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@BOOK{harold:2001,
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@ARTICLE{hedley:2001,
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@MISC{hedley:2001b,
       AUTHOR = {Warren~J. Hedley and Melanie~R. Nelson and David Bullivant and
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@INPROCEEDINGS{hucka:2000,
       AUTHOR = {M. Hucka and D. Beeman and K. Shankar and S. Emardson and
                  J.~M. Bower},
        TITLE = {The {M}odeler's {W}orkspace: A Tool for Computational Neuroscientists},
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         YEAR = 2000,
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@MISC{hucka:2000b,
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        TITLE = {{SCHUCS}: A Notation for Describing Model Representations
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@MISC{hucka:2000c,
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        TITLE = {Preliminary High-Level Design for {BMF}, the {Biology Modeling Framework}},
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         YEAR = 2000
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@MISC{hucka:2001,
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        TITLE = {{Systems Biology Markup Language} ({SBML}) {L}evel 1: Structures
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@MISC{hucka:2001b,
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        TITLE = {Introduction to the {Systems Biology Workbench}},
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                 \url{http://www.sbw-sbml.org/}},
         YEAR = 2001
}

@MISC{hucka:2001c,
       AUTHOR = {M. Hucka and A. Finney and H.~M. Sauro and H. Bolouri},
        TITLE = {A Comparison of Two Alternative Message-Passing
                 Approaches for {SBW}},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.sbw-sbml.org/}},
         YEAR = 2001
}

@INCOLLECTION{hucka:2001d,
       AUTHOR = {Michael Hucka and Herbert~M. Sauro and Andrew Finney and
                 Hamid Bolouri and John Doyle and Hiroaki Kitano},
        TITLE = {The {ERATO} {S}ystems {B}iology {W}orkbench: An Integrated Environment
                 for Multiscale and Multitheoretic Simulations in Systems Biology},
    BOOKTITLE = {Foundations of Systems Biology},
       EDITOR = {H. Kitano},
    PUBLISHER = MITP,
      CHAPTER = {6},
         YEAR = 2001
}

@MISC{hucka:2001e,
       AUTHOR = {Michael Hucka and Andrew Finney},
        TITLE = {Source Code for {XML-RPC} versus {SBW-RPC} Comparison},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{ftp://ftp.cds.caltech.edu/pub/caltech-erato/message-comparison}},
         YEAR = 2001
}

@INPROCEEDINGS{hucka:2001f,
       AUTHOR = {Michael Hucka and Andrew Finney and Herbert~M. Sauro and
                 Hamid Bolouri and John~C. Doyle and Hiroaki Kitano},
        TITLE = {The {ERATO} {S}ystems {B}iology {W}orkbench: Architectural Evolution},
    BOOKTITLE = {Proceedings of the Second International Conference on Systems Biology},
        PAGES = {352--361},
         YEAR = 2001,
       EDITOR = {Tau-Mu Yi and Michael Hucka and Mineo Morohashi and Hiroaki Kitano},
    PUBLISHER = {Omnipress, Inc.}
}

@MISC{hucka:2001g,
       AUTHOR = {M. Hucka and A. Finney and H.~M. Sauro and H. Bolouri},
        TITLE = {{Systems Biology Markup Language} ({SBML}) {L}evel 1: Structures
                  and Facilities for Basic Model Definitions},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://sbml.org/documents/}},
         YEAR = 2001
}

@INPROCEEDINGS{hucka:2002,
       AUTHOR = {Michael Hucka and Andrew Finney and Herbert~M. Sauro and
                 Hamid Bolouri and John~C. Doyle and Hiroaki Kitano},
        TITLE = {The {ERATO} {S}ystems {B}iology {W}orkbench: Enabling Interaction and
                 Exchange Between Software Tools for Computational Biology},
    BOOKTITLE = {Pacific Symposium on Biocomputing 2002},
         YEAR = 2002,
       EDITOR = {Russ~B. Altman and A.~Keith Dunker and Lawrence~Hunker and Kevin
                 Lauderdale and Teri~E. Klein},
    PUBLISHER = {World Scientific Press}
}

@MISC{hucka:2002b,
       AUTHOR = {Michael Hucka and Andrew Finney and Herbert~M. Sauro and Hamid Bolouri},
        TITLE = {Systems {B}iology {W}orkbench {Java}\textsuperscript{\tiny{\texttrademark}} Programmer's Manual},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.sbw-sbml.org/}},
         YEAR = 2002
}

@MISC{hucka:2002c,
       AUTHOR = {Michael Hucka and Andrew Finney},
        TITLE = {The {SBW-CORBA} {G}ateway},
         YEAR = 2002
}

