KBase: An Open and Extensible Cyberinfrastructure to Accelerate Predictive Systems Biology

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 provides open access to quality-controlled data, and modeling and simulation tools that enable researchers to gain new insight, infer missing information, conduct predictive modeling, test hypotheses, design experiments, and share findings so they can be reproduced and extended by others.

KBase has a Jupyter-based, socially-oriented user interface that supports a persistent and provenanced environment enabling experimental and computational biologists to work together to share and publish data, approaches, workflows, and conclusions, leading to transparent and reproducible computational experiments that give credit where credit is due. KBase’s Software Development Kit (SDK) enables developers to integrate open source tools as KBase Apps.

KBase provides analysis apps that include genome assembly and annotation, transcriptomics, metabolic modeling, phylogenetics, comparative genomics and microbial community analysis. A distinguishing feature of KBase is its integrated data model that enables comparison across biological domains and interoperability with both standard and next-generation tools. Users can upload their own data and access public data to execute and share customized, ordered analyses.

Back to: Bioinformatics: Software

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