combine_archive.bib

@misc{Adams:2012,
  author= {Adams, Richard and Bergmann, Frank T and Le Nov\`{e}re, Nicolas},
  title={COMBINE archive format proposal},
  url={https://docs.google.com/document/d/10tI1NwehBVDTxE5Q11APx7bZVoeNVJdFMiBdPywZKZM/edit},
  year={2012}
}

@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{Cuellar:2003,
  author = {Cuellar, A.A. and Lloyd, C.M. and Nielsen, P.F. and Bullivant, D.P. and Nickerson,
	D.P. and Hunter, P.J.},
  title = {An overview of CellML 1.1, a biological model description language.},
  journal = {SIMULATION},
  year = {2003},
  volume = {79},
  pages = {740-747},
  number = {12},
}

@BOOK{eriksson:1998,
       AUTHOR = {H.-E. Eriksson and M. Penker},
	TITLE = {{UML} Toolkit},
    PUBLISHER = {John Wiley \& Sons},
	 YEAR = 1998,
      ADDRESS =	{New York}
}

@MISC{fallside:2000,
       AUTHOR = {D.~C. Fallside},
        TITLE = {{XML} {S}chema Part 0: Primer ({W3C} Candidate
                 Recommendation 24 {O}ctober 2000)},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.w3.org/TR/xmlschema-0/}},
         YEAR = 2000
}

@ARTICLE{Galdzicki:2014,
  author = {Michal Galdzicki and Kevin P Clancy and Ernst Oberortner and Matthew
	Pocock and Jacqueline Y Quinn and Cesar A Rodriguez and Nicholas
	Roehner and Mandy L Wilson and Laura Adam and J. Christopher Anderson
	and Bryan A Bartley and Jacob Beal and Deepak Chandran and Joanna
	Chen and Douglas Densmore and Drew Endy and Raik Grünberg and Jennifer
	Hallinan and Nathan J Hillson and Jeffrey D Johnson and Allan Kuchinsky
	and Matthew Lux and Goksel Misirli and Jean Peccoud and Hector A
	Plahar and Evren Sirin and Guy-Bart Stan and Alan Villalobos and
	Anil Wipat and John H Gennari and Chris J Myers and Herbert M Sauro},
  title = {The Synthetic Biology Open Language (SBOL) provides a community standard
	for communicating designs in synthetic biology.},
  journal = {Nat Biotechnol},
  year = {2014},
  volume = {32},
  pages = {545--550},
  number = {6},
  month = {Jun},
}

@ARTICLE{Gleeson:2010,
  author = {Padraig Gleeson and Sharon Crook and Robert C Cannon and Michael
	L Hines and Guy O Billings and Matteo Farinella and Thomas M Morse
	and Andrew P Davison and Subhasis Ray and Upinder S Bhalla and Simon
	R Barnes and Yoana D Dimitrova and R. Angus Silver},
  title = {NeuroML: a language for describing data driven models of neurons
	and networks with a high degree of biological detail.},
  journal = {PLoS Comput Biol},
  year = {2010},
  volume = {6},
  pages = {e1000815},
  number = {6},
  month = {Jun},
}

@ARTICLE{hucka:2003,
  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. Minch 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 {S}ystems {B}iology {M}arkup {L}anguage ({SBML}): a medium for representation and exchange of biochemical network models},
  journal = {Bioinformatics},
  year = {2003},
  volume = {19},
  pages = {524-31},
  number = {4},
}

@article{libsbml,
   author = {Bornstein, Benjamin J. and Keating, Sarah M. and Jouraku, Akiya and Hucka, Michael},
   title = {{LibSBML}: an {API} {L}ibrary for {SBML}},
   journal = {Bioinformatics},
   volume = {24},
   number = {6},
   pages = {880-881},
   abstract = {Summary: LibSBML is an application programming interface library for reading, writing, manipulating and validating content expressed in the Systems Biology Markup Language (SBML) format. It is written in ISO C and C++, provides language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many features that facilitate adoption and use of both SBML and the library. Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software.Availability: LibSBML 3 was released in August 2007. Source code, binaries and documentation are freely available under LGPL open-source terms from http://sbml.org/software/libsbml.Contact: sbml-team@caltech.edu},
   year = {2008}
}

@MISC{Moodie:2013,
       AUTHOR = {Stuart L. Moodie and Maciej J. Swat and Niels R. Kristensen and Nicolas Le Nov\`{e}re},
        TITLE = {PharmML: The Pharmacometrics Markup Language},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://ddmore.eu/pharmml}.},
         YEAR = {2013}
}

@BOOK{oestereich:1999,
       AUTHOR = {B. Oestereich},
    TITLE = {Developing Software with {UML}: {O}bject-{O}riented {A}nalysis and
                  Design in Practice},
    PUBLISHER = {Addison-Wesley},
     YEAR = 1999
}

@article{oberhardt_2009,
	author = {Oberhardt, Matthew A. and Palsson, Bernhard {\O}.  and Papin, Jason A.},
	title = {Applications of genome-scale metabolic reconstructions.},
	journal = {Molecular Systems Biology},
	volume = {5},
	pages = {320},
	year = {2009},
}

