Refinement of Whole-genome Metabolic Models of a Hot Lake Bacterial Community Using Phenotype Simulations in the Systems Biology Knowledgebase (KBase) Environment

Event Sponsor: 
Mathematics and Computer Science Division Seminar
Start Date: 
Jan 18 2017 - 11:00am
Building/Room: 
Building 240/Room 4301
Location: 
Argonne National Laboratory
Speaker(s): 
Ronald C. Taylor
Speaker(s) Title: 
Pacific Northwest National Laboratory
Host: 
Chris Henry

Whole-genome metabolic modeling can provide valuable insights to how species interact in microbial communities.  Here, I report on the use of phenotype simulations in the DOE Systems Biology Knowledgebase (KBase) environment, combined with experimental growth/no growth data, to improve individual species models being used for a hot lake bacterial community modeling project at Pacific Northwest National Laboratory. We compare the growth predictions to experimental evidence to provide guidance as to which missing reactions can be safely added to improve a species model or otherwise used for further investigation on model improvement, and show how an iterative improvement process could be employed.