% Encoding: UTF-8

@article{campbell2018,
   author = {Richard A. Campbell and Yussif Saaka and Yanan Shao and Yuri Gerelli and Robert Cubitt and Ewa Nazaruk and Dorota Matyszewska and M. Jayne Lawrence},
    title = {Structure of surfactant and phospholipid monolayers at the air/water interface modeled from neutron reflectivity data},
  journal = {Journal of Colloid and Interface Science},
     year = 2018,
   volume = 531,
    pages = {98-108},
      doi = {10.1016/j.jcis.2018.07.022}
}

@article{emcee,
   author = {{Foreman-Mackey}, D. and {Hogg}, D.~W. and {Lang}, D. and {Goodman}, J.},
    title = {emcee: The MCMC Hammer},
  journal = {Publications of the Astronomical Society of the Pacific},
     year = 2013,
   volume = 125,
    pages = {306-312},
   eprint = {1202.3665},
      doi = {10.1086/670067}
}

@article{pauw2013,
   author = {{Pauw}, B.~R},
   title = {Everything SAXS: small-angle scattering pattern collection and correction},
   journal = {Journal of Physics: Condensed Matter},
   year = 2013,
   volume = 25,
   pages = {383201},
   doi = {10.1088/0953-8984/26/23/239501}
}

@article{corner,
    Author = {Daniel Foreman-Mackey},
    Doi = {10.21105/joss.00024},
    Title = {corner.py: Scatterplot matrices in {P}ython},
    Journal = {The Journal of Open Source Software},
    Year = 2016,
    volume = 1,
    number = 2,
    pages = 24,
    XUrl = {http://dx.doi.org/10.5281/zenodo.45906}
}

@Article{Majkrzak1999,
  author  = {Charles Majkrzak},
  title   = {Neutron Reflectometry Studies of Thin Films and Multilayered Materials},
  journal = {Acta Physica Polonica},
  year    = {1999},
  volume  = {96},
  number  = {1},
  pages   = {81},
}

@Article{Heinrich2009,
  author  = {Frank Heinrich and Tiffany Ng and David J. Vanderah and Prabhanshu Shekhar and Mihaela Mihailescu and Hirsh Nanda and Mathias Losche},
  title   = {A New Lipid Anchor for Sparsely Tethered Bilayer Lipid Membranes},
  journal = {Langmuir},
  year    = {2009},
  volume  = {25},
  number  = {7},
  pages   = {4219-4229},
  doi     = {10.1021/la8033275},
}

@Article{Helliwell2017,
  doi = {10.1107/s2052252517013690},
  Xurl = {https://doi.org/10.1107%2Fs2052252517013690},
  year = 2017,
  month = {oct},
  publisher = {International Union of Crystallography ({IUCr})},
  volume = {4},
  number = {6},
  pages = {714--722},
  author = {John R. Helliwell and Brian McMahon and J. Mitchell Guss and Loes M. J. Kroon-Batenburg},
  title = {The science is in the data},
  journal = {{IUCrJ}}
}

@article{Chirigati2013,
  author    = {Fernando Seabra Chirigati and
               Matthias Troyer and
               Dennis E. Shasha and
               Juliana Freire},
  title     = {A Computational Reproducibility Benchmark},
  journal   = {{IEEE} Data Eng. Bull.},
  volume    = {36},
  number    = {4},
  pages     = {54--59},
  year      = {2013},
  Xurl       = {http://sites.computer.org/debull/A13dec/p54.pdf},
  timestamp = {Thu, 11 Aug 2016 11:10:44 +0200},
  biburl    = {https://dblp.org/rec/bib/journals/debu/ChirigatiTSF13},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@Misc{Kienzle2011,
  author       = {P. A. Kienzle and J. Krycka and N. Patel and I. Sahin},
  title        = {Refl1D -- depth profile modelling},
  Xhowpublished = {http://reflectometry.org/danse/},
  year         = {2011},
  url          = {http://reflectometry.org/danse/docs/refl1d/},
  version      = {0.7.9a2},
}

@Conference{Kluyver:2016aa,
  author       = {Thomas Kluyver and Benjamin Ragan-Kelley and Fernando P{\'e}rez and Brian Granger and Matthias Bussonnier and Jonathan Frederic and Kyle Kelley and Jessica Hamrick and Jason Grout and Sylvain Corlay and Paul Ivanov and Dami{\'a}n Avila and Safia Abdalla and Carol Willing},
  title        = {Jupyter Notebooks -- a publishing format for reproducible computational workflows},
  booktitle    = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},
  year         = {2016},
  editor       = {F. Loizides and B. Schmidt},
  pages        = {87 - 90},
  organization = {IOS Press},
}