@misc{RDF,
  title = "{RDF} 1.1 Concepts and Abstract Syntax",
  author = "Cyganiak, Richard and Wood, David and Lanthaler, Markus and Klyne, Graham and Carroll, Jeremy J and McBride, Brian",
  year="2014",
  HOWPUBLISHED="Available via the World Wide Web at \url{http://www.w3.org/TR/rdf11-concepts/}"
}

@misc{rfc6350,
  author="S. Perreault",
  title="{vCard Format Specification}",
  series="Request for Comments",
  number="6350",
  publisher="IETF",
  organization="Internet Engineering Task Force",
  year=2011,
  month=aug,
    note="Updated by RFC 6868",
  HOWPUBLISHED="http://www.ietf.org/rfc/rfc6350.txt",
}


@misc{sedmll1v1,
   author = {Waltemath, Dagmar and Bergmann, Frank T. and Adams, Richard and Le Nov\`{e}re, Nicolas.},
   year = {2011},
	 title = {Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1},
   HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://co.mbine.org/specifications/sed-ml.level-1.version-1.pdf}}
}

@MISC{thompson:2000,
       AUTHOR = {H.~S. Thompson and D. Beech and M. Maloney and N. Mendelsohn},
        TITLE = {{XML} {S}chema Part 1: Structures ({W3C} Candidate Recommendation
                 24 {O}ctober 2000)},
 HOWPUBLISHED = {Available online via the World Wide Web at the address
                 \url{http://www.w3.org/TR/xmlschema-1/}},
         YEAR = 2000
}

@misc{tracker,
title = {The {SBML} {I}ssue {T}racker},
author = {{SBML Team}},
year = 2010,
HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://sbml.org/issue-tracker}}
}

@misc{vCardOnto,
title = {Ianella, Renato and McKinney, James},
author = {vCard Ontology - for describing People and Organizations},
year = {2014},
HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.w3.org/TR/vcard-rdf/}}
}

@article {Waltemath:2011,
	title = {Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.},
	journal = {BMC Syst Biol},
	volume = {5},
	year = {2011},
	pages = {198},
	author = {Waltemath, Dagmar and Adams, Richard and Bergmann, Frank T and Hucka, Michael and Kolpakov, Fedor and Miller, Andrew K and Moraru, Ion I and Nickerson, David and Sahle, Sven and Snoep, Jacky L and Le Nov{\`e}re, Nicolas}
}

@misc{zipFile,
author = "Wikipedia",
   title = "{Zip (file format)} --- {W}ikipedia{,} The Free Encyclopedia",
   year = "2014",
   howpublished = {\url{http://en.wikipedia.org/w/index.php?title=Zip%20(file%20format)&oldid=588974210}},
   note = "[Online; accessed 13-January-2014]"
 }


@misc{zipSpec,
author = "{PKWARE Inc.}",
   title = "{A}{P}{P}{N}{O}{T}{E}.{T}{X}{T} - .{Z}{I}{P} {F}ile {F}ormat {S}pecification",
   year = "2012",
   howpublished = {\url{http://www.pkware.com/documents/casestudies/APPNOTE.TXT}},
   note = "[Online; accessed 13-January-2014]"
 }


@misc{rfc2046,
  author= {Freed, N. and N. Borenstein},
  title="{Multipurpose Internet Mail Extensions (MIME) Part Two: Media Types}",
  series="Request for Comments",
  number="2046",
  publisher="IETF",
  organization="Internet Engineering Task Force",
  year=1996,
  month=November,
    note="Updated by RFC 6868",
  HOWPUBLISHED={\url{http://www.rfc-editor.org/rfc/rfc2046.txt} \url{http://www.ietf.org/rfc/rfc6350.txt} \url{http://www.iana.org/assignments/media-types/media-types.xhtml}},
}


@MISC{ro2013,
       AUTHOR = {Soiland-Reyes, S.},
        TITLE = {Wf4Ever Research Object Bundle},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://wf4ever.github.io/ro/bundle/}.},
         YEAR = 2013
}

@MISC{ucf,
 KEY = {UCF},
        TITLE = {Universal Container Format},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{https://wikidocs.adobe.com/wiki/display/PDFNAV/Universal+Container+Format}.},
         YEAR = 2013
}

@MISC{OCF,
 KEY = {OCF},
        TITLE = {EPUB Open Container Format (OCF) 3.0.},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://www.idpf.org/epub/30/spec/epub30-ocf.html}.},
         YEAR = 2011
}

@MISC{ODF,
 KEY = {ODF},
        TITLE = {OpenDocument technical specification},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://en.wikipedia.org/wiki/OpenDocument_technical_specification}.},
         YEAR = 2011
}

@MISC{OPC,
 KEY = {OPC},
        TITLE = {Open Packaging Convention},
 HOWPUBLISHED = {Available via the World Wide Web at
                 \url{http://en.wikipedia.org/wiki/Open_Packaging_Convention}.},
         YEAR = 2008
}