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@article{Bezgin2023, title={JAX-Fluids: A fully-differentiable high-order computational fluid dynamics solver for compressible two-phase flows}, volume={282}, ISSN={0010-4655}, url={http://dx.doi.org/10.1016/j.cpc.2022.108527}, DOI={10.1016/j.cpc.2022.108527}, journal={Computer Physics Communications}, publisher={Elsevier BV}, author={Bezgin, Deniz A. and Buhendwa, Aaron B. and Adams, Nikolaus A.}, year={2023}, month=jan, pages={108527} }

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@article{Golightly2011, title={Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo}, volume=1, ISSN={2042-8901}, url={http://dx.doi.org/10.1098/rsfs.2011.0047}, DOI={10.1098/rsfs.2011.0047}, number=6, journal={Interface Focus}, publisher={The Royal Society}, author={Golightly, Andrew and Wilkinson, Darren J.}, year=2011, month=sep, pages={807–820} }

@software{JAX,
  author = {James Bradbury and Roy Frostig and Peter Hawkins and Matthew James Johnson and Chris Leary and Dougal Maclaurin and George Necula and Adam Paszke and Jake Vander{P}las and Skye Wanderman-{M}ilne and Qiao Zhang},
  title = {{JAX}: composable transformations of {P}ython+{N}um{P}y programs},
  url = {http://github.com/google/jax},
  version = {0.3.13},
  year = {2018},
}

@phdthesis{Kidger2021,
    title={{O}n {N}eural {D}ifferential {E}quations},
    author={Patrick Kidger},
    year=2021,
    school={University of Oxford},
}

@article{Marin2011, title={Approximate Bayesian computational methods}, volume=22, ISSN={1573-1375}, url={http://dx.doi.org/10.1007/s11222-011-9288-2}, DOI={10.1007/s11222-011-9288-2}, number=6, journal={Statistics and Computing}, publisher={Springer Science and Business Media LLC}, author={Marin, Jean-Michel and Pudlo, Pierre and Robert, Christian P. and Ryder, Robin J.}, year=2011, month=oct, pages={1167–1180} }


@Article{      NumPy,
 title         = {Array programming with {NumPy}},
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                 Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del
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                 Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
                 Travis E. Oliphant},
 year          = 2020,
 month         = sep,
 journal       = {Nature},
 volume        = 585,
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 pages         = {357--362},
 doi           = {10.1038/s41586-020-2649-2},
 publisher     = {Springer Science and Business Media {LLC}},
 url           = {https://doi.org/10.1038/s41586-020-2649-2}
}

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  year={2004}
}

@article{Panch2021, title={The systems biology simulation core library}, volume={38}, ISSN={1367-4811}, url={http://dx.doi.org/10.1093/bioinformatics/btab669}, DOI={10.1093/bioinformatics/btab669}, number={3}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Panchiwala, Hemil and Shah, Shalin and Planatscher, Hannes and Zakharchuk, Mykola and König, Matthias and Dräger, Andreas}, editor={Xu, Jinbo}, year={2021}, month=sep, pages={864–865} }

@book{Python,
 author = {Van Rossum, Guido and Drake, Fred L.},
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 isbn = {1441412697},
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}

@Manual{R,
    title = {R: A Language and Environment for Statistical Computing},
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  }

@article{SBML, title={SBML Level 3: an extensible format for the exchange and reuse of biological models}, volume={16}, ISSN={1744-4292}, url={http://dx.doi.org/10.15252/msb.20199110}, DOI={10.15252/msb.20199110}, number={8}, journal={Molecular Systems Biology}, publisher={Springer Science and Business Media LLC}, author={Keating, Sarah M and Waltemath, Dagmar and König, Matthias and Zhang, Fengkai and Dräger, Andreas and Chaouiya, Claudine and Bergmann, Frank T and Finney, Andrew and Gillespie, Colin S and Helikar, Tomáš and Hoops, Stefan and Malik‐Sheriff, Rahuman S and Moodie, Stuart L and Moraru, Ion I and Myers, Chris J and Naldi, Aurélien 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 Gómez, 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 Červený, Jan and Courtot, Mélanie 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 MT and Fröhlich, Martina and Glont, Mihai and Gonçalves, 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 de 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 Knüpfer, 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 MF 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 von Kamp, Axel and Wittig, Ulrike and Wrzodek, Clemens and Wrzodek, Finja and Xenarios, Ioannis and Zhukova, Anna and Zucker, Jeremy}, year={2020}, month=aug }


