b.bib

@ARTICLE{bader:2003,
AUTHOR={Bader, G. D. and Betel, D. and Hogue, C. W.},
YEAR=2003,
TITLE={{BIND}: the Biomolecular Interaction Network Database},
JOURNAL={Nucleic Acids Res.},
VOLUME=31,
NUMBER=1,
PAGES={248--50}
}

@Article{ball:2006,
  author = 	 {K. Ball and T. G. Kurtz and L. Popovic and G. Rempala},
  title = 	 {Asymptotic analysis of multiscale approximations to reaction networks},
  journal = 	 {Annals of Applied Probability},
  year = 	 2006,
  volume =	 16,
  number =	 4,
  pages =	 {1925--1961}
}

@BOOK{barrett:2001,
       AUTHOR = {Daniel~J. Barrett and Richard~E. Silverman},
    TITLE = {{SSH}, the Secure Shell},
    PUBLISHER = OREILLY,
     YEAR = 2001,
      ADDRESS = {Sebastopol, CA, USA}
}

@MISC{bartol:2002,
       AUTHOR = {Thomas M. Bartol and Joel R. Stiles},
        TITLE = {{MCell}},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.mcell.cnl.salk.edu/}},
         YEAR = 2002
}

@MISC{beckett:2002,
       AUTHOR = {Beckett, Dave and Miller, Eric and Brickley, Dan},
        TITLE = {Expressing Simple Dublin Core in {RDF/XML}},
 HOWPUBLISHED = {Available via the World Wide Web at \url{http://dublincore.org/documents/dcmes-xml/index.shtml}},
         YEAR = 2002
}

@MISC{belta:2003,
       AUTHOR = {Calin Belta and Mark Goulian and Sharon Gowen and Franjo Ivancic and
                 Vijay Kumar and Arch Owen and Harvey Rubin and Matt Rubin and
                 Jonathan Schug and Oleg Sokolsky and Jonathan Webb and Lois Welber},
        TITLE = {{Bio Sketch Pad}},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://bio.bbn.com/biospice/biosketchpad/}},
         YEAR = 2003
}

@ARTICLE{berman:2000,
AUTHOR = {H.M. Berman and J. Westbrook and Z. Feng and G. Gilliland and T.N. Bhat and H. Weissig and I.N. Shindyalov and P.E. Bourne},
TITLE = {The Protein Data Bank},
JOURNAL = {Nucleic Acids Research},
VOLUME = 28,
PAGES = {235--242},
YEAR = 2000
}

@MISC{biggs:2001,
       AUTHOR = {Wes Biggs},
        TITLE = {Package \texttt{gnu.regexp}: Regular expressions for {Java}},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.cacas.org/java/gnu/regexp/}.},
         YEAR = 2001
}

@MISC{bipm:1998,
       AUTHOR = {{Bureau International des Poids et Mesures}},
        TITLE = {The {International} {System} of {Units} ({SI})},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.bipm.fr/pdf/si-brochure.pdf}.},
         YEAR = 1998
}

% The capitalization on the title of the next one is goofy and
% appears as shown:

@MISC{bipm:2000,
       AUTHOR = {{Bureau International des Poids et Mesures}},
        TITLE = {The {International} {System} of {Units} ({SI}) Supplement 2000: addenda
                 and corrigenda to the 7th edition (1998)},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.bipm.fr/pdf/si-supplement2000.pdf}.},
         YEAR = 2000
}

@MISC{bipm:2006,
       AUTHOR = {{Bureau International des Poids et Mesures}},
        TITLE = {The {International} {System} of {Units} ({SI}) 
                 8th edition (2006)},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.bipm.org/utils/common/pdf/si_brochure_8.pdf}.},
         YEAR = 2006
}

@MISC{biron:2000,
       AUTHOR = {P.~V. Biron and A. Malhotra},
        TITLE = {{XML} {S}chema Part 2: Datatypes ({W3C} Candidate
                 Recommendation 24 {O}ctober 2000)},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.w3.org/TR/xmlschema-2/}.},
         YEAR = 2000
}

@article{blinov:2004,
  title={BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains},
  author={Blinov, Michael L and Faeder, James R and Goldstein, Byron and Hlavacek, William S},
  journal={Bioinformatics},
  volume={20},
  number={17},
  pages={3289--3291},
  year={2004},
  publisher={Oxford University Press}
}

@TECHREPORT{borenstein:1992,
       AUTHOR = {N. Borenstein and N. Freed},
        TITLE = {{MIME} ({Multipurpose Internet Mail Extensions})},
  INSTITUTION = {Bellcore},
         TYPE = {Internet Request for Comments},
       NUMBER = 1341,
         NOTE = {Available via the World Wide Web at
                 \url{http://www.faqs.org/rfcs/rfc1341.html}},
         YEAR = 1992
}

