refs.bib

@article{Norsigian2019,
    author   = {Norsigian, Charles J. and Pusarla, Neha and McConn, John Luke and Yurkovich,
               James T. and Dr\"ager, Andreas and Palsson, Bernhard O. and King, Zachary},
    title    = {{BiGG Models 2020: multi-strain genome-scale models and expansion across the
               phylogenetic tree}},
    journal  = {Nucleic Acids Research},
    volume   = {48},
    number   = {D1},
    year     = {2019},
    month    = {11},
    abstract = {The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized
               repository for high-quality genome-scale metabolic models. For the past 12 years,
               the website has allowed users to browse and search metabolic models. Within this
               update, we detail new content and features in the repository, continuing the
               original effort to connect each model to genome annotations and external
               databases as well as standardization of reactions and metabolites. We describe
               the addition of 31 new models that expand the portion of the phylogenetic tree
               covered by BiGG Models. We also describe new functionality for hosting
               multi-strain models, which have proven to be insightful in a variety of studies
               centered on comparisons of related strains. Finally, the models in the knowledge
               base have been benchmarked using Memote, a new community-developed validator for
               genome-scale models to demonstrate the improving quality and transparency of
               model content in BiGG Models.},
    issn     = {0305-1048},
    doi      = {10.1093/nar/gkz1054},
    url      = {https://doi.org/10.1093/nar/gkz1054},
    note     = {gkz1054},
    eprint   = {https://academic.oup.com/nar/article-pdf/48/D1/D402/31697906/gkz1054.pdf},
}

@article{Neal2018,
  author    = {Neal, Maxwell Lewis and K\"onig, Matthias and Nickerson, David and M{\i}s{\i}rl{\i},
    G\"oksel and Kalbasi, Reza and Dr\"ager, Andreas and Atalag, Koray and Chelliah, Vijayalakshmi
    and Cooling, Michael T. and Cook, Daniel L. and Crook, Sharon and {de Alba}, Miguel and Friedman,
    Samuel H. and Garny, Alan and Gennari, John H. and Gleeson, Padraig and Golebiewski, Martin and
    Hucka, Michael and Juty, Nick and Myers, Chris and Olivier, Brett G. and Sauro, Herbert M. and
    Scharm, Martin and Snoep, Jacky L and Tour\'e, Vasundra and Wipat, Anil and Wolkenhauer, Olaf
    and Waltemath, Dagmar},
  title     = {Harmonizing semantic annotations for computational models in biology},
  abstract  = {Life science researchers use computational models to articulate and test hypotheses
    about the behavior of biological systems. Semantic annotation is a critical component for
    enhancing the interoperability and reusability of such models as well as for the integration of
    the data needed for model parameterization and validation. Encoded as machine-readable links to
    knowledge resource terms, semantic annotations describe the computational or biological meaning
    of what models and data represent. These annotations help researchers find and repurpose models,
    accelerate model composition and enable knowledge integration across model repositories and
    experimental data stores. However, realizing the potential benefits of semantic annotation
    requires the development of model annotation standards that adhere to a community-based
    annotation protocol. Without such standards, tool developers must account for a variety of
    annotation formats and approaches, a situation that can become prohibitively cumbersome and
    which can defeat the purpose of linking model elements to controlled knowledge resource terms.
    Currently, no consensus protocol for semantic annotation exists among the larger biological
    modeling community. Here, we report on the landscape of current annotation practices among the
    COmputational Modeling in BIology NEtwork community and provide a set of recommendations for
    building a consensus approach to semantic annotation.},
  keywords  = {semantic annotation, computational modeling, knowledge representation, modeling
    standards, data integration},
  journal   = {Briefings in Bioinformatics},
  volume    = {20},
  number    = {2},
  pages     = {540--550},
  year      = {2018},
  month     = nov,
  issn      = {1477-4054},
  doi       = {10.1093/bib/bby087},
  url       = {https://doi.org/10.1093/bib/bby087},
  eprint    = {https://academic.oup.com/bib/article-pdf/20/2/540/28834058/bby087.pdf},
}

