The DOE Systems Biology Knowledgebase (KBase): Introduction to a System for Collaborative and Reproducible Inference and Modeling of Biological Function

The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) aims to provide a computational environment to meet the key challenges of systems biology: predicting and ultimately designing biological function. KBase supports the sharing and integration of reference and experimental data with analysis tools that enable researchers to design computational experiments, test hypotheses, and share findings that can be reproduced and extended by other researchers.

KBase integrates a growing set of commonly used data types and analysis tools, overlaying them with new capabilities for visualization, exploration, and predictive analysis. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics. 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.

KBase’s Narrative Interface enables users to upload their own data or access public data to execute and share customized, ordered analyses that target their specific systems biology hypotheses. In KBase, computational experiments are captured in dynamic, interactive documents called Narratives that promote collaboration and reproducibility of scientific results. In addition to data and analysis steps, Narratives can include images, notes, and commentary.  They can be kept private, shared with colleagues and collaborators, or made public for the benefit of the research community.

KBase tutorials (http://kbase.us/tutorials/) such as Build Plant Metabolic Model provide a good starting place to understand how KBase might be useful in your research and how to get started.