User Working Groups

User Working Groups

Partnering with researchers and data scientists, KBase is working to advance a joint mission of sharing data and knowledge with the science community.


Microbes are diverse and pervasive, existing across space and time. Collaborations focused on understanding microbiome communities explore what microbes are where, and what they are doing there. Much of this work delves into the genetic potential of organisms, especially how they are capable of interacting with each other and their surrounding environment. Understanding the potential of microbiomes helps us predict ecosystem resilience and how they might respond to change.

ENIGMA Science Focus Area

Research within the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) project, led by Lawrence Berkeley National Lab (LBNL), emphasizes achieving a multiscale, causal, and predictive understanding of microbial biology. This includes understanding the relationship between molecules, microbes, communities, and the impact on the ecosystems they inhabit 

To find out more about ENIGMA community developer contributions to KBase, check out the ENIGMA collaboration page.

ENIGMA SFA home page
ENIGMA Science Focus Area
Microbes Persist Science Focus Area

The Microbes Persist: Systems Biology of the Soil Microbiome (Microbe Persist) Science Focus Area, led by Lawrence Livermore National Lab (LLNL), explores how microbial ecophysiology and population dynamics, as well as biotic-abiotic interactions regulate the microbial resilience soil under changing soil moisture conditions.

To find out more about Microbe Persist community developer contributions to KBase, check out the Microbes Persist collaboration page.

Microbes Persist SFA home page
Bacterial-Fungal Interactions Science Focus Area

The Bacterial-Fungal Interactions Science Focus Area (SFA) at Los Alamos National Lab (LANL) uses a multi-omics approach to address knowledge gaps and gain a predictive understanding of the bacterial-fungal interactions in the soil, with the goal of understanding how microbial interactions affect ecosystem services such as plant productivity, nutrient cycling, and carbon flux.

To find out more about Bacterial-Fungal Interaction community developer contributions to KBase, check out the Bacterial-Fungal Interaction collaboration page.

Bacterial-Fungal Interactions SFA home page


Collaborations around metabolic networks explore how cells (free-living, host-associated, or multicellular) communicate with other cells, collaborate or compete for resources, and interact with their environment. Research in this area connects the genetic potential of cells/communities to environmental conditions and aims to understand how life responds to change.


Biofuels Science Focus Area

The Biofuels Scientific Focus Area (SFA) at Lawrence Livermore National Lab (LLNL) looks at systems biology of microbial consortia associated with bioenergy-relevant plants and algae. The aim is to create better predictive models that aid our understanding of how plants and photosynthetic algae, in concert with their associated microbiomes, harness solar energy and impact nutrient cycling in their environments.

To find out more about Biofuels community developer contributions to KBase, check out the Biofuels collaboration page.

Biofuels SFA home page
Soil Microbiome Science Focus Area

The Phenotypic Response of the Soil Microbiome to Environmental Perturbations (Soil Microbiome) Science Focus Area (SFA), led by Pacific Northwest National Laboratory (PNNL), is tackling the challenge of understanding how soil ecosystems (plants, microbes, nutrients, etc.) respond to changes in the environment, such as drought.

To find out more about the Soil Microbiome community developer contributions to KBase, check out the Soil Microbiome collaboration page.

Soil Microbiome SFA home page
Persistence Control Science Focus Area

The Persistence Control of Engineered Functions in Complex Soil Microbiomes (PerCon) Science Focus Area (SFA), led by Pacific Northwest National Laboratory (PNNL), explores genome-scale engineering of rhizosphere microbiomes as a way to create resilient and productive bioenergy crops. Understanding the genetics, metabolomics, spatial distribution of microbes in the rhizosphere will help PerCon create and establish persistent host-microbe symbioses.

To find out more about the PerCon community developer contributions to KBase, check out the PerCon collaboration page.