@article{malik2020biomodels,
  title={BioModels--15 years of sharing computational models in life science},
  author={Malik-Sheriff, Rahuman S and Glont, Mihai and Nguyen, Tung VN and Tiwari, Krishna and Roberts, Matthew G and Xavier, Ashley and Vu, Manh T and Men, Jinghao and Maire, Matthieu and Kananathan, Sarubini and others},
  journal={Nucleic acids research},
  volume={48},
  number={D1},
  pages={D407--D415},
  year={2020},
  publisher={Oxford University Press}
}

@manual{rfc2119,
  title={Key words for use in RFCs to Indicate Requirement Levels},
  author={Bradner, S.},
  series={RFC},
  number={2119},
  year={1997},
  month={3},
  doi={10.17487/RFC2119},
  url={https://www.rfc-editor.org/info/rfc2119}
}

@manual{rfc8259,
  title={The JavaScript Object Notation (JSON) Data Interchange Format},
  author={Bray, Tim},
  series={RFC},
  number={8259},
  year={2017},
  month={12},
  doi={10.17487/RFC8259},
  url={https://www.rfc-editor.org/info/rfc8259}
}

@manual{rfc3629,
  title={UTF-8, a transformation format of ISO 10646},
  author={Yergeau, Francois},
  series={RFC},
  number={3629},
  year={2003},
  month={11},
  doi={10.17487/RFC3629},
  url={https://www.rfc-editor.org/info/rfc3629}
}

@manual{iso8601,
  title={Date and time: Representations for information interchange -- Part 1: Basic rules},
  series={ISO},
  number={8601-1},
  year={2019},
  url={https://www.iso.org/iso-8601-date-and-time-format.html}
}

@article{orth2010reconstruction,
  title={Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide},
  author={Orth, Jeffrey D and Fleming, Ronan MT and Palsson, Bernhard {\O}},
  journal={EcoSal plus},
  volume={4},
  number={1},
  year={2010},
  publisher={Am Soc Microbiol}
}

@misc{ianatsv,
  title={Definition of tab-separated-values},
  author={Internet Gopher Team},
  publisher={IANA},
  url={https://www.iana.org/assignments/media-types/text/tab-separated-values}
}

@misc{rfc1321,
  title={The MD5 message-digest algorithm},
  author={Rivest, Ronald},
  series={RFC},
  number={1321},
  year={1992},
  month={4},
  doi={10.17487/RFC1321},
  url={https://www.rfc-editor.org/info/rfc1321}
}

@book{national2008secure,
  title={Secure Hash Standard (SHS)},
  author={National Institute of Standards and Technology (US)},
  year={2008},
  publisher={US Department of Commerce, National Institute of Standards and Technology}
}

@article{lieven2020memote,
  title={MEMOTE for standardized genome-scale metabolic model testing},
  author={Lieven, Christian and Beber, Moritz E and Olivier, Brett G and Bergmann, Frank T and Ataman, Meric and Babaei, Parizad and Bartell, Jennifer A and Blank, Lars M and Chauhan, Siddharth and Correia, Kevin and others},
  journal={Nature biotechnology},
  volume={38},
  number={3},
  pages={272--276},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{olivier2018sbmlfbc,
  title={SBML level 3 package: flux balance constraints version 2},
  author={Olivier, Brett G and Bergmann, Frank T},
  journal={Journal of integrative bioinformatics},
  volume={15},
  number={1},
  year={2018},
  publisher={De Gruyter}
}

@article{hucka2003systems,
  title={The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models},
  author={Hucka, Michael and Finney, Andrew and Sauro, Herbert M and Bolouri, Hamid and Doyle, John C and Kitano, Hiroaki and Arkin, Adam P and Bornstein, Benjamin J and Bray, Dennis and Cornish-Bowden, Athel and others},
  journal={Bioinformatics},
  volume={19},
  number={4},
  pages={524--531},
  year={2003},
  publisher={Oxford University Press}
}

