The DOE Systems Biology Knowledgebase: Progress Toward a System for Collaborative and Reproducible Inference and Modeling of Biological Function in Plant Research

The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) integrates commonly used core tools, reference and experimental data, and overlays them with new capabilities for visualization, exploration, and predictive analysis with KBase-generated recommendations designed to accelerate our understanding of microbes, plants and their communities.

KBase offers open access to quality-controlled data and high-performance modeling and simulation tools that enable researchers to build new knowledge, interpret missing information necessary for predictive modeling, test hypotheses, design experiments, and share findings. KBase empowers researchers with a variety of plant resources and analytical services including plant genomes such as poplar and Arabidopsis that are integrated with phenotype experiments, gene expression profiles, regulatory, interaction, and metabolic networks. These data sources can be used as input to KBase analysis tools to build models and generate new hypotheses such as metabolic reconstruction and flux balance analyses based on transcriptomes. An example with Sphagnum sequenced by JGI will be shown. In addition, user-furnished data can be uploaded, analyzed using high-performance bioinformatics tools, and overlaid visually and analytically on KBase-provided data already available.

As the project matures, partnerships with plant resources such as iPlant and Gramene/Ensembl will lead to a broader research platform for predictive plant and microbial biology.

This work is supported by the U.S. Department of Energy, Office of Biological and Environmental Research under Contract DE-AC02-06CH11357.