bibliography.bib

@inproceedings{pyarelal2019,
	Author = {Adarsh Pyarelal and Marco A.~Valenzuela-Esc\'{a}rcega and Rebecca Sharp and Paul D.~Hein and Jon Stephens and Pratik Bhandari and HeuiChan Lim and Saumya Debray and Clayton T.~Morrison},
	Booktitle = {Modeling the World's Systems},
	Date-Added = {2019-05-28 17:43:37 -0700},
	Date-Modified = {2019-05-28 17:51:51 -0700},
	Title = {{AutoMATES}: Automated Model Assembly from Text, Equations, and Software},
	Year = {2019}
}

@inproceedings{EidosIndraDelphi,
	Author = {Rebecca Sharp and Adarsh Pyarelal and Benjamin M.~Gyori and Keith Alcock and Egoitz Laparra and Marco A.~Valenzuela-Esc\'{a}rcega and Ajay Nagesh and Vikas Yadav and John A.~Bachman and Zheng Tang and Heather Lent and Fan Luo and Mithun Paul and Steven Bethard and Kobus Barnard and Clayton T.~Morrison and Mihai Surdeanu},
	Booktitle = {Proceedings of the Conference of the North American Chapter of the Association for Computational Linguistics - Human Language Technologies (NAACL HLT): Software Demonstrations},
	Date-Modified = {2019-05-28 17:51:45 -0700},
	Publisher = {Association for Computational Linguistics},
	Title = {Eidos, {INDRA}, \& {D}elphi: From Free Text to Executable Causal Models},
	Url = {http://clulab.cs.arizona.edu/papers/NAACL2019_2.pdf},
	Year = {2019},
	Bdsk-Url-1 = {http://clulab.cs.arizona.edu/papers/NAACL2019_2.pdf}
}

@article{gyori2017word,
  title={From word models to executable models of signaling networks using automated assembly},
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}

@article{cerami2010pathway,
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  author={Cerami, Ethan G and Gross, Benjamin E and Demir, Emek and Rodchenkov, Igor and Babur, {\"O}zg{\"u}n and Anwar, Nadia and Schultz, Nikolaus and Bader, Gary D and Sander, Chris},
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@inproceedings{nigam2015datums,
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  author={Nigam, Vivek and Donaldson, Robin and Knapp, Merrill and McCarthy, Tim and Talcott, Carolyn},
  booktitle={International Conference on Computational Methods in Systems Biology},
  pages={90--103},
  year={2015},
  organization={Springer}
}

@inproceedings{gil2018mint,
  title={MINT: model integration through knowledge-powered data and process composition},
  author={Gil, Yolanda and Cobourn, Kelly and Deelman, Ewa and Duffy, Chris and da Silva, Rafael Ferreira and Kemanian, Armen and Knoblock, Craig and Kumar, Vipin and Peckham, Scott and Carvalho, Lucas and others},
  booktitle={9th International Congress on Environmental Modelling and Software},
  year={2018}
}

@inproceedings{semanticModels2019,
	Author = {Herlihy, Christine and Cao, Kun and Reparti, Sreenath and Briscoe, Erica and Fairbanks, James},
	Booktitle = {Modeling the World's Systems},
	Title = {Semantic Program Analysis for Scientific Model Augmentation},
	Year = {2019}
}

@article{johnston2004dataflowadvances,
  title={Advances in dataflow programming languages},
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@article{camargo2016six,
	Author = {Camargo, GGT and Kemanian, AR},
	Journal = {Agricultural and forest meteorology},
	Pages = {116--129},
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	Volume = {220},
	Year = {2016}
}

@article{adams2009dakota,
	Author = {Adams, Brian M and Bohnhoff, WJ and Dalbey, KR and Eddy, JP and Eldred, MS and Gay, DM and Haskell, K and Hough, Patricia D and Swiler, Laura P},
	Journal = {Sandia National Laboratories, Tech. Rep. SAND2010-2183},
	Title = {DAKOTA, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis: version 5.0 user's manual},
	Year = {2009}
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@article{fei2010dataflow,
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@article{DSSAT,
	Author = {J.W Jones and G Hoogenboom and C.H Porter and K.J Boote and W.D Batchelor and L.A Hunt and P.W Wilkens and U Singh and A.J Gijsman and J.T Ritchie},
	Doi = {https://doi.org/10.1016/S1161-0301(02)00107-7},
	Issn = {1161-0301},
	Journal = {European Journal of Agronomy},
	Keywords = {Crop simulation, Weather, Research tool, Decision aid},
	Note = {Modelling Cropping Systems: Science, Software and Applications},
	Number = {3},
	Pages = {235 - 265},
	Title = {The DSSAT cropping system model},
	Url = {http://www.sciencedirect.com/science/article/pii/S1161030102001077},
	Volume = {18},
	Year = {2003},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1161030102001077},
	Bdsk-Url-2 = {https://doi.org/10.1016/S1161-0301(02)00107-7}
}

@inproceedings{valenzuela2015Odin,
  title={Odin's Runes: A Rule Language for Information Extraction},
  author={Marco Antonio Valenzuela-Escarcega and Gus Hahn-Powell and Mihai Surdeanu},
  booktitle={LREC},
  year={2016}
}

@article{peckham2017reproducible,
  title={Reproducible, component-based modeling with TopoFlow, a spatial hydrologic modeling toolkit},
  author={Peckham, Scott D and Stoica, Maria and Jafarov, Elchin and Endalamaw, Abraham and Bolton, W Robert},
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  number={6},
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  year={2017},
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}

@inproceedings{allen1970CFG,
	Author = {Allen, Frances E},
	Booktitle = {ACM Sigplan Notices},
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@book{chartrand1977introGraphTheory,
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@book{pearl2009causality,
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@book{pearl2014probabilistic,
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@book{bishop2006pattern,
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@misc{sedgewick2002algorithmsInC,
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@InCollection{frigg2006models,
	author       =	{Frigg, Roman and Hartmann, Stephan},
	title        =	{Models in Science},
	booktitle    =	{The Stanford Encyclopedia of Philosophy},
	editor       =	{Edward N. Zalta},
	howpublished =	{\url{https://plato.stanford.edu/archives/sum2018/entries/models-science/}},
	year         =	{2018},
	edition      =	{Summer 2018},
	publisher    =	{Metaphysics Research Lab, Stanford University}
}

@book{giere2010explaining,
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@article{morrison2009models,
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@article{Patterson2017DataflowRO,
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@article{Patterson2018TeachingMT,
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  year={2018},
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}

@inproceedings{Unbehauen2012KnowledgeEF,
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@article{Wimalasuriya2010OntologybasedIE,
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@article{Fayyad1996FromDM,
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@inproceedings{Fayyad1997KnowledgeDI,
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}