Persistence Control SFA home page

Functional Genomics

Functional genomics collaborations investigate a range of multivariate genotype-phenotype relationships to study how genes or genomic regions are predictive of biological function in a particular environmental context. Associated data include genomic and phenotypic assessments, along with integrations of epigenomic, transcriptomic, proteomic, metabolomic and other data necessary to improve predictions. Studies can be direct or indirect, with the goal of linking function to genes and understanding the impact of genetic variation in populations.


Biofuels & Protein Structure Science Focus Area

The Biofuels and Protein Structure Science Focus Area (SFA) at Oak Ridge National Laboratory (ORNL) aims to understand how to efficiently develop renewable biofuels from lignocellulosic biomass. This includes understanding the process of biomass deconstruction, the enzymes responsible and the byproducts they generate to maximize biofuel production.

To find out more about Biofuel and Protein Structure community developer contributions, check out the Biofuels and Protein Structure collaboration page.

Biofuels and Protein Stucture SFA home page
Plant Microbe Interfaces Science Focus Area

The Plant Microbe Interfaces (PMI) Science Focus Area (SFA) at Oak Ridge National Laboratory (ORNL) explores the dynamic interface between plants, microbes, and their environment. With a focus on Populus (poplar trees), PMI aims to understand carbon sequestration and cycling in terrestrial systems, and how those processes may respond to climate change and provide renewable sources of energy.

To find out more about the PMI community developer contributions to KBase, check out the PMI collaboration page.

Plant Microbe Interfaces SFA home page
Plant Genomics

The Ware lab at Cold Spring Harbor Laboratory (CSHL) looks at functional and comparative plant genomics, with an emphasis on agricultural crops, and develops tools for the plant genomics research community.

To find out more about the Ware lab contributions to KBase, check out the Ware lab collaboration page.

Ware Lab at CSHL
Protein Data Bank

A core component to linking genotype to phenotype includes linking genomics to proteins and their structures. The Protein Data Bank (PDB) provides 3D protein structures derived from experimental and computational approaches, and KBase provides diverse systems biology data that provides context to protein function. 

To find out more about how PDB and KBase are connecting these complementary resources, check out the PDB collaboration page.

Protein Data Bank

Data Science

Developing detailed models of biological function within an environmental context enables researchers to explore prediction and design of ecosystem services that address challenges of climate change, land and water use, and other anthropogenic impacts. Data science employs a diverse and sophisticated set of statistical transformations and machine learning methods built from a suite of measurement technologies, spanning the molecular to the ecological, that are being linked together by increasingly sophisticated experimental designs.


Exascale Networks

In collaboration with the Daniel Jacobson Lab at Oak Ridge National Lab (ORNL), an exascale network prototype for the model organism Arabidopsis thaliana using layered data that encompasses DNA, RNA, proteins, metabolites, phenotype, and environmental conditions.

To find out more about the Exascale Network community developer contributions to KBase, check out the Exascale Network collaboration page (coming soon).

This activity is still in beta testing, and we are looking for beta testers! Sign up here.

Co-development with the Joint Genome Institute

Data science methodology requires well curated and consistent data sources for success. To support the community’s data science research efforts, KBase and the Joint Genome Institute (JGI) are developing shared microservices so our users can expect consistent and reliable results across our platforms. 

To find out more about how JGI and KBase are working together, check out the JGI collaboration page (coming soon).

Joint Genome Institute
Data center network maintenance 1/22-1/23

Update Jan 19: we have been told that different network maintenance will be performed over the weekend of January 22-23.  We have not been told an exact time, nor whether there will be an outage, nor a duration of any possible outages.  We will continue to post updates if we get them.

Our data center will be performing network maintenance on Monday, January 24, 2022.  This outage should last approximately 10 minutes, and will cause disruption to,, and possibly compute jobs.  We have not yet been notified of a specific time, if we are told a time we will update this message.

Holiday reduced support

The KBase helpdesk will have limited or no staff during the last two weeks of the year (Dec. 20-Jan. 1). There will be delays in responding to tickets.