Adapting tools and functionalities in KBase to support a systems biology approach to understanding interactions in bioenergy-relevant microbial communities

Abstract

A science focus area (SFA) is a research project funded by the Department of Energy (DOE) to further scientific advancement and support the DOE’s Office of Science mission. The LLNL Biofuels SFA, at Lawrence Livermore National Laboratory, is focused on the community systems biology of microbial consortia that are closely associated with bioenergy-relevant plants and algae. They focus on linking microscale impacts of single cells on system scale processes, applying quantitative isotope tracing of elemental exchanges and various ‘omics-based approaches. They also utilize constraint-based genome-scale metabolic modeling to predict and test interactions within microbial communities.

In the immediate future, they are seeking to improve the quality of genome annotations to improve draft metabolic models within KBase, by developing tools for importing, comparing, and merging metabolic annotations. This will both expedite the curation process during model building and produce the high-quality, multi-evidenced curated models needed to investigate the complex interactions within microbial communities.

Longer term, they seek to engage with KBase to interpret and integrate their data streams to further their goal to understand and predict ecological, biophysical, and biochemical dynamics of multi-taxa communities, as well as the metabolite fluxes that regulate trophic interactions.

Collaborative Data Object

New Functionality:

  • Create annotation tools that accept multiple lines of evidence to determine an optimal consensus annotation
    • This would allow annotation data like EC numbers, KEGG, and MetaCyc reaction identifiers to be combined for more accurate draft metabolic models

New Apps:

Additional Information

Meet the Members

SFA Manager for LLNL: Henry Shaw1
SFA Lead Investigator: Rhona Stuart1
SFA Contacts: Patrik D’haeseleer1, Rhona Stuart1
KBase Contact: Chris Henry2,3
Lead Developers: Patrik D’haeseleer1 and Jeffrey Kimbrel1
LLNL SFA Team: Xavier Mayali1, Jennifer Pett-Ridge1, Peter Weber1, Ali Navid1, Erin Nuccio1, Michael Thelen1, Ty Samo1, Steve Blazewicz1
Collaborators: Todd Lane4, Eoin Brodie5, Yiwei Cheng5, Trent Northen5, Sabeeha Merchant6, Cullen Buie7, Christine Hawkes8, Kelly Craven9, Paul Zimba10, Mary Lipton11
Postdocs/Students: Christopher Ward1, Vanessa Brisson1, Rachel Hestrin1, Rachel Neurath1,2, Colleen Hui4, Katie Harding10, Carolyn Fisher4, Kristina Mahan4, Hyungseok Kim7
Affiliations: 1Lawrence Livermore National Laboratory, 2Argonne National Laboratory, 3KBase, 4Sandia National Laboratory, 5Lawrence Berkeley National Laboratory, 6UC Berkeley, 7Massachusetts Institute of Technology, 8North Carolina State University, 9Noble Research Institute, 10Texas A&M, 11Pacific Northwest National Laboratory

Resources