@ARTICLE{bosak:1999,
       AUTHOR = {J. Bosak and T. Bray},
        TITLE = {{XML} and the Second-Generation {Web}},
      JOURNAL = SA,
         YEAR = 1999,
        PAGES = {89--93},
        MONTH = may,
       VOLUME = 280,
       NUMBER = 5
}

@MISC{box:2000,
       AUTHOR = {D. Box and D. Ehnebuske and G. Kakivaya and A. Layman and
                  N. Mendelsohn and H.~F. Nielsen and S. Thatte and D. Winer},
        TITLE = {Simple {O}bject {A}ccess {P}rotocol ({SOAP}) 1.1: {W3C} Note 08 {M}ay 2000},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.w3.org/TR/SOAP/}},
         YEAR = 2000
}

@INPROCEEDINGS{bramley:2000,
       AUTHOR = {Randall Bramley and Kenneth Chiu and Shridhar Diwan and Dennis
                 Cannon and Madhusudhan Govindaraju and Nirmal Mukhi and
                 Benjamin Temko and Madhuri Yechuri},
        TITLE = {A Component Based Services Architecture for Building
                 Distributed Applications},
    BOOKTITLE = {Proceedings of the 9th {IEEE} International Symposium on High
                 Performance Distributed Computing, Pittsburgh, PA, Aug. 2000},
         YEAR = 2000
}

@MISC{bray:1998,
       AUTHOR = {T. Bray and J. Paoli and C.~M. Sperberg-McQueen},
        TITLE = {Extensible Markup Language ({XML}) 1.0, {W3C} Recommendation
                  10-{F}ebruary-1998},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.w3.org/TR/1998/REC-xml-19980210}},
         YEAR = 1998
}

@MISC{bray:1999,
       AUTHOR = {T. Bray and D. Hollander, D and A. Layman},
        TITLE = {Namespaces in {XML}.  {W3C} 14-{J}anuary-1999},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.w3.org/TR/1999/REC-xml-names-19990114/}},
         YEAR = 1999
}

@MISC{bray:2000,
       AUTHOR = {T. Bray and J. Paoli and C.~M. Sperberg-McQueen and Eve Maler},
        TITLE = {Extensible Markup Language ({XML}) 1.0 (Second Edition),
                 {W3C} Recommendation 6-{October}-2000},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.w3.org/TR/1998/REC-xml-19980210}},
         YEAR = 2000
}

@MISC{bray:2004,
       AUTHOR = {T. Bray and J. Paoli and C.~M. Sperberg-McQueen and Eve Maler
                 and Fran\c{c}ois Yergeau},
        TITLE = {Extensible Markup Language ({XML}) 1.0 (Third Edition),
                 {W3C} Recommendation 4-{February}-2004},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.w3.org/TR/2004/REC-xml-20040204}},
         YEAR = 2004
}

@MISC{bray:2001,
       AUTHOR = {Dennis Bray and Carl Firth and Nicolas {Le Nov\`{e}re} and Thomas Shimizu},
        TITLE = {\emph{StochSim}},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.zoo.cam.ac.uk/comp-cell/StochSim.html}},
         YEAR = 2001
}

@ARTICLE{brown:2002,
       AUTHOR = {C.~T. Brown and A.~G. Rust and P.~J.~C. Clarke and Z. Pan and
                 M.~.J. Schilstra and T. {De Buysshcher} and G. Griffin and
                 B.~J. Wold and R.~A. Cameron and E.~H. Davidson and H. Bolouri},
        TITLE = {New Computational Approaches for Analysis of Cis-Regulatory Networks},
      JOURNAL = {Developmental Biology},
         YEAR = 2002,
       VOLUME = 246,
       NUMBER = 1,
        PAGES = {86--102},
        MONTH = jun,
     ABSTRACT = {
The investigation and modeling of gene regulatory networks requires
computational tools specific to the task. We present several locally
developed software tools that have been used in support of our ongoing
research into the embryogenesis of the sea urchin. These tools are
especially well suited to iterative refinement of models through
experimental and computational investigation. They include: BioArray, a
macroarray spot processing program; SUGAR, a system to display and
correlate large-BAC sequence analyses; SeqComp and FamilyRelations,
programs for comparative sequence analysis; and NetBuilder, an environment
for creating and analyzing models of gene networks. We also present an
overview of the process used to build our model of the Strongylocentrotus
purpuratus endomesoderm gene network. Several of the tools discussed in
this paper are still in active development and some are available as open
source.}
}

@BOOK{buschmann:1996,
       AUTHOR = {Frank Buschmann and Regine Meunier and Hans Rohnert and
                 Peter Sommerlad and Michael Stal},
    TITLE = {Pattern-Oriented Software Architecture: A System of Patterns},
    PUBLISHER = WI,
     YEAR = 1996
}