KBase: The United States Department of Energy Systems Biology Knowledgebase
Adam P. ArkinDepartment of Bioengineering, University of California, Berkeley, California, USARobert W. CottinghamBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAChristopher S. HenryMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USANomi L. HarrisEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USARick StevensComputer Science Department and Computation Institute, University of Chicago, Chicago, Illinois, USASergei MaslovBiology Department, Brookhaven National Laboratory, Upton, New York, USAParamvir DehalEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USADoreen WareCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USAFernando PérezBerkeley Institute for Data Science, University of California, Berkeley, California, USAShane CanonNational Energy Research Scientific Computing Center, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USAMichael W. SneddonEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USAMatthew HendersonEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USAWilliam J. RiehlEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USADan Murphy-OlsonMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAStephen Y. ChanEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USARoy T. KamimuraEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USASunita KumariCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USAMeghan M. DrakeBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAThomas BrettinComputing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USAElizabeth M. GlassMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USADylan ChivianEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USADan GunterComputational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USADavid J. WestonBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USABenjamin AllenBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAJason K. BaumohlEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USAAaron A. BestDepartment of Biology, Hope College, Holland, Michigan, USABen BowenEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USASteven E. BrennerDepartment of Plant and Microbial Biology, University of California, Berkeley, California, USAChristopher BunMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAJohn‐Marc ChandoniaEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USAJer-Ming ChiaCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USARic ColasantiMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USANeal ConradComputing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USAJames J. DavisComputing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USABrian H. DavisonBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAMatthew DeJonghDepartment of Computer Science, Hope College, Holland, Michigan, USAScott DevoidMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAEmily DietrichComputing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USAInna DubchakEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USAJanaka N. EdirisingheComputation Institute, University of Chicago, Chicago, Illinois, USAGang FangDepartment of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)José P. FariaMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAPaul M FrybargerMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAWolfgang GerlachMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAMark GersteinProgram in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USAAnnette GreinerNational Energy Research Scientific Computing Center, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USAJames GurtowskiCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USAHolly L HaunBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAFei HeBiology Department, Brookhaven National Laboratory, Upton, New York, USARashmi JainDepartment of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USAMarcin P. JoachimiakEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USAKevin KeeganMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAShinnosuke KondoDepartment of Computer Science, Hope College, Holland, Michigan, USAVivek KumarCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USAMiriam LandBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAFolker MeyerMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAMarissa MillsBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAPavel S. NovichkovEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USATaeyun OhDepartment of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)Gary J. OlsenDepartment of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USARobert OlsonMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USABruce ParrelloMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAShiran PasternakCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USAErik PearsonEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USASarah PoonComputational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USAGavin A PriceEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USASrividya RamakrishnanCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USAPriya RanjanBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAPamela C. RonaldDepartment of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USAMichael C. SchatzCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USASamuel M. D. SeaverMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAMaulik ShuklaComputing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USARoman A. SutorminEnvironmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USAMustafa SyedBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAJames ThomasonCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USANathan TintleDepartment of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)Daifeng WangDepartment of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)Fangfang XiaComputing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USAHyunseung YooComputing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USAShinjae YooComputer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USADantong YuComputer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA
2018en
ABI
Аннотация
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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