2018 PlantSEED Metabolic Modeling Workshop

A two-day workshop on plant genome annotation, metabolic modeling, and reconstruction comprising formal lectures and hands-on instruction held at Northwestern University, Evanston, IL from the 16th to the 17th of August, 2018. The workshop content is of interest to computational scientists associated to agriculture and biology departments as well as plant scientists interested in metabolic modeling including plant breeders, geneticists, physiologists and biochemists.

Participants

• Chris Henry, Argonne National Laboratory, Co-PI, Faculty and Workshop Instructor
• Jose Gonzalez, South Dakota State Univesity, Faculty
• Robert Kleps, Morton Arboretum, Visiting Faculty
• Kathleen Beilsmith, University of Chicago, Graduate Student
• Crysten Blaby-Haas, Brookhaven National Laboratory, Faculty
• Caroline Oldstone-Moore, University of Chicago, Graduate Student
• Don McCarty, University of Florida, Co-PI and Faculty
• Rongkui Han, University of California, Davis, Graduate Student
• Zeeshan Banday, University of Chicago, Graduate Student
• Kateel Shetty, Flordia International University, Faculty
• Ian Blaby, Brookhaven National Laboratory, Faculty
• Megan Kennedy, University of Chicago, Graduate Student
• Sam Seaver, Argonne National Laboratory, Faculty and Workshop Instructor
• Feng Huang, University of Chicago, Graduate Student

Program

Day 1: Flux Balance Analysis in PlantSEED

• A. Overview.
• B. Plastidial Sandbox Model.
• C. Flux Balance Analysis.
• D. Transcript-constrained Flux Balance Analysis.

Day 2: Annotation and Reconstruction in PlantSEED

• E. Overview.
• F. Annotation and Metabolic Reconstruction.
• G. Future of PlantSEED.

Grant Support

The PlantSEED resource was created with support by the National Science Foundation Grant IOS-1025398, by an endowment from the C. V. Griffin Sr. Foundation, and by the Office of Science, Office of Biological and Environmental Research, of the US Department of Energy (DOE) under Contract DE-ACO2-06CH11357, as part of the DOE Systems Biology Knowledgebase.

The National Science Foundation Grant IOS-1444202 has provided support for both the improvement of the PlantSEED resource and the production of new modeling tools within ModelSEED to be able to annotate plant genomes using the PlantSEED platform and develop plant metabolism models. This grant also supports the implementation of four PlantSEED metabolic modeling workshops to train faculty, post-doctoral fellows and graduate students of American universities (with an emphasis on recruitment of faculty from minority serving institutions) in the use of these novel computational tools.