Plant Genomics Outreach Consortium; Lisa Harper, USDA ARS; Ethalinda Cannon, Iowa State University; Carolyn J. Dill, Bioinformatics and Computational Biology Program, Iowa State University

5:55 PM
Plant Metabolomics and Network Analysis
Julie Dickerson, Iowa State University

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