semsim-L1V1.bib

@article{LLH+08,
  title={{The CellML model repository}},
  author={Lloyd, C.M. and Lawson, J.R. and Hunter, P.J. and Nielsen, P.F.},
  journal={Bioinformatics},
  volume=24,
  number=18,
  pages=2122,
  year=2008,
  publisher={Oxford Univ Press}
}


@misc{xpath:1999,
       author = {Clarke, J. and DeRose, S.},
       year= 1999,
       TITLE = {{XML Path Language (XPath) Version 1.0}},
       url = {http://www.w3.org/TR/xpath/}
}

@misc{Berners-Lee:2005,
       author = {Berners-Lee, T. and Fielding, R. and Masinter, L.},
       year= 2005,
       TITLE = {{Uniform Resource Identifier ({URI}): Generic Syntax}},
       url = {http://www.ietf.org/rfc/rfc3986.txt}
}

@Misc{bpmnPoster,
  author = 	 {{Business Process Technology group}},
  title = 	 {{BPMN} -- Business Process Modeling Notation},
  organisation = {HPI},
  howpublished = {poster},
  year = 	 2009,
  url= {http://bpt.hpi.uni-potsdam.de/Public/BPMNCorner}
}
@article{P+02,
  title={{XHTML 1.0: The Extensible HyperText Markup Language—W3C Recommendation 26 January 2000}},
  author={Pemberton, S. and others},
  year = 2002,
  journal={World Wide Web Consortium (W3C)(August 2002)}
}
@Misc{bpmnSpce,
  author = 	 {OMG},
  title = 	 {BPMN 1.2 Specification},
  year = 	 2008,
  url  = {http://www.omg.org/spec/BPMN/1.2/PDF/}
}
@misc{Bray:2006,
        author = {Bray, T. and Paoli, J. and Sperberg-McQueen, C.M. and Maler, E. and Yergeau, F. and Cowan, J.},
        title  = {{Extensible Markup Language (XML) 1.1 (Second Edition)}},
        url = {http://www.w3.org/TR/xml11/},
        year = 2006
}
@Article{Elowitz:2000,
  author = 	 {Elowitz, M.B. and Leibler, S.},
  title = 	 {A synthetic oscillatory network of transcriptional regulators},
  journal = 	 {Nature},
  year = 	 2000,
  month =        Jan,
  volume = 	 403,
  number =       6767,
  pages = 	 {335-338}
}
@article{Fallside:2001,
  title={{XML schema part 0: Primer}},
  author={Fallside, D.C. and Walmsley, P. and others},
  journal={W3C recommendation},
  volume={2},
  year={2001},
  publisher={http:∥ www. w3. org/TR/xmlschema-0}
}

@Article{Goddard:2001,
  author =       {Goddard, N. and Hucka, M. and Howell, F. and Cornelis, H. and Skankar, K. and Beeman, D.},
  title =        {{Towards NeuroML: Model Description Methods for Collaborative Modeling in Neuroscience}},
  journal =      {Phil. Trans. Royal Society series B},
  year =         2001,
  volume =       356,
  pages =        {1209-1228}
}

@article{DSM10,
    author = {Dada, J.O. and Spasi\'{c}, I. and Paton, N.W. and Mendes, P.},
    citeulike-article-id = 6722016,
    citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btq069},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20176582},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20176582},
    day = 1,
    doi = {10.1093/bioinformatics/btq069},
    issn = {1367-4811},
    journal = {Bioinformatics (Oxford, England)},
    keywords = {sbrml, simulation\_results},
    month = {April},
    number = 7,
    pages = {932--938},
    posted-at = {2010-03-11 15:42:33},
    priority = 2,
    title = {{SBRML: a markup language for associating systems biology data with models.}},
    volume = 26,
    year = 2010
}

@article{Hoops:2006,
    author = {Hoops, S. and Sahle, S. and Lee, C. and Pahle, J. and Simus, N. and Singhal, M. and Xu, L. and Mendes, P. and Kummer, U.},
    doi = {10.1093/bioinformatics/btl485},
    issn = {1460-2059},
    journal = {Bioinformatics (Oxford, England)},
    keywords = {composition, copasi, pathways, sbml, simulation, standards},
    month = {December},
    number = 24,
    pages = {3067--3074},
    posted-at = {2007-04-20 11:25:43},
    priority = 4,
    publisher = {Oxford University Press},
    title = {{COPASI} - a {CO}mplex {PA}thway {SI}mulator},
    volume = 22,
    year = 2006
}
@article{Hucka:2003,
    address = {Control and Dynamical Systems, MC 107-81, California Institute of Technology, Pasadena, CA 91125, USA. sysbio-team@caltech.edu},
    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 Novere, 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.},
    doi = {10.1093/bioinformatics/btg015},
    issn = {1367-4803},
    journal = {Bioinformatics},
    month = {March},
    number = 4,
    pages = {524--531},
    title = {{The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models}},
    volume = 19,
    year = 2003
}


