KBase: The United States Department of Energy Systems Biology Knowledgebase

Adam P. Arkin(Lawrence Berkeley National Laboratory), Robert W. Cottingham(Oak Ridge National Laboratory), Christopher S. Henry(Argonne National Laboratory), Nomi L. Harris(Lawrence Berkeley National Laboratory), Rick Stevens(Argonne National Laboratory), Sergei Maslov(Brookhaven National Laboratory), Paramvir Dehal(Lawrence Berkeley National Laboratory), Doreen Ware(Cold Spring Harbor Laboratory), Fernando Pérez(Lawrence Berkeley National Laboratory), Shane Canon(Lawrence Berkeley National Laboratory), Michael W. Sneddon(Lawrence Berkeley National Laboratory), Matthew Henderson(Lawrence Berkeley National Laboratory), William J. Riehl(Lawrence Berkeley National Laboratory), Dan Murphy-Olson(Argonne National Laboratory), Stephen Y. Chan(Lawrence Berkeley National Laboratory), Roy T. Kamimura(Lawrence Berkeley National Laboratory), Sunita Kumari(Cold Spring Harbor Laboratory), Meghan M. Drake(Oak Ridge National Laboratory), Thomas Brettin(Argonne National Laboratory), Elizabeth M. Glass(Argonne National Laboratory), Dylan Chivian(Lawrence Berkeley National Laboratory), Dan Gunter(Lawrence Berkeley National Laboratory), David J. Weston(Oak Ridge National Laboratory), Benjamin Allen(Oak Ridge National Laboratory), Jason K. Baumohl(Lawrence Berkeley National Laboratory), Aaron A. Best(Hope College), Ben Bowen(Lawrence Berkeley National Laboratory), Steven E. Brenner(University of California, Berkeley), Christopher Bun(Argonne National Laboratory), John‐Marc Chandonia(Lawrence Berkeley National Laboratory), Jer-Ming Chia(Cold Spring Harbor Laboratory), Ric Colasanti(Argonne National Laboratory), Neal Conrad(Argonne National Laboratory), James J. Davis(Argonne National Laboratory), Brian H. Davison(Oak Ridge National Laboratory), Matthew DeJongh(Hope College), Scott Devoid(Argonne National Laboratory), Emily Dietrich(Argonne National Laboratory), Inna Dubchak(Lawrence Berkeley National Laboratory), Janaka N. Edirisinghe(Argonne National Laboratory), Gang Fang(Yale University), José P. Faria(Argonne National Laboratory), Paul M Frybarger(Argonne National Laboratory), Wolfgang Gerlach(Argonne National Laboratory), Mark Gerstein(Yale University), Annette Greiner(Lawrence Berkeley National Laboratory), James Gurtowski(Cold Spring Harbor Laboratory), Holly L Haun(Oak Ridge National Laboratory), Fei He(Brookhaven National Laboratory), Rashmi Jain(Lawrence Berkeley National Laboratory), Marcin P. Joachimiak(Lawrence Berkeley National Laboratory), Kevin Keegan(Argonne National Laboratory), Shinnosuke Kondo(Hope College), Vivek Kumar(Cold Spring Harbor Laboratory), Miriam Land(Oak Ridge National Laboratory), Folker Meyer(Argonne National Laboratory), Marissa Mills(Oak Ridge National Laboratory), Pavel S. Novichkov(Lawrence Berkeley National Laboratory), Taeyun Oh(Lawrence Berkeley National Laboratory), Gary J. Olsen(University of Illinois Urbana-Champaign), Robert Olson(Argonne National Laboratory), Bruce Parrello(Argonne National Laboratory), Shiran Pasternak(Cold Spring Harbor Laboratory), Erik Pearson(Lawrence Berkeley National Laboratory), Sarah Poon(Lawrence Berkeley National Laboratory), Gavin A Price(Lawrence Berkeley National Laboratory), Srividya Ramakrishnan(Cold Spring Harbor Laboratory), Priya Ranjan(Oak Ridge National Laboratory), Pamela C. Ronald(Lawrence Berkeley National Laboratory), Michael C. Schatz(Cold Spring Harbor Laboratory), Samuel M. D. Seaver(Argonne National Laboratory), Maulik Shukla(Argonne National Laboratory), Roman A. Sutormin(Lawrence Berkeley National Laboratory), Mustafa Syed(Oak Ridge National Laboratory), James Thomason(Cold Spring Harbor Laboratory), Nathan Tintle(Hope College), Daifeng Wang(Yale University), Fangfang Xia(Argonne National Laboratory), Hyunseung Yoo(Argonne National Laboratory), Shinjae Yoo(Brookhaven National Laboratory), Dantong Yu(Brookhaven National Laboratory)
Nature Biotechnology
July 1, 2018
10.1038/nbt.4163
Cited by 1,649Open Access
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Abstract

The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) is an open-source software and data platform designed to tackle the grand challenge of systems biology—predicting and designing biological function at scales ranging from the biomolecular to the ecological. KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large analyses on scalable computing infrastructure; and combine experimental evidence and conclusions to model plant and microbial physiology and community dynamics. The KBase platform has extensible analytical capabilities that currently include (meta)genome assembly, annotation, comparative genomics, transcriptomics, and metabolic modeling; a web-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; and a software development kit that enables the community to add functionality to the system.

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