sbol.bib

\LDtodo{I added further references from the Overview to this section - KC}

@article{roehner2014proposed,
  title={Proposed data model for the next version of the Synthetic Biology Open Language},
  author={Roehner, Nicholas and Oberortner, Ernst and Pocock, Matthew and Beal, Jacob and Clancy, Kevin and Madsen, Curtis and Misirli, Goksel and Wipat, Anil and Sauro, Herbert and Myers, Chris J},
  journal={ACS synthetic biology},
  year={2015},
  publisher={ACS Publications},
  volume=4,
  number={1},
  pages={57--71}
}

@article{galdzicki2014synthetic,
  title={The Synthetic Biology Open Language ({SBOL}) provides a community standard for communicating designs in synthetic biology},
  author={Galdzicki, Michal and Clancy, Kevin P and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline Y and Rodriguez, Cesar A and Roehner, Nicholas and Wilson, Mandy L and Adam, Laura and Anderson, J Christopher and others},
  journal={Nature biotechnology},
  volume={32},
  number={6},
  pages={545--550},
  year={2014},
  publisher={Nature Publishing Group}
}

@article{canton-natbio-2008,
    author = "Barry Canton and Anna Labno and  Drew Endy",
    title = "Refinement and standardization of synthetic biological parts and devices",
    journal = "Nature Biotechnology",
    volume = 26,
    number = 7,
    year = 2008,
    pages = "787--793",
}

@article{rdfxml,
  title={{RDF/XML} syntax specification (revised)},
  author={Beckett, Dave and McBride, Brian},
  journal={W3C recommendation},
  volume={10},
  year={2004}
}

@article{COBRA,
  title={Quantitative prediction of cellular metabolism with constraint-based models: the {COBRA} Toolbox v2.0},
  author={Schellenberger, Jan and Que, Richard and Fleming, Ronan MT and Thiele, Ines and Orth, Jeffrey D and Feist, Adam M and Zielinski, Daniel C and Bordbar, Aarash and Lewis, Nathan E and Rahmanian, Sorena and others},
  journal={Nature protocols},
  volume={6},
  number={9},
  pages={1290--1307},
  year={2011},
  publisher={Nature Publishing Group}
}

@article{CellML,
	Author = {A Garny and DP Nickerson and J Cooper and R Weber dos Santos and AK Miller and S McKeever and PM Nielsen and PJ Hunter},
	Journal = {Philos. Transact. A: Math Phys Eng Sci},
	Month = {September},
	Number = {1878},
	Pages = {3017--43},
	Title = {CellML and associated tools and techniques},
	Volume = {366},
	Year = {2008}}

@incollection{SBML,
	Author = {Finney, Andrew and Hucka, Michael and Bornstein, Benjamin J. and Keating, Sarah M. and Shapiro, Bruce M. and Matthews, Joanne and Kovitz, Benjamin K. and Schilstra, Maria J. and Funahashi, Akira and Doyle, John and Kitano, Hiroaki},
	Booktitle = {System Modeling in Cell Biology: From Concepts to Nuts and Bolts},
	Editor = {Zoltan Szallasi and J{\"o}rg Stelling and Vipul Periwal},
	Publisher = {MIT Press},
	Title = {Software Infrastructure for Effective Communication and Reuse of Computational Models},
	Year = {2006}}

@misc{matlab,
year = {2015},
author = {MathWorks},
title = {MATLAB},
publisher = {The MathWorks Inc.},
address = {Natick, Massachusetts}
}

@Article{Gardner2000,
  author =       "Timothy S. Gardner and Charles R. Cantor and James J. Collins",
  title =        "Construction of a genetic toggle switch in Escherichia coli",
  journal =      "Nature",
  volume =       "403",
  pages =        "339-342",
  year =         "2000"
}

@techreport{dcmi2012,
  author = {{DCMI Usage Board}},
  institution = {Dublin Core Metadata Initiative},
  keywords = {dc rdf semweb},
  month = {June},
  title = {{DCMI} Metadata Terms},
  type = {{DCMI} Recommendation},
  url = {http://dublincore.org/documents/2012/06/14/dcmi-terms/},
  year = 2012
}

@article{ L08752.1,
author = {Norrander,J and Kempe,T and Messing,J},
title = {Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis},
journal =      {Gene},
  volume =       26,
  pages =        {101-106},
  year =         {1983},
  url = {http://www.ncbi.nlm.nih.gov/nuccore/L08752.1}
}

@article{ genbank,
author = {Dennis A. Benson and Mark Cavanaugh and Karen Clark and Ilene Karsch-Mizrachi and David J. Lipman and James Ostell and Eric W. Sayers},
title = {GenBank},
journal =      {Nucleic Acids Research},
  volume =       41,
  pages =        {D36-D42},
  year =         {2013},
  url = {http://nar.oxfordjournals.org/content/41/D1/D36.short}
}

@article{ chebi,
author = {Kirill Degtyarenko and Paula de Matos and Marcus Ennis and Janna Hastings and Martin Zbinden and Alan McNaught and Rafael Alcántara and Michael Darsow and Mickaël Guedj and Michael Ashburner},
title = {ChEBI: a database and ontology for chemical entities of biological interest},
journal =      {Nucleic Acids Research},
  volume =       36,
  pages =        {D344-D350},
  year =         {2008},
  url = {http://nar.oxfordjournals.org/content/36/suppl_1/D344.short}
}

@article{ so,
author = {Karen Eilbeck and Suzanna E Lewis and Christopher J Mungall and Mark Yandell and Lincoln Stein and Richard Durbin and Michael Ashburner},
title = {The Sequence Ontology: a tool for the unification of genome annotations},
journal =      {Genome Biology},
  volume =       6,
  pages =        {R44},
  year =         {2005},
  url = {http://genomebiology.com/content/6/5/R44}
}

@article{ swissprot,
author = {Brigitte Boeckmann and Marie-Claude Blatter and Livia Famiglietti and Ursula Hinz and  Lydie Lane and Bernd Roechert and Amos Bairoch},
title = {Protein variety and functional diversity: Swiss-Prot annotation in its biological context},
journal =      {Comptes Rendus Biologies},
  volume =       328,
  pages =        {882-899},
  year =         {2005},
  url = {http://www.sciencedirect.com/science/article/pii/S1631069105001101}
}

@misc{wolf1997,
year = {1997},
author = {Wolf, Misha and Wicksteed, Charles},
title = {Date and Time Formats},
url = {https://www.w3.org/TR/NOTE-datetime}
}

@misc{Biron2004,
year = {2004},
author = {Biron, Paul V. and Permanente, Kaiser and Malhotra, Ashok},
title = {XML Schema Part 2: Datatypes Second Edition},
url = {https://www.w3.org/TR/xmlschema-2}
}