@article{Hucka2019,
  author   = {Hucka, Michael and Bergmann, Frank T. and Chaouiya, Claudine and  Dr\"ager, Andreas
    and Hoops, Stefan and Keating, Sarah M. and K\"onig, Matthias and {Le Nov\`{e}re}, Nicolas and
    Myers, Chris J. and Olivier, Brett G. and Sahle, Sven and Schaff, James C. and Sheriff, Rahuman
    and Smith, Lucian P. and Waltemath, Dagmar and Wilkinson, Darren J. and Zhang, Fengkai},
  title    = {{Systems Biology Markup Language (SBML): Language Specification for Level~3 Version~2
    Core Release~2}},
  journal  = {Journal of Integrative Bioinformatics},
  volume   = {16},
  number   = {2},
  pages    = {1},
  month    = may,
  year     = {2019},
  issn     = {1613-4516},
  abstract = {Computational models can help researchers to interpret data, understand biological
    functions, and make quantitative predictions. The \textbf{S}ystems \textbf{B}iology
    \textbf{M}arkup \textbf{L}anguage (SBML) is a file format for representing computational models
    in a declarative form that different software systems can exchange. 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. By supporting SBML as an
    input/output format, different tools can all operate on an identical representation of a model,
    removing opportunities for translation errors and assuring a common starting point for analyses
    and simulations. This document provides the specification for Release 2 of Version 2 of SBML
    Level 3 Core. The specification defines the data structures prescribed by SBML as well as their
    encoding in XML, the eXtensible Markup Language. Release 2 corrects some errors and clarifies
    some ambiguities discovered in Release 1. This specification also defines validation rules that
    determine the validity of an SBML document, and provides many examples of models in SBML form.
    Other materials and software are available from the SBML project website at
    \url{http://sbml.org/}.},
  nlm-id   = {101503361},
  pii      = {/j/jib.2019.16.issue-2/jib-2019-0021/jib-2019-0021.xml},
  pmc      = {PMC6798823},
  pmid     = {31219795},
  doi      = {10.1515/jib-2019-0021},
  url      = {https://www.degruyter.com/view/journals/jib/16/2/article-20190021.xml},
  pdf      = {https://www.degruyter.com/view/journals/jib/16/2/article-20190021.pdf},
  keywords = {Computer Simulation; Models, Biological; Programming Languages; Systems Biology;
    Representation; Standards; Systems Biology Markup Language; Visualization},
}

@article{Hucka2018b,
  author = {Hucka, Michael and Bergmann, Frank T. and Dr\"ager, Andreas and
        Hoops, Stefan and Keating, Sarah M. and {Le Nov\`{e}re}, Nicolas and Myers,
        Chris J. and Olivier, Brett G. and Sahle, Sven and Schaff, James C. and
        Smith, Lucian P. and Waltemath, Dagmar and Wilkinson, Darren J.},
  title = {{Systems Biology Markup Language (SBML) Level~3 Version~1 Core}},
  journal = {Journal of Integrative Bioinformatics},
  volume = {15},
  number = {1},
  pages = {1},
  month = apr,
  year = {2018},
  doi = {10.1515/jib-2017-0080},
  abstract = {Computational models can help researchers to interpret data,
        understand biological functions, and make quantitative predictions. The
        Systems Biology Markup Language (SBML) is a file format for representing
        computational models in a declarative form that different software
        systems can exchange. 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. By supporting
        SBML as an input/output format, different tools can all operate on an
        identical representation of a model, removing opportunities for translation
        errors and assuring a common starting point for analyses and simulations.
        This document provides the specification for Release 2 of Version 1 of
        SBML Level 3 Core. The specification defines the data structures prescribed
        by SBML, their encoding in XML (the eXtensible Markup Language), validation
        rules that determine the validity of an SBML document, and examples of
        models in SBML form. No design changes have been made to the description of
        models between Release 1 and Release 2; changes are restricted to the
        format of annotations, the correction of errata and the addition of
        clarifications. Other materials and software are available from the SBML
        project website at \url{http://sbml.org}},
  URL = {https://www.degruyter.com/view/j/jib.2018.15.issue-1/jib-2017-0080/jib-2017-0080.xml},
  pdf = {https://www.degruyter.com/downloadpdf/j/jib.2018.15.issue-1/jib-2017-0080/jib-2017-0080.pdf},
}


