labop.bib

@misc{om2,
  title={Ontology of units of Measure ({OM}), version 2.0.31},
  author={Hajo Rijgersberg and Don Willems and Xin-Ying Ren and Mari Wigham and Jan Top},
  howpublished={\url{http://www.ontology-of-units-of-measure.org/resource/om-2}},
  month={June},
  year={2021}
}

@misc{uml251,
  title={OMG Unified Modeling Language (OMG UML) Version 2.5.1},
  author={{Object Management Group}},
  month={December},
  year={2017},
  howpublished={\url{https/www.omg.org/spec/UML/}}
}

@article{SBOL3,
author = {Hasan Baig and Pedro Fontanarrosa and Vishwesh Kulkarni and James Alastair McLaughlin and Prashant Vaidyanathan and Bryan Bartley and Jacob Beal and Matthew Crowther and Thomas E. Gorochowski and Raik Grunberg and Goksel Misirli and James Scott-Brown and Ernst Oberortner and Anil Wipat and Chris J. Myers},
doi = {doi:10.1515/jib-2020-0017},
url = {https://doi.org/10.1515/jib-2020-0017},
title = {Synthetic biology open language {(SBOL)} version 3.0.0},
journal = {Journal of Integrative Bioinformatics},
number = {2-3},
volume = {17},
year = {2020}
}

@article{Peccoud2011,
  doi = {10.1038/nbt.1753},
  url = {https://doi.org/10.1038/nbt.1753},
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  number = {1},
  pages = {22--22},
  author = {Jean Peccoud and J Christopher Anderson and Deepak Chandran and Douglas Densmore and Michal Galdzicki and Matthew W Lux and Cesar A Rodriguez and Guy-Bart Stan and Herbert M Sauro},
  title = {Essential information for synthetic {DNA} sequences},
  journal = {Nature Biotechnology}
}

@article{SBO,
  title={Controlled vocabularies and semantics in systems biology},
  author={Courtot, M{\'e}lanie and Juty, Nick and Kn{\"u}pfer, Christian and Waltemath, Dagmar and Zhukova, Anna and Dr{\"a}ger, Andreas and Dumontier, Michel and Finney, Andrew and Golebiewski, Martin and Hastings, Janna and others},
  journal={Molecular systems biology},
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}


@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},
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  number={1},
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}

@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},
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  pages={545--550},
  year={2014},
  publisher={Nature Publishing Group}
}

@article{hucka2017sbmlpkgspec,
 title={{SBMLPkgSpec}: a \latex style file for {SBML} package
specification documents},
 author={Hucka, Michael},
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 number={1},
 pages={451},
 year={2017},
 publisher={BioMed Central}
}

@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",
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    year = 2008,
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}

@article{rdfxml,
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  volume={10},
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}

@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},
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  year={2011},
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}

@article{CellML,
  doi = {10.1177/0037549703040939},
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  year = 2003,
  month = {dec},
  publisher = {{SAGE} Publications},
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  title = {An Overview of {CellML} 1.1, a Biological Model Description Language},
  journal = {{SIMULATION}}
}

@incollection{SBML,
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  url = {https://doi.org/10.1093%2Fbioinformatics%2Fbtg015},
  year = 2003,
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  title = {The systems biology markup language ({SBML}): a medium for representation and exchange of biochemical network models},
  journal = {Bioinformatics}
}

@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 \textit{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}
}

@article{biopax,
  title={The {BioPAX} community standard for pathway data sharing},
  author={Demir, Emek and Cary, Michael P and Paley, Suzanne and Fukuda, Ken and Lemer, Christian and Vastrik, Imre and Wu, Guanming and D'eustachio, Peter and Schaefer, Carl and Luciano, Joanne and others},
  journal={Nature Biotechnology},
  volume={28},
  number={9},
  pages={935},
  year={2010},
  publisher={Nature Publishing Group}
}