@Misc{ipywidgets,
  author       = {{Project Jupyter Contributors}},
  title        = {ipywidgets},
  Xhowpublished = {https://github.com/jupyter-widgets/ipywidgets},
  year         = {2015-2016},
  url          = {https://github.com/jupyter-widgets/ipywidgets},
}

@Article{Moeller2017a,
  author    = {Möller, Steffen and Prescott, Stuart W. and Wirzenius, Lars and Reinholdtsen, Petter and Chapman, Brad and Prins, Pjotr and Soiland-Reyes, Stian and Klötzl, Fabian and Bangnacani, Andrea and Kalaš, Matús and Tille, Andreas and Crusoe, Michael R},
  title     = {{Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis}},
  journal   = {Data Science and Engineering},
  year      = {2017},
  volume    = {2},
  pages     = {232--244},
  month     = DEC,
  abstract  = {Information integration and workflow technologies for data analysis have always been major fields of investigation in bioinformatics. A range of popular workflow suites are available to support analyses in computational biology. Commercial providers tend to offer prepared applications remote to their clients. However, for most academic environments with local expertise, novel data collection techniques or novel data analysis, it is essential to have all the flexibility of open-source tools and open-source workflow descriptions. Workflows in data-driven science such as computational biology have considerably gained in complexity. New tools or new releases with additional features arrive at an enormous pace, and new reference data or concepts for quality control are emerging. A well-abstracted workflow and the exchange of the same across work groups have an enormous impact on the efficiency of research and the further development of the field. High-throughput sequencing adds to the avalanche of data available in the field; efficient computation and, in particular, parallel execution motivate the transition from traditional scripts and Makefiles to workflows. We here review the extant software development and distribution model with a focus on the role of integration testing and discuss the effect of common workflow language on distributions of open-source scientific software to swiftly and reliably provide the tools demanded for the execution of such formally described workflows. It is contended that, alleviated from technical differences for the execution on local machines, clusters or the cloud, communities also gain the technical means to test workflow-driven interaction across several software packages.},
  doi       = {10.1007/s41019-017-0050-4},
  file      = {Moeller2017a.pdf:Moeller2017a.pdf:PDF},
  owner     = {stuart},
  timestamp = {2017.11.24},
}

@Article{Stark2018,
  author  = {Philip Stark},
  title   = {Before reproducibility must come preproducibility},
  journal = {Nature},
  year    = {2018},
  volume  = {557},
  pages   = {613},
  doi     = {10.1038/d41586-018-05256-0},
}

@Article{Trewhella:jc5010,
  author   = {Trewhella, Jill and Duff, Anthony P. and Durand, Dominique and Gabel, Frank and Guss, J. Mitchell and Hendrickson, Wayne A. and Hura, Greg L. and Jacques, David A. and Kirby, Nigel M. and Kwan, Ann H. and P{\'{e}}rez, Javier and Pollack, Lois and Ryan, Timothy M. and Sali, Andrej and Schneidman-Duhovny, Dina and Schwede, Torsten and Svergun, Dmitri I. and Sugiyama, Masaaki and Tainer, John A. and Vachette, Patrice and Westbrook, John and Whitten, Andrew E.},
  title    = {{2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update}},
  journal  = {Acta Crystallographica Section D},
  year     = {2017},
  volume   = {73},
  number   = {9},
  pages    = {710--728},
  month    = {Sep},
  abstract = {In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Bio{\-}molecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.},
  doi      = {10.1107/S2059798317011597},
  keywords = {small-angle scattering, SAXS, SANS, biomolecular structure, proteins, DNA, RNA, structural modelling, hybrid structural modelling, publication guidelines, integrative structural biology},
  Xurl      = {https://doi.org/10.1107/S2059798317011597},
}

@Misc{conda,
  author       = {{Continuum Analytics}},
  title        = {Conda -- Package, dependency and environment management for any language},
  year         = {2017},
  url          = {https://conda.io/docs/},
}

@Article{Nelson2006,
  author  = {Andrew Nelson},
  title   = {Co-refinement of multiple-contrast neutron/{X}-ray reflectivity data using MOTOFIT},
  journal = {Journal of Applied Crystallography},
  year    = {2006},
  volume  = {39},
  pages   = {273-276},
  doi     = {10.1107/S0021889806005073},
}

@Book{Heavens1955,
  title     = {Optical Properties of Thin Films},
  publisher = {Butterworth: London},
  year      = {1955},
  author    = {Heavens, O},
}

