2016 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 4th to the 5th of August, 2016. 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
- Sam Seaver, Argonne National Laboratory, Faculty and Workshop Instructor
- Yang Shen, Texas A&M, Faculty
- Janaka Edirisinghe, Argonne National Laboratory, Faculty and Workshop Instructor
- Jiayi Sun, University of Florida, Post-doc
- Francisco Iacobelli, Northeastern Illinois University, Faculty
- Sunita Kumari, Cold Spring Harbor Laboratory, Faculty and Workshop Instructor
- Danielle Garceau, University of California, Riverside, Graduate Student
- Don McCarty, University of Florida, Co-PI and Faculty
- Elizabeth Fitzek, Northern Illinois University, Post-doc
- Joe Song, New Mexico State University, Faculty
- Amancio De Souza, University of California, Davis, Post-doc
- Patrick Thomas, University of California, Riverside, Graduate Student
- Neal Conrad, Argonne National Laboratory, Workshop Instructor
- David Still, California State Polytechnic University, Pomona, Faculty
- Ryan Fuller, University of Chicago, Graduate Student
- Chris Henry, Argonne National Laboratory, Co-PI, Faculty and Workshop Instructor
- Jose Faria, Argonne National Laboratory, Post-doc and Workshop Instructor
Program
Day 1: Annotation and modeling of plant genomes in PlantSEED
- A. Introduction to PlantSEED
- B. Annotation of transcripts (Learn about signature k-mers and FIGFams)
- C. View and Comparison of PlantSEED annotations
- D. Introduction to metabolic modeling
- E. Interactive Walkthrough of PlantSEED using Sandbox Model
Day 2: Application of models to understand and discover plant biology
- A. Demonstration of model applications with sandbox model
- B. Question and answer session
- C. Application of full genomes, transcriptomes, and models to answer biological questions
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.