skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: KBase: The United States Department of Energy Systems Biology Knowledgebase

Authors:
ORCiD logo; ; ; ORCiD logo; ; ; ; ORCiD logo; ORCiD logo; ; ; ; ; ; ; ; ; ; ; more »; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ORCiD logo; ; ; ORCiD logo; ; ; ; ORCiD logo; ; ; ; ; ; ORCiD logo; ORCiD logo; ; ; ORCiD logo; ; ; ; ; ; ; ; ; ; ; ORCiD logo; ; ; ; ; ; ; ORCiD logo; ; ; ; « less
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science - Office of Biological and Environmental Research; USDOE Office of Science (SC)
OSTI Identifier:
1474150
DOE Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article
Journal Name:
Nature Biotechnology
Additional Journal Information:
Journal Volume: 36; Journal Issue: 7; Journal ID: ISSN 1087-0156
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English

Citation Formats

Arkin, Adam P., Cottingham, Robert W., Henry, Christopher S., Harris, Nomi L., Stevens, Rick L., Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W., Henderson, Matthew L., Riehl, William J., Murphy-Olson, Dan, Chan, Stephen Y., Kamimura, Roy T., Kumari, Sunita, Drake, Meghan M., Brettin, Thomas S., Glass, Elizabeth M., Chivian, Dylan, Gunter, Dan, Weston, David J., Allen, Benjamin H., Baumohl, Jason, Best, Aaron A., Bowen, Ben, Brenner, Steven E., Bun, Christopher C., Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J., Davison, Brian H., DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N., Fang, Gang, Faria, José P., Frybarger, Paul M., Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L., He, Fei, Jain, Rashmi, Joachimiak, Marcin P., Keegan, Kevin P., Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L., Meyer, Folker, Mills, Marissa, Novichkov, Pavel S., Oh, Taeyun, Olsen, Gary J., Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S., Price, Gavin A., Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C., Schatz, Michael C., Seaver, Samuel M. D., Shukla, Maulik, Sutormin, Roman A., Syed, Mustafa H., Thomason, James, Tintle, Nathan L., Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, and Yu, Dantong. KBase: The United States Department of Energy Systems Biology Knowledgebase. United States: N. p., 2018. Web. doi:10.1038/nbt.4163.
Arkin, Adam P., Cottingham, Robert W., Henry, Christopher S., Harris, Nomi L., Stevens, Rick L., Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W., Henderson, Matthew L., Riehl, William J., Murphy-Olson, Dan, Chan, Stephen Y., Kamimura, Roy T., Kumari, Sunita, Drake, Meghan M., Brettin, Thomas S., Glass, Elizabeth M., Chivian, Dylan, Gunter, Dan, Weston, David J., Allen, Benjamin H., Baumohl, Jason, Best, Aaron A., Bowen, Ben, Brenner, Steven E., Bun, Christopher C., Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J., Davison, Brian H., DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N., Fang, Gang, Faria, José P., Frybarger, Paul M., Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L., He, Fei, Jain, Rashmi, Joachimiak, Marcin P., Keegan, Kevin P., Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L., Meyer, Folker, Mills, Marissa, Novichkov, Pavel S., Oh, Taeyun, Olsen, Gary J., Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S., Price, Gavin A., Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C., Schatz, Michael C., Seaver, Samuel M. D., Shukla, Maulik, Sutormin, Roman A., Syed, Mustafa H., Thomason, James, Tintle, Nathan L., Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, & Yu, Dantong. KBase: The United States Department of Energy Systems Biology Knowledgebase. United States. doi:10.1038/nbt.4163.
Arkin, Adam P., Cottingham, Robert W., Henry, Christopher S., Harris, Nomi L., Stevens, Rick L., Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W., Henderson, Matthew L., Riehl, William J., Murphy-Olson, Dan, Chan, Stephen Y., Kamimura, Roy T., Kumari, Sunita, Drake, Meghan M., Brettin, Thomas S., Glass, Elizabeth M., Chivian, Dylan, Gunter, Dan, Weston, David J., Allen, Benjamin H., Baumohl, Jason, Best, Aaron A., Bowen, Ben, Brenner, Steven E., Bun, Christopher C., Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J., Davison, Brian H., DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N., Fang, Gang, Faria, José P., Frybarger, Paul M., Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L., He, Fei, Jain, Rashmi, Joachimiak, Marcin P., Keegan, Kevin P., Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L., Meyer, Folker, Mills, Marissa, Novichkov, Pavel S., Oh, Taeyun, Olsen, Gary J., Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S., Price, Gavin A., Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C., Schatz, Michael C., Seaver, Samuel M. D., Shukla, Maulik, Sutormin, Roman A., Syed, Mustafa H., Thomason, James, Tintle, Nathan L., Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, and Yu, Dantong. Fri . "KBase: The United States Department of Energy Systems Biology Knowledgebase". United States. doi:10.1038/nbt.4163.
@article{osti_1474150,
title = {KBase: The United States Department of Energy Systems Biology Knowledgebase},
author = {Arkin, Adam P. and Cottingham, Robert W. and Henry, Christopher S. and Harris, Nomi L. and Stevens, Rick L. and Maslov, Sergei and Dehal, Paramvir and Ware, Doreen and Perez, Fernando and Canon, Shane and Sneddon, Michael W. and Henderson, Matthew L. and Riehl, William J. and Murphy-Olson, Dan and Chan, Stephen Y. and Kamimura, Roy T. and Kumari, Sunita and Drake, Meghan M. and Brettin, Thomas S. and Glass, Elizabeth M. and Chivian, Dylan and Gunter, Dan and Weston, David J. and Allen, Benjamin H. and Baumohl, Jason and Best, Aaron A. and Bowen, Ben and Brenner, Steven E. and Bun, Christopher C. and Chandonia, John-Marc and Chia, Jer-Ming and Colasanti, Ric and Conrad, Neal and Davis, James J. and Davison, Brian H. and DeJongh, Matthew and Devoid, Scott and Dietrich, Emily and Dubchak, Inna and Edirisinghe, Janaka N. and Fang, Gang and Faria, José P. and Frybarger, Paul M. and Gerlach, Wolfgang and Gerstein, Mark and Greiner, Annette and Gurtowski, James and Haun, Holly L. and He, Fei and Jain, Rashmi and Joachimiak, Marcin P. and Keegan, Kevin P. and Kondo, Shinnosuke and Kumar, Vivek and Land, Miriam L. and Meyer, Folker and Mills, Marissa and Novichkov, Pavel S. and Oh, Taeyun and Olsen, Gary J. and Olson, Robert and Parrello, Bruce and Pasternak, Shiran and Pearson, Erik and Poon, Sarah S. and Price, Gavin A. and Ramakrishnan, Srividya and Ranjan, Priya and Ronald, Pamela C. and Schatz, Michael C. and Seaver, Samuel M. D. and Shukla, Maulik and Sutormin, Roman A. and Syed, Mustafa H. and Thomason, James and Tintle, Nathan L. and Wang, Daifeng and Xia, Fangfang and Yoo, Hyunseung and Yoo, Shinjae and Yu, Dantong},
abstractNote = {},
doi = {10.1038/nbt.4163},
journal = {Nature Biotechnology},
issn = {1087-0156},
number = 7,
volume = 36,
place = {United States},
year = {2018},
month = {7}
}

