Journal Article

KBase: The United States Department of Energy Systems Biology Knowledgebase

Olson, Robert, Riehl, William J, Murphy-Olson, Dan, Conrad, Neal, Oh, Taeyun, Sneddon, Michael W, Kondo, Shinnosuke, Dubchak, Inna, Stevens, Rick L, Yoo, Hyunseung, Haun, Holly L, Dietrich, Emily, Parrello, Bruce, Chia, Jer-Ming, Gerlach, Wolfgang, Colasanti, Ric, Harris, Nomi L, Fang, Gang, Kumari, Sunita, Greiner, Annette, Gurtowski, James, Sutormin, Roman A, Pasternak, Shiran, Chivian, Dylan, Henderson, Matthew L, Price, Gavin A, Syed, Mustafa H, Gerstein, Mark, Davis, James J, Faria, José P, Seaver, Samuel M D, Weston, David J, Brenner, Steven E, Novichkov, Pavel S, Keegan, Kevin P, Baumohl, Jason, Meyer, Folker, Thomason, James, Schatz, Michael C, Kumar, Vivek, Pearson, Erik, Best, Aaron A, Ware, Doreen, Bowen, Ben, Jain, Rashmi, Ranjan, Priya, Allen, Benjamin H, Poon, Sarah S, Yu, Dantong, Maslov, Sergei, Gunter, Dan, Chandonia, John-Marc, Wang, Daifeng, Henry, Christopher S, Arkin, Adam P, Bun, Christopher C, Ronald, Pamela C, Yoo, Shinjae, Shukla, Maulik, Brettin, Thomas S, Drake, Meghan M, Kamimura, Roy T, Chan, Stephen Y, Edirisinghe, Janaka N, He, Fei, Devoid, Scott, Perez, Fernando, Mills, Marissa, Dehal, P

2018

Overview

To the Editor: Over the past two decades, the scale and complexity of genomics technologies and data have advanced from sequencing genomes of a few organisms to generating metagenomes, genome variation, gene expression, metabolites, and phenotype data for thousands of organisms and their communities. A major challenge in this data-rich age of biology is integrating heterogeneous and distributed data into predictive models of biological function, ranging from a single gene to entire organisms and their ecologies. Here we present the DOE Systems Biology Knowledgebase (KBase, http://kbase.us), an open-source software and data platform that enables data sharing, integration, and analysis of microbes, plants, and their communities. Once a Narrative has been shared or made public, other users can copy the Narrative and rerun it on their own data, or modify it to suit their scientific needs. [...]public Narratives serve as resources for the user community by capturing valuable data sets, associated computational analyses, and scientific context describing the rationale behind a scientific study in a form that is immediately reproducible and reusable.

• Publisher: Springer New York,Nature Publishing Group,Springer Nature,Nature Publishing Group US
• Subject: 38/39 / 45/23 / 49/91 / 631/114/129 / 631/114/2398 / 631/114/2401 / 631/114/794 / Agriculture / BASIC BIOLOGICAL SCIENCES / Bioinformatics / Biology / Biomedical Engineering/Biotechnology / Biomedicine / Biotechnology / Collaboration / Computational Biology - methods / correspondence / Data analysis / Data models / Database Management Systems - trends / Energy policy / Gene expression / Gene sequencing / Genomes / Genomics / Government agencies / Humans / Knowledge Bases / Knowledge bases (artificial intelligence) / KNOWLEDGE MANAGEMENT AND PRESERVATION / Life Sciences / MATHEMATICS AND COMPUTING / Metabolism / Metabolites / Narratives / Open source software / Organisms / Phenotypes / Prediction models / Reproducibility / Software development / Systems Biology - trends / Technology application / United States / User interface