@Article{Nevot1980,
  author  = {Névot, L. and Croce, P.},
  title   = {Caractérisation des surfaces par réflexion rasante de rayons {X}. Application à l'étude du polissage de quelques verres silicates},
  journal = {Rev. Phys. Appl.},
  year    = {1980},
  volume  = {15},
  number  = {761-769},
  doi     = {10.1051/rphysap:01980001503076100},
}

@Article{Nelson2014,
  author    = {Andrew Nelson and Charles Dewhurst},
  title     = {Toward a detailed resolution smearing kernel for time-of-Flight neutron reflectometers.},
  journal   = {Journal of Applied Crystallography},
  year      = {2014},
  volume    = {47},
  pages     = {1162},
  doi       = {10.1107/S1600576714009595},
  owner     = {anz},
  timestamp = {2014.05.22},
}

@Article{Gerelli2016,
  author  = {Yuri Gerelli},
  title   = {Aurore: new software for neutron reflectivity data analysis},
  journal = {Journal of Applied Crystallography},
  year    = {2016},
  volume  = {49},
  pages   = {330-339},
  doi     = {10.1107/S1600576716002466},
}

@Misc{refnx,
  author       = {Andrew Nelson and Stuart W. Prescott},
  title        = {refnx - Neutron and {X}-ray reflectometry analysis in {P}ython},
  Xhowpublished = {https://www.github.com/refnx/refnx},
  year         = {2018},
  doi          = {10.5281/zenodo.1345464},
  url          = {https://www.github.com/refnx/refnx},
}

@Misc{Jones2001-2017,
  author       = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
  title        = {{SciPy}: Open source scientific tools for {P}ython},
  Xhowpublished = {https://www.scipy.org/},
  year         = {2001-2017},
  url          = {http://www.scipy.org/},
}

@Article{Wood2017,
  author  = {Mary Wood and Stuart Clarke},
  title   = {Neutron Reflectometry for Studying Corrosion and Corrosion Inhibition},
  journal = {Metals},
  year    = {2017},
  volume  = {7},
  number  = {8},
  pages   = {304},
  doi     = {10.3390/met7080304},
}

@Book{Daillant2009,
  title     = {{X}-ray and Neutron Reflectivity: Principles and Applications},
  publisher = {Springer Verlag},
  year      = {2009},
  editor    = {Jean Daillant and Alain Gibaud},
  volume    = {770},
  series    = {Lecture Notes in Physics},
  isbn      = {978-3-540-88588-7},
}

@Article{Bjorck2007,
  author  = {Matts Bjorck and Gabriella Andersson},
  title   = {{GenX}: an extensible {X}-ray reflectivity refinement program utilizing differential evolution},
  journal = {Journal of Applied Crystallography},
  year    = {2007},
  volume  = {40},
  pages   = {1174-1178},
  doi     = {10.1107/S0021889807045086},
}

@Book{Sivia2006,
  title     = {Data Analysis: A Bayesian Tutorial},
  publisher = {Oxford Science Publications},
  year      = {2006},
  author    = {Devinderjit Sivia and John Skilling},
  isbn      = {978-0198568322},
}

@Article{Hogg2010,
  author        = {David W. Hogg and Jo Bovy and Dustin Lang},
  title         = {Data analysis recipes: Fitting a model to data},
  journal       = {ArXiv e-prints},
  year          = {2010},
  Xvolume        = {arXiv:1008.4686},
  month         = aug,
  archiveprefix = {arXiv},
  url           = {arXiv:1008.4686},
  eprint        = {1008.4686},
}

@article{Hogg2018a,
  author={David W. Hogg and Daniel Foreman-Mackey},
  title={Data Analysis Recipes: Using Markov Chain Monte Carlo},
  journal={The Astrophysical Journal Supplement Series},
  volume={236},
  number={1},
  pages={11},
  url={http://stacks.iop.org/0067-0049/236/i=1/a=11},
  year={2018},
  abstract={Markov Chain Monte Carlo (MCMC) methods for sampling probability density functions (combined with abundant computational resources) have transformed the sciences, especially in performing probabilistic inferences, or fitting models to data. In this primarily pedagogical contribution, we give a brief overview of the most basic MCMC method and some practical advice for the use of MCMC in real inference problems. We give advice on method choice, tuning for performance, methods for initialization, tests of convergence, troubleshooting, and use of the chain output to produce or report parameter estimates with associated uncertainties. We argue that autocorrelation time is the most important test for convergence, as it directly connects to the uncertainty on the sampling estimate of any quantity of interest. We emphasize that sampling is a method for doing integrals; this guides our thinking about how MCMC output is best used.}
}


@Article{ptemcee,
  author        = {Will Vousden and Will M. Farr and Ilya Mandel},
  title         