Works referenced in this record:

Enhancing reproducibility for computational methods
journal, December 2016


Ten Simple Rules for the Open Development of Scientific Software
journal, December 2012


NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
journal, January 2007

  • Pruitt, K. D.; Tatusova, T.; Maglott, D. R.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl842

Phytozome: a comparative platform for green plant genomics
journal, November 2011

  • Goodstein, David M.; Shu, Shengqiang; Howson, Russell
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr944

Global phenotypic characterization of bacteria
journal, January 2009


KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000

  • Kanehisa, Minoru; Goto, Susumu
  • Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
  • DOI: 10.1093/nar/28.1.27

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
journal, January 2010

  • Schellenberger, Jan; Park, Junyoung O.; Conrad, Tom M.
  • BMC Bioinformatics, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2105-11-213

MetaCyc: a multiorganism database of metabolic pathways and enzymes
journal, January 2006


IPython: A System for Interactive Scientific Computing
journal, January 2007

  • Perez, Fernando; Granger, Brian E.
  • Computing in Science & Engineering, Vol. 9, Issue 3
  • DOI: 10.1109/MCSE.2007.53

Modeling central metabolism and energy biosynthesis across microbial life
journal, August 2016


Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
journal, November 2016

  • Magnúsdóttir, Stefanía; Heinken, Almut; Kutt, Laura
  • Nature Biotechnology, Vol. 35, Issue 1
  • DOI: 10.1038/nbt.3703

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction: COMMUNITY DATA-DRIVEN METABOLIC NETWORK MODELING
journal, June 2016