@ARTICLE{hucka:2002d,
       AUTHOR = {M. Hucka and A. Finney and H.~M. Sauro
                 and H. Bolouri and J.~C. Doyle and H. Kitano
                 and A.~P. Arkin and B.~J. Bornstein
                 and D. Bray and A. Cornish-Bowden
                 and A.~A. Cuellar and S. Dronov
                 and E.~D. Gilles and M. Ginkel
                 and V. Gor and I.~I. Goryanin
                 and W.~J. Hedley and T.~C. Hodgman
                 and J-H. Hofmeyr and P.~J. Hunter
                 and N.~S. Juty and J.~L. Kasberger
                 and A. Kremling and U. Kummer
                 and N. Le~Nov\`{e}re and L.~M. Loew
                 and D. Lucio and P. Mendes and E.~D. Mjolsness
                 and Y. Nakayama and M.~R. Nelson and P.~F. Nielsen
                 and T. Sakurada and J.~C. Schaff and B.~E. Shapiro
                 and T.~S. Shimizu and H.~D. Spence and J. Stelling
                 and K. Takahashi and M. Tomita and J. Wagner
                 and J. Wang},
        TITLE = {The Systems Biology Markup Language (SBML):
                 A Medium for Representation and Exchange
                 of Biochemical Network Models},
      JOURNAL = {Bioinformatics},
         YEAR = 2002,
         NOTE = {To appear}
}

@article{hucka:2003,
     AUTHOR = {Hucka, M. and Finney, A. and Sauro, H.~M. and Bolouri, H.
               and Doyle, J.~C. and Kitano, H. and Arkin, A.~P.
               and Bornstein, B.~J. and Bray, D. and Cornish-Bowden, A.
               and Cuellar, A.~A. and Dronov, S. and Gilles, E.~D.
               and Ginkel, M. and Gor, V. and Goryanin, I.~I.
               and Hedley, W.~J. and Hodgman, T.~C. and Hofmeyr, J.-H.
               and Hunter, P.~J. and Juty, N.~S. and Kasberger, J.~L.
               and Kremling, A. and Kummer, U. and Le Nov\`{e}re, N.
               and Loew, L.~M.  and Lucio, D. and Mendes, P. and Minch, E.
               and Mjolsness, E.~D.  and Nakayama, Y. and Nelson, M.~R.
               and Nielsen, P.~F. and Sakurada, T. and Schaff, J.~C.
               and Shapiro, B.~E. and Shimizu, T.~S.  and Spence, H.~D.
               and Stelling, J. and Takahashi, K. and Tomita, M.
               and Wagner, J. and Wang, J.},
      TITLE = {The {S}ystems {B}iology {M}arkup {L}anguage ({SBML}): A Medium
               for Representation and Exchange of Biochemical Network Models},
    JOURNAL = {Bioinformatics},
     VOLUME = {19},
     NUMBER = {4},
      PAGES = {524-531},
       YEAR = 2003
}

@MISC{hucka:2003a,
       AUTHOR = {Michael Hucka and Ben Kovitz and Jo Matthews and Maria Schilstra and
                  Andrew Finney and Ben Bornstein and Bruce Shapiro and Sarah Keating and Akira Funahashi},
        TITLE = {The {SBML} Website},
 HOWPUBLISHED = {Available via the World Wide Web at \url{http://www.sbml.org/}.},
         YEAR = 2003
}

@MISC{hudson:1999,
       AUTHOR = {Scott~E. Hudson and Frank Flannery and C.~Scott Ananian},
        TITLE = {{CUP} Parser Generator for {Java}},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.cs.princeton.edu/~appel/modern/java/CUP/}.},
         YEAR = 1999
}

@article{hucka:2004,
     AUTHOR = {Hucka, M. and Finney, A. and Bornstein, B.~J. and Keating, S.~M. and
                Shapiro, B.~E. and Matthews, J. and Kovitz, B.~L. and Schilstra,
                M.~J. and Funahashi, A. and Doyle J.~C. and Kitano, H.},
      TITLE = {Evolving a lingua franca and assoicated software infrastructure for
                computational systems biology: the {Systems Biology Markup Language (SBML)}
                project},
    JOURNAL = {IEE Systems Biology},
     VOLUME = {1},
     NUMBER = {1},
      PAGES = {41-53},
       YEAR = 2004
}

@BOOK{hughes:1999,
       AUTHOR = {Merlin Hughes and Michael Shoffner and Derek Hamner},
        TITLE = {Java Network Programming},
    PUBLISHER = {Manning Publications Co.},
         YEAR = 1999
}