Learn about KBase at PAG 33, January 9-14, 2026
In preparation for those planning to attend KBase-related workshops at PAG, we recommend first creating a free KBase account so you can use the system. This short KBase Quick Start video demonstrates how-to along with a very brief introduction to the platform or follow the step-by-step sign-up guide.
KBase for Plant Science
Lead: Priya Ranjan
Location: Palm 3-4
Date: Friday, Jan 9 10:30 AM
KBase is a collaborative, reproducible cyberinfrastructure that enables integrated analysis, modeling, and interpretation of plant and plant-associated microbiome data. Designed to support transparent and shareable research, KBase provides a point-and-click, narrative-based user interface that captures data, parameters, intermediate results, and analytical workflows in a single executable record.
Presentations will demonstrate how KBase supports end-to-end analyses across multiple biological scales. First an overview of KBase functionality is provided in a context illustrating how plant RNA-seq data can be processed, normalized, and analyzed for differential gene expression. Workflows for modeling and predicting microbial interactions relevant to plant-associated communities are then presented. Finally, we introduce a network-based tool for refining large gene sets derived from GWAS and other omics studies.
If you’re interested in follow-up, please sign up on our interest form: https://bit.ly/pag_2026_kbase_workshop
POSTER: A poster will also be available for discussion on these topics:
Presenter: Bob Cottingham
Location: Exhibit Hall & Lower Level Poster Area
Date: Monday, Jan 12 3:00 – 4:30 PM
Metagenomics in KBase
Presenter: Bob Cottingham
Location: Pacific H-I (2nd Floor)
Date: Saturday, Jan 10 4:20 PM (20 minutes)
Metagenomics has transformed researchers ability to characterize and understand complex microbial communities directly from environmental and host-associated samples. However translating raw sequencing data into biological insight remains an analytical challenge. KBase (The DOE Systems Biology Knowledgebase) provides an integrated, open-access platform that enables reproducible, scalable, and collaborative metagenomic analyses by combining curated reference data, standardized workflows, and interactive narrative-driven computing.
Apps in KBase include tools for metabolic modeling and comparative phylogenomics of microbial genomes that can be used for developing mechanistic understanding of functional interactions between species in microbial ecosystems. Essential to this process is obtaining high-quality genomes to annotate, either via cultivation or genome extraction from metagenome assembly. KBase has a suite of microbiome analysis Apps meant to be used in concert. After assembly and binning, the resulting high-quality bins are annotated and can then be used in Comparative Phylogenomics analyses and Metabolic Reconstruction and Community Interaction Modeling.
An overview of metagenomic analysis in KBase will be presented highlighting end-to-end workflows from raw read processing and assembly through binning, genome quality assessment, and functional annotation will be presented including how KBase supports comparative analysis of metagenome-assembled genomes (MAGs), metabolic reconstruction, and linkage of community structure to predicted functional potential. Emphasis will be placed on the use of Narratives to capture complete, reproducible analyses and to facilitate collaboration across research teams and in educational settings; and showing how KBase enables rapid hypothesis testing, transparent data integration, and FAIR-compliant computational research in metagenomics.
BER Plant Genomic Science
Lead: Jeremy Schmutz and Bob Cottingham
Location: Palm 3-4
Date: Monday, Jan 12 6:20 PM
The Department of Energy Biological and Environmental Research (DOE-BER) currently funds both a large-scale user facility for plant genomics at the DOE Joint Genome Institute and a large-scale computational resource for comparative functional genomics and systems biology of microbes, plants and their communities called the DOE Systems Biology Knowledgebase (KBase). The core mission of both of these endeavors is to help scientists carry out experiments and analyses in areas such as improving biofuel development, understanding plant model systems, advancing plant comparative science, and investigating global carbon cycling. In this workshop, we will present current and ongoing developments at the JGI and KBase toward integrative biology and hear from researchers who are applying genomic sequence information to BER-funded activities of plant systems. We will describe how to apply for a project with the JGI Community Science Program and how you can use the KBase system to accelerate your plant genomics research.