@article{Schoenholz2021,
doi = {10.1088/1742-5468/ac3ae9},
url = {https://dx.doi.org/10.1088/1742-5468/ac3ae9},
year = 2021,
month = {dec},
publisher = {IOP Publishing and SISSA},
volume = 2021,
number = 12,
pages = 124016,
author = {Samuel S Schoenholz and Ekin D Cubuk},
title = {JAX-MD: A framework for differentiable physics},
journal = {Journal of Statistical Mechanics: Theory and Experiment},
}

@ARTICLE{SciPy,
  author  = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and
            Haberland, Matt and Reddy, Tyler and Cournapeau, David and
            Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and
            Bright, Jonathan and {van der Walt}, St{\'e}fan J. and
            Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and
            Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and
            Kern, Robert and Larson, Eric and Carey, C J and
            Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and
            {VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef and
            Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and
            Harris, Charles R. and Archibald, Anne M. and
            Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and
            {van Mulbregt}, Paul and {SciPy 1.0 Contributors}},
  title   = {{{SciPy} 1.0: Fundamental Algorithms for Scientific
            Computing in Python}},
  journal = {Nature Methods},
  year    = 2020,
  volume  = 17,
  pages   = {261--272},
  adsurl  = {https://rdcu.be/b08Wh},
  doi     = {10.1038/s41592-019-0686-2},
}

@article{Toni2008, title={Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems}, volume={6}, ISSN={1742-5662}, url={http://dx.doi.org/10.1098/rsif.2008.0172}, DOI={10.1098/rsif.2008.0172}, number={31}, journal={Journal of The Royal Society Interface}, publisher={The Royal Society}, author={Toni, Tina and Welch, David and Strelkowa, Natalja and Ipsen, Andreas and Stumpf, Michael P.H}, year={2008}, month=jul, pages={187–202} }

@article{Welsh2022, title={libRoadRunner 2.0: a high performance SBML simulation and analysis library}, volume={39}, ISSN={1367-4811}, url={http://dx.doi.org/10.1093/bioinformatics/btac770}, DOI={10.1093/bioinformatics/btac770}, number={1}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Welsh, Ciaran and Xu, Jin and Smith, Lucian and König, Matthias and Choi, Kiri and Sauro, Herbert M}, editor={Martelli, Pier Luigi}, year={2022}, month=dec }

@article{Wilkinson2009, title={Stochastic modelling for quantitative description of heterogeneous biological systems}, volume=10, ISSN={1471-0064}, url={http://dx.doi.org/10.1038/nrg2509}, DOI={10.1038/nrg2509}, number=2, journal={Nature Reviews Genetics}, publisher={Springer Science and Business Media LLC}, author={Wilkinson, Darren J.}, year=2009, month=feb, pages={122–133} }

@Book{Wilkinson2018,
  author = 	 {Darren J. Wilkinson},
  title = 	 {Stochastic Modelling for Systems Biology, third edition},
  publisher = 	 {Chapman\& Hall/CRC Press},
  year = 	 2018}

@misc{Wilkinson2019,
  author = {Darren J. Wilkinson},
  title = {scala-smfsb},
  year = {2019},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/darrenjw/scala-smfsb}
}

@misc{Wilkinson2023,
  author = {Darren J. Wilkinson},
  title = {python-smfsb},
  year = {2023},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/darrenjw/python-smfsb}
}

@Manual{Wilkinson2024,
    title = {smfsb: Stochastic Modelling for Systems Biology},
    author = {Darren J. Wilkinson},
    year = 2024,
    note = {R package version 1.5},
    url = {https://CRAN.R-project.org/package=smfsb},
  }