@article{HBH+10,
    abstract = {This is the specification for Release 1 Candidate of SBML Level 3 Version 1 Core, an electronic model representation format for systems biology.SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML. This document contains many examples of SBML models written in XML. More information about SBML and this specification is available online at http://sbml.org/Documents/Specifications/.},
    author = {Hucka, M. and Bergmann, F.T. and Hoops, S. and Keating, S. and Sahle, S. and Wilkinson, D.J.},
    citeulike-article-id = 6626627,
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/npre.2010.4123.1},
    citeulike-linkout-1 = {http://precedings.nature.com/documents/4123/version/1},
    day = 2,
    doi = {10.1038/npre.2010.4123.1},
    issn = {1756-0357},
    journal = {Nature Precedings},
    keywords = {sbml, spec},
    month = {January},
    posted-at = {2010-02-04 13:00:30},
    priority = 2,
    publisher = {Nature Publishing Group},
    title = {{The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate)}},
    year = 2010
}

@article{cuellar:2003,
  author = {Cuellar, A A and Lloyd, C M and Nielson, P F and Halstead, M D B
	and Bullivant, D P and Nickerson, D P and Hunter, P J},
  title = {An Overview of {C}ell{ML} 1.1, a biological model description language},
  journal = {Simulation},
  year = {2003},
  volume = {79},
  pages = {740--747},
  number = {12},
  owner = {andre},
  timestamp = {2010.01.29}
}

@manual{uml22,
  title = 	 {UML 2.2 Superstructure and Infrastructure},
  author = 	 {OMG},
  month = 	 {February},
  year = 	 {2009},
  url  = {http://www.omg.org/spec/UML/2.2/}
}



@article{CWK+10,
  author = 	 {Courtot, Melanie and  Juty, N. and Kn{\"u}pfer, Christian and Waltemath, D. and Dr{\"a}ger, A. andFinney, A. and Golebiewski, M. and Hoops, S. and Keating, S. and Kell, D.B. and Kerrien, S. and Lawson, J.  and Lister, A. and Lu, J. and Machne, R. and Mendes, P. and Pocock, M. and Rodriguez, N. and Villeger, A. and Wimalaratne, S. and Laibe, C. and Hucka, M. and Le Nov{\`e}re, N.},
  title = 	 {Controlled vocabularies and semantics in Systems Biology},
  year = 	 2011,
  journal = {Mol Sys Biol},
  volume = 7,
  month = oct,
  doi = {10.1038/msb.2011.77}
}

@article{WAB+11,
  title={Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language},
  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 others},
  journal={BMC systems biology},
  volume={5},
  number={1},
  pages={198},
  year={2011},
  publisher={BioMed Central Ltd}
}


@article{Waltemath:2011,
  author = 	 {Waltemath, D. and Adams, R. and Beard, D.A. and Bergmann, F.T. and Bhalla, U.S. and Britten, R. and Chelliah, V. and Cooling, M.T. and Cooper, J. and Crampin, E. and Garny, A. and Hoops, S. and Hucka, M. and Hunter, P. and Klipp, E. and Laibe, C. and Miller, A. and Moraru, I. and Nickerson, D. and Nielsen, P. and Nikolski, M. and Sahle, S. and Sauro, H. and Schmidt, H. and Snoep, J.L. and Tolle, D. and Wolkenhauer, O. and Le Novère, N.},
  title = 	 {Minimum Information About a Simulation Experiment ({MIASE})},
  journal =      {PLoS Comput Biol},
  pages =	 {e1001122},
  volume = 7,
  year = 2011,
  doi = {10.1371/journal.pcbi.1001122}
}
@article{White:2004,
  title={Business Process Modeling Notation ({BPMN}) Version 1.0},
  author={White, S.A. and others},
  journal={Business Process Management Initiative, BPMI. org},
  year="2004"
}
@misc{xmls,
  author = 	 {W3C},
  title = 	 {{XML Schema Part 1: Structures Second Edition}},
  howpublished = {W3C Recommendation},
  month = 	 {October},
  year = 	 2004,
  url = {http://www.w3.org/TR/xmlschema-1/}
}


@article{CIM+01,
  title={{Mathematical Markup Language (MathML) version 2.0}},
  author={Carlisle, D. and Ion, P. and Miner, R. and Poppelier, N.},
  journal={W3C Recommendation},
  volume=21,
  year=2001
}



