Ecosystems and Networks Integrated with Genes and Molecular Assemblies

Improving metagenomics workflows in KBase




The Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Science Focus Area (SFA), managed by Dr. Paul D. Adams and led by Dr. Adam P. Arkin at Lawrence Berkeley National Laboratory (LBNL), aims to advance knowledge of microbial biology and better understand effects of the microbial community on the organisms and abiotic factors around them across multiple scales. ENIGMA studies everything from single molecules to ecosystems at large to unlock how they are interconnected.

The goal is to develop a mechanistic understanding of microbial community formation and activity in complex environments. To do this, ENGIMA is exploring interactions between microbial communities in ground water and sediment at various locations within the Oak Ridge Field Research Site. The site has well-mapped hydrology and geology, as well as complex gradients of nutrients, stressors, and contaminants. This provides a robust framework to explore spatial and temporal impacts of environmental factors on microbial communities.

Collaborative Development Projects

Starting Fall 2021 – Long read assembly of microbial isolates and metagenomes

Reference-based metagenome workflow

Functionality and Tools:

Additional Information

Meet the Members

SFA Principal Investigator: Paul D. Adams1,2
SFA Technical Co-Manager, Science Lead: Adam P. Arkin1,2,3
SFA Contact: Astrid Terry1
KBase Contact: Dylan Chivian1,3
Lead Developers: John-Marc Chandonia1,3, Alexey Kazakov1, Lauren Lui1, Torben Nielsen1, Anni Zhang4
Project Team: Eric J. Alm4
Affiliations: 1Lawrence Berkeley National Laboratory, 2University of California at Berkeley, 3KBase, 4Massachussetts Institute of Technology


appdev maintenance Feb 8

We will be performing maintenance on appdev.kbase.us on Wednesday, February 8, from 1pm-6pm CST (11am-4pm PST).  Parts of appdev will be unavailable during this time.

We do not anticipate any interruption to other KBase services.