  • Henry, Christopher S.; Bernstein, Hans C.; Weisenhorn, Pamela
  • Journal of Cellular Physiology, Vol. 231, Issue 11
  • DOI: 10.1002/jcp.25428

MetaCyc: a multiorganism database of metabolic pathways and enzymes
journal, January 2004


NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
journal, December 2004

  • Pruitt, K. D.
  • Nucleic Acids Research, Vol. 33, Issue Database issue
  • DOI: 10.1093/nar/gki025

    Works referencing / citing this record:

    iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
    journal, July 2019


    Ten Simple Rules for the Open Development of Scientific Software
    journal, December 2012


    Current status and applications of genome-scale metabolic models
    journal, June 2019


    Global phenotypic characterization of bacteria
    journal, January 2009


    Enhancing reproducibility for computational methods
    journal, December 2016


    KEGG: Kyoto Encyclopedia of Genes and Genomes
    journal, January 2000

    • Kanehisa, Minoru; Goto, Susumu
    • Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
    • DOI: 10.1093/nar/28.1.27

    BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
    journal, January 2010

    • Schellenberger, Jan; Park, Junyoung O.; Conrad, Tom M.
    • BMC Bioinformatics, Vol. 11, Issue 1
    • DOI: 10.1186/1471-2105-11-213

    MetaCyc: a multiorganism database of metabolic pathways and enzymes
    journal, January 2006


    IPython: A System for Interactive Scientific Computing
    journal, January 2007

    • Perez, Fernando; Granger, Brian E.
    • Computing in Science & Engineering, Vol. 9, Issue 3
    • DOI: 10.1109/mcse.2007.53

    A systematic assessment of current genome-scale metabolic reconstruction tools
    journal, August 2019


    Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
    journal, November 2016

    • Magnúsdóttir, Stefanía; Heinken, Almut; Kutt, Laura
    • Nature Biotechnology, Vol. 35, Issue 1
    • DOI: 10.1038/nbt.3703

    NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    journal, January 2007

    • Pruitt, K. D.; Tatusova, T.; Maglott, D. R.
    • Nucleic Acids Research, Vol. 35, Issue Database
    • DOI: 10.1093/nar/gkl842

    Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome
    journal, June 2019

    • Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel
    • eLife, Vol. 8
    • DOI: 10.7554/elife.39733

    Methods for automated genome-scale metabolic model reconstruction
    journal, July 2018

    • Faria, José P.; Rocha, Miguel; Rocha, Isabel
    • Biochemical Society Transactions, Vol. 46, Issue 4
    • DOI: 10.1042/bst20170246

    Phytozome: a comparative platform for green plant genomics
    journal, November 2011

    • Goodstein, David M.; Shu, Shengqiang; Howson, Russell
    • Nucleic Acids Research, Vol. 40, Issue D1
    • DOI: 10.1093/nar/gkr944

    Modeling central metabolism and energy biosynthesis across microbial life
    journal, August 2016


    Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction: COMMUNITY DATA-DRIVEN METABOLIC NETWORK MODELING
    journal, June 2016

    • Henry, Christopher S.; Bernstein, Hans C.; Weisenhorn, Pamela
    • Journal of Cellular Physiology, Vol. 231, Issue 11
    • DOI: 10.1002/jcp.25428

    Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica
    journal, August 2019


    Methods for automated genome-scale metabolic model reconstruction
    journal, July 2018

    • Faria, José P.; Rocha, Miguel; Rocha, Isabel
    • Biochemical Society Transactions, Vol. 46, Issue 4
    • DOI: 10.1042/bst20170246

    iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
    journal, July 2019


    Current status and applications of genome-scale metabolic models
    journal, June 2019


    Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica
    journal, August 2019


    Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome
    journal, June 2019

    • Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel
    • eLife, Vol. 8
    • DOI: 10.7554/elife.39733

    Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions
    dataset, January 2020

    • St. James, Andrew; Crockett, Zachary
    • Cornell Univ., Ithaca, NY (United States);Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
    • DOI: 10.25982/51077.6/1637903

    Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions
    journal, March 2020

    • St. James, Andrew R.; Richardson, Ruth E.
    • FEMS Microbiology Ecology, Vol. 96, Issue 5
    • DOI: 10.1093/femsec/fiaa050

    Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots
    journal, March 2020

    • Pelletier, Dale A.; Burdick, Leah H.; Podar, Mircea
    • Microbiology Resource Announcements, Vol. 9, Issue 12
    • DOI: 10.1128/mra.00159-20

    A systematic assessment of current genome-scale metabolic reconstruction tools
    journal, August 2019