	
@article{BBC+09,
	author = {Beard, D. A. and Britten, R. and Cooling, M. T. and Garny, A. and Halstead, M. D. and Hunter, P. J. and Lawson, J. and Lloyd, C. M. and Marsh, J. and Miller, A. and Nickerson, D. P. and Nielsen, P. M. and Nomura, T. and Subramanium, S. and Wimalaratne, S. M. and Yu, T.},
	citeulike-article-id = 4371567,
	doi = {10.1098/rsta.2008.0310},
	issn = {1364-503X},
	journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
	keywords = {cellml, meta\_data},
	month = {May},
	number = 1895,
	pages = {1845--1867},
	posted-at = {2009-06-30 07:10:06},
	priority = 4,
	title = {{CellML metadata standards, associated tools and repositories.}},
	volume = 367,
	year = 2009
}
@article{N+06,
	address = {European Bioinformatics Institute EMBL, Wellcome-Trust Genome Campus, Hinxton, CB10 1SD, UK. lenov@ebi.ac.uk},
	author = {Le Nov\`{e}re, N.  and Bornstein, B.  and Broicher, A.  and Courtot, M.  and Donizelli, M.  and Dharuri, H.  and Li, L.  and Sauro, H.  and Schilstra, M.  and Shapiro, B.  and Snoep, J. L.  and Hucka, M. },
	citeulike-article-id = 1081165,
	issn = {1362-4962},
	journal = {Nucleic Acids Res},
	keywords = {biomodels database ebi sbml},
	month = {January},
	number = {Database issue},
	priority = 4,
	title = {{BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.}},
	volume = 34,
	year = 2006
}

@article{LDR+10,
    author = {Li, C. and Donizelli, M. and Rodriguez, N. and Dharuri, H. and Endler, L. and Chelliah, V. and Li, L. and He, E. and Henry, A. and Stefan, M. and Snoep, J. and Hucka, M. and Le Nov{\`e}re, N. and Laibe, C.},
    citeulike-article-id = 7371796,
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/1752-0509-4-92},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20587024},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20587024},
    day = 29,
    doi = {10.1186/1752-0509-4-92},
    issn = {1752-0509},
    journal = {BMC Systems Biology},
    keywords = {biomodelsdb},
    month = {June},
    number = 1,
    pages = {92+},
    posted-at = {2010-08-02 19:55:57},
    priority = 2,
    title = {{BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models}},
    volume = 4,
    year = 2010
}


@manual{BM05,
	Author = {Gary D. Bader AND Michael P. Cary},
	Date-Added = {2006-04-22 18:42:09 +0200},
	Date-Modified = {2006-06-10 16:42:32 +0200},
	Editor = {Gary D. Bader AND Michael P. Cary},
	Mm = {[25]},
	Month = {December},
	Organization = {BioPAX workgroup},
	Title = {{BioPAX - Biological Pathways Exchange Language Level 2, Version 1.0 Documentation}},
	Year = 2005}

@article{Cue+03,
	author = {Cuellar, Autumn  A.  and Lloyd, Catherine  M.  and Nielsen, Poul  F.  and Bullivant, David  P.  and Nickerson, David  P.  and Hunter, Peter  J. },
	citeulike-article-id = 1526654,
	comment = {use for pikm},
	doi = {10.1177/0037549703040939},
	journal = {SIMULATION},
	keywords = {cellml},
	month = {December},
	number = 12,
	pages = {740--747},
	priority = 4,
	title = {An Overview of CellML 1.1, a Biological Model Description Language},
	url = {http://dx.doi.org/10.1177/0037549703040939},
	volume = 79,
	year = 2003
}

@inproceedings{KL08a,
  title={{SED-ML---An XML Format for the Implementation of the MIASE Guidelines}},
  author={K{\"o}hn, D. and Le Nov{\`e}re, N.},
  booktitle={CMSB},
  pages={176--190},
  year=2008,
  organization={Springer}
}
	



@article{BFM05,
  title={{RFC 3986: Uniform resource identifier (uri): Generic syntax}},
  author={Berners-Lee, T. and Fielding, R. and Masinter, L.},
  journal={The Internet Society},
  year=2005
}

@misc{KL08,
  title={{The KInetic Simulation Algorithm Ontology (KiSAO)-A Proposal for the Classification of Simulation Algorithms in Systems Biology}, oral presentation at the {SBGN} Workshop, Japan},
  author={K{\"o}hn, D. and Le Nov{\`e}re, N.},
  notes={SBGN Workshop, Japan},
  year=2008
}


@Misc{Bel03,
  author = 	 {Bell, D.},
  title = 	 {{UML basics, Part III}: The class diagram},
  howpublished = {IBM, the rational edge},
  year = 	 2003,
  note = 	 {\url{http://download.boulder.ibm.com/ibmdl/pub/software/dw/rationaledge/nov03/t_modelinguml_db.pdf}}}