@article{keating2020sbml,
  author     = {Keating, Sarah M. and Waltemath, Dagmar and K\"onig, Matthias and Zhang, Fengkai and
    Dr\"ager, Andreas and Chaouiya, Claudine and Bergmann, Frank T. and Finney, Andrew and
    Gillespie, Colin S. and Helikar, Tom\'{a}\v{s} and Hoops, Stefan and Malik-Sheriff, Rahuman S.
    and Moodie, Stuart L. and Moraru, Ion I. and Myers, Chris J. and Naldi, Aur\'elien and Olivier,
    Brett G. and Sahle, Sven and Schaff, James C. and Smith, Lucian P. and Swat, Maciej J. and
    Thieffry, Denis and Watanabe, Leandro and Wilkinson, Darren J. and Blinov, Michael L. and
    Begley, Kimberly and Faeder, James R. and G\'omez, Harold F. and Hamm, Thomas M. and Inagaki,
    Yuichiro and Liebermeister, Wolfram and Lister, Allyson L. and Lucio, Daniel and Mjolsness, Eric
    and Proctor, Carole J. and Raman, Karthik and Rodriguez, Nicolas and Shaffer, Clifford A. and
    Shapiro, Bruce E. and Stelling, Joerg and Swainston, Neil and Tanimura, Naoki and Wagner, John
    and Meier-Schellersheim, Martin and Sauro, Herbert M. and Palsson, Bernhard and Bolouri, Hamid
    and Kitano, Hiroaki and Funahashi, Akira and Hermjakob, Henning and Doyle, John C. and Hucka,
    Michael and Adams, Richard R. and Allen, Nicholas A. and Angermann, Bastian R. and Antoniotti,
    Marco and Bader, Gary D. and \v{C}erven\'y, Jan and Courtot, M\'elanie and Cox, Chris D. and
    Dalle Pezze, Piero and Demir, Emek and Denney, William S. and Dharuri, Harish and Dorier, Julien
    and Drasdo, Dirk and Ebrahim, Ali and Eichner, Johannes and Elf, Johan and Endler, Lukas and
    Evelo, Chris T. and Flamm, Christoph and Fleming, Ronan M.~T. and Fr\"ohlich, Martina and Glont,
    Mihai and Gon\c{c}alves, Emanuel and Golebiewski, Martin and Grabski, Hovakim and Gutteridge,
    Alex and Hachmeister, Damon and Harris, Leonard A. and Heavner, Benjamin D. and Henkel, Ron and
    Hlavacek, William S. and Hu, Bin and Hyduke, Daniel R. and Jong, Hidde and Juty, Nick and Karp,
    Peter D. and Karr, Jonathan R. and Kell, Douglas B. and Keller, Roland and Kiselev, Ilya and
    Klamt, Steffen and Klipp, Edda and Kn\"upfer, Christian and Kolpakov, Fedor and Krause, Falko
    and Kutmon, Martina and Laibe, Camille and Lawless, Conor and Li, Lu and Loew, Leslie M. and
    Machne, Rainer and Matsuoka, Yukiko and Mendes, Pedro and Mi, Huaiyu and Mittag, Florian and
    Monteiro, Pedro T. and Natarajan, Kedar Nath and Nielsen, Poul M.~F. and Nguyen, Tramy and
    Palmisano, Alida and Pettit, Jean-Baptiste and Pfau, Thomas and Phair, Robert D. and
    Radivoyevitch, Tomas and Rohwer, Johann M. and Ruebenacker, Oliver A. and Saez-Rodriguez, Julio
    and Scharm, Martin and Schmidt, Henning and Schreiber, Falk and Schubert, Michael and Schulte,
    Roman and Sealfon, Stuart C. and Smallbone, Kieran and Soliman, Sylvain and Stefan, Melanie I.
    and Sullivan, Devin P. and Takahashi, Koichi and Teusink, Bas and Tolnay, David and Vazirabad,
    Ibrahim and Kamp, Axel von and Wittig, Ulrike and Wrzodek, Clemens and Wrzodek, Finja and
    Xenarios, Ioannis and Zhukova, Anna and Zucker, Jeremy},
  journal    = {Molecular Systems Biology},
  title      = {{SBML Level~3: an extensible format for the exchange and reuse of biological
               models}},
  year       = {2020},
  issn       = {1744-4292},
  month      = aug,
  volume     = {16},
  number     = {8},
  pages      = {e9110},
  publisher  = {John Wiley \& Sons, Ltd},
  address    = {New York, NY, USA},
  abstract   = {Abstract Systems biology has experienced dramatic growth in the number, size, and
    complexity of computational models. To reproduce simulation results and reuse models,
    researchers must exchange unambiguous model descriptions. We review the latest edition of the
    Systems Biology Markup Language (SBML), a format designed for this purpose. A community of
    modelers and software authors developed SBML Level 3 over the past decade. Its modular form
    consists of a core suited to representing reaction-based models and packages that extend the
    core with features suited to other model types including constraint-based models,
    reaction-diffusion models, logical network models, and rule-based models. The format leverages
    two decades of SBML and a rich software ecosystem that transformed how systems biologists build
    and interact with models. More recently, the rise of multiscale models of whole cells and
    organs, and new data sources such as single-cell measurements and live imaging, has precipitated
    new ways of integrating data with models. We provide our perspectives on the challenges
    presented by these developments and how SBML Level 3 provides the foundation needed to support
    this evolution.},
  doi        = {10.15252/msb.20199110},
  keywords   = {computational modeling, file format, interoperability, reproducibility, systems
               biology},
  pdf        = {https://www.embopress.org/doi/epdf/10.15252/msb.20199110},
  url        = {https://www.embopress.org/doi/abs/10.15252/msb.20199110},
  eprint     = {https://www.embopress.org/doi/pdf/10.15252/msb.20199110},
}

@book{palsson2015systems,
  title={Systems biology},
  author={Palsson, Bernhard},
  year={2015},
  publisher={Cambridge university press}
}

@misc{semver,
  title={Semantic Versioning 2.0.0},
  author={Tom Preston-Werner},
  url={https://semver.org/}
}

@article{bergmann2014omex,
  title={COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project},
  author={Bergmann, Frank T and Adams, Richard and Moodie, Stuart and Cooper, Jonathan and Glont, Mihai and Golebiewski, Martin and Hucka, Michael and Laibe, Camille and Miller, Andrew K and Nickerson, David P and others},
  journal={BMC bioinformatics},
  volume={15},
  number={1},
  pages={1--9},
  year={2014},
  publisher={BioMed Central}
}

@misc{stall2019make,
  title={Make scientific data FAIR},
  author={Stall, Shelley and Yarmey, Lynn and Cutcher-Gershenfeld, Joel and Hanson, Brooks and Lehnert, Kerstin and Nosek, Brian and Parsons, Mark and Robinson, Erin and Wyborn, Lesley},
  year={2019},
  publisher={Nature Publishing Group}
}

@inproceedings{pezoa2016jsonschema,
  title={Foundations of JSON schema},
  author={Pezoa, Felipe and Reutter, Juan L and Suarez, Fernando and Ugarte, Mart{\'\i}n and Vrgo{\v{c}}, Domagoj},
  booktitle={Proceedings of the 25th International Conference on World Wide Web},
  pages={263--273},
  year={2016}
}

@article{raman2005flux,
  title={Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs},
  author={Raman, Karthik and Rajagopalan, Preethi and Chandra, Nagasuma},
  journal={PLoS computational biology},
  volume={1},
  number={5},
  pages={e46},
  year={2005},
  publisher={Public Library of Science San Francisco, USA}
}