The DOE systems biology knowledgebase (KBase): progress towards a system for collaborative and reproducible inference and modeling of biological function

KBase (http://kbase.us) is an integrated software and data platform designed to meet the grand challenge of systems biology---predicting and designing biological function on a range of scales, from the biomolecular to the ecological. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics.

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 such that they can be reproduced and extended by others. KBase is being built to integrate a growing collection of data resources and analytical services including microbial and 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. In addition, user-furnished data can be uploaded, analyzed using high-performance bioinformatics tools, and overlaid visually and analytically on KBase-provided data.

We envision KBase as a comprehensive environment that accelerates the integration of new information from external reference sources and users, improving predictions of biological function from individual enzymes to ecosystems and thereby enabling users to greatly amplify the results of their own work by most effectively leveraging that of others.