report.bib

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    CTLuse_forced_etal = "yes",
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@article{smith2013sbml,
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  author={Smith, Lucian P and Hucka, Michael and Hoops, Stefan and Finney, Andrew and Ginkel, Martin and Myers, Chris J and Moraru, Ion I and Liebermeister, Wolfram},
  year={2013}
}


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@misc{SBMLArrays,
        title = {{SBML Level~3 Package Specification: Arrays (Draft of April 6, 2015)}},
        author = {Leandro Watanabe and Chris J. Myers and Lucian P. Smith},
        year = {2015},
        url = {http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/arrays},
        note = {Accessed: 2015-05-25}
}

@misc{SBMLMulti,
        title = {{SBML Level~3 Package Specification: Multistate/Multicomponent Species (Version 1, Release 0.1 Draft 369)}},
        author = {Fengkai Zhang and Martin Meier-Schellersheim},
        year = {2015},
        url = {http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/multi},
        note = {Accessed: 2015-05-25}
}

@webpage{COMBINE2012,
	Author = {{COMBINE}},
	Date-Added = {2015-06-15 03:34:58 +0000},
	Date-Modified = {2015-06-15 03:38:07 +0000},
	Title = {{COMBINE 2012}},
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	Title = {{GPML} Pathway Format},
	Year = {2014}}

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@article{olivier2013sbml,
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}


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@misc{mamo_2014,
	Author = {Anna Zhukova and Dagmar Waltemath and Maciej J. Swat and Jon Olav Vik and Nicolas Rodriguez and Nicolas {Le Nov\`{e}re}},
	Howpublished = {\url{https://sourceforge.net/p/mamo-ontology/wiki/Home/}},
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@article{Juty2012,
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@article{hucka_2004,
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@misc{hucka_2010,
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	Howpublished = {Available via the World Wide Web at \url{http://sbml.org/Documents/Specifications}},
	Institution = {California Institute of Technology},
	Publisher = {Nature Precedings},
	Title = {The {S}ystems {B}iology {M}arkup {L}anguage ({{SBML}}): Language Specification for {L}evel 3 {V}ersion 1 {Core}},
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	Howpublished = {\url{http://grants.nih.gov/grants/guide/notice-files/NOT-CA-14-054.html}},
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@webpage{ERASysBio2015,
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@webpage{CaSYM2015,
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@article{Karr2015,
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@article{Sneddon2011,
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@article{Somogyi17062015,
	Abstract = {Motivation: This article presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML). SBML is the most widely used standard for representing dynamic networks, especially biochemical networks. libRoadRunner is fast enough to support large-scale problems such as tissue models, studies that require large numbers of repeated runs and interactive simulations.Results: libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python interface. Its Python Application Programming Interface (API) is similar to the APIs of MATLAB (www.mathworks.com) and SciPy (http://www.scipy.org/), making it fast and easy to learn. libRoadRunner uses a custom Just-In-Time (JIT) compiler built on the widely used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) including several SBML extensions (composition and distributions). It offers multiple deterministic and stochastic integrators, as well as tools for steady-state analysis, stability analysis and structural analysis of the stoichiometric matrix.Availability and implementation: libRoadRunner binary distributions are available for Mac OS X, Linux and Windows. The library is licensed under Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi. http://www.libroadrunner.org provides online documentation, full build instructions, binaries and a git source repository.Contacts: hsauro@u.washington.edu or somogyie@indiana.eduSupplementary information: Supplementary data are available at Bioinformatics online.},
	Author = {Somogyi, Endre T. and Bouteiller, Jean-Marie and Glazier, James A. and K{\"o}nig, Matthias and Medley, J. Kyle and Swat, Maciej H. and Sauro, Herbert M.},
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	Eprint = {http://bioinformatics.oxfordjournals.org/content/early/2015/07/13/bioinformatics.btv363.full.pdf+html},
	Journal = {Bioinformatics},
	Title = {{libRoadRunner}: a high performance {SBML} simulation and analysis library},
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	Year = {2015},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/early/2015/07/13/bioinformatics.btv363.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btv363}}

@article{ebrahim2013cobrapy,
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	Title = {{COBRApy}: constraints-based reconstruction and analysis for python},
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@misc{sbwfba,
	Author = {Bergmann, Frank T.},
	Howpublished = {Available via the World Wide Web at \url{https://github.com/fbergmann/FluxBalance}},
	Title = {{SBW} Flux Balance},
	Year = 2012}

@misc{sedml_web_tools,
	Author = {Bergmann, Frank T.},
	Howpublished = {Available via the World Wide Web at \url{http://sysbioapps.dyndns.org/SED-ML_Web_Tools}},
	Title = {{SED-ML} Web Tools},
	Year = 2015}

@article{bornstein_2008,
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@article{Hastings2013,
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@article{Karr2015b,
	Author = {Karr, J R and Williams, A H and Zucker, J D and Raue, A and Steiert, B and Timmer, J and Kreutz, C and {DREAM8 Parameter Estimation Challenge Consortium} and Wilkinson, S and Allgood, B A and Bot, B M and Hoff, B R and Kellen, M R and Covert, M W and Stolovitzky, G A and Meyer, P},
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@article{Karr2014,
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	Title = {{WholeCellSimDB}: a hybrid relational/HDF database for whole-cell model predictions},
	Volume = 2014,
	Year = {2014}}

@article{Sanghvi2013,
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@article{Lee2013,
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@article{Purcell2013,
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