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Research Article

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

  • Ramy K. Aziz mail,

    ramy.aziz@gmail.com (RKA); Ross@thefig.info (RO)

    Affiliations: Computation Institute, University of Chicago, Chicago, Illinois, United States of America, Department of Computer Science, San Diego State University, San Diego, California, United States of America, Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt

    Current address: Systems Biology Research Group, University of California San Diego, La Jolla, California, United States of America

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  • Scott Devoid,

    Affiliations: Computation Institute, University of Chicago, Chicago, Illinois, United States of America, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America

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  • Terrence Disz,

    Affiliations: Computation Institute, University of Chicago, Chicago, Illinois, United States of America, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America

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  • Robert A. Edwards,

    Affiliations: Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America, Department of Computer Science, San Diego State University, San Diego, California, United States of America

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  • Christopher S. Henry,

    Affiliations: Computation Institute, University of Chicago, Chicago, Illinois, United States of America, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America

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  • Gary J. Olsen,

    Affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America

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  • Robert Olson,

    Affiliations: Computation Institute, University of Chicago, Chicago, Illinois, United States of America, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America

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  • Ross Overbeek mail,

    ramy.aziz@gmail.com (RKA); Ross@thefig.info (RO)

    Affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, United States of America

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  • Bruce Parrello,

    Affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, United States of America

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  • Gordon D. Pusch,

    Affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, United States of America

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  • Rick L. Stevens,

    Affiliations: Computation Institute, University of Chicago, Chicago, Illinois, United States of America, Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, Illinois, United States of America

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  • Veronika Vonstein,

    Affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, United States of America

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  • Fangfang Xia

    Affiliations: Computation Institute, University of Chicago, Chicago, Illinois, United States of America, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America

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  • Published: October 24, 2012
  • DOI: 10.1371/journal.pone.0048053
  • Featured in PLOS Collections

About the Authors

Ramy K. Aziz, Scott Devoid, Terrence Disz, Christopher S. Henry, Robert Olson, Rick L. Stevens, Fangfang Xia
Computation Institute, University of Chicago, Chicago, Illinois, United States of America
Scott Devoid, Terrence Disz, Robert A. Edwards, Christopher S. Henry, Robert Olson, Fangfang Xia
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America
Ross Overbeek, Bruce Parrello, Gordon D. Pusch, Veronika Vonstein
Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, United States of America
Ramy K. Aziz, Robert A. Edwards
Department of Computer Science, San Diego State University, San Diego, California, United States of America
Ramy K. Aziz
Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
Gary J. Olsen
Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
Rick L. Stevens
Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, Illinois, United States of America

Corresponding Authors

Competing Interests

RKA is a volunteer member of the editorial board of PLOS ONE, and as such had no access to the peer review or acceptance process for this manuscript. Other than that, the authors have declared that no competing interests exist. The submitted manuscript has been created in part by UChicago Argonne, LLC, Operator of Argonne National Laboratory (“Argonne”). Argonne, a U.S. Department of Energy Office of Science laboratory, is operated under Contract No. DE-AC02-06CH11357 and Award DE-SC0004921. The U.S. Government retains for itself, and others acting on its behalf, a paid-up nonexclusive, irrevocable worldwide license in said article to reproduce, prepare derivative works, distribute copies to the public, and perform publicly and display publicly, by or on behalf of the Government. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.

Author Contributions

Conceived and designed the experiments: TD R. Overbeek BP RLS VV. Performed the experiments: RKA SD TD CSH RAE GJO R. Olson R. Overbeek BP GDP RLS VV FX. Analyzed the data: TD CSH GJO R. Overbeek BP GDP RLS VV. Wrote the paper: RKA TD CSH R. Overbeek BP VV. Developed the SEED servers and client code: TD CSH R. Olson R. Overbeek BP GDP. Developed the JAVA version: RAE. Contributed to the curation of the SEED annotations and subsystems: RKA RAE CSH GJO R. Overbeek RLS VV. Contributed to the SEED codebase: SD TD RAE CSH GJO R. Olson R. Overbeek TP BP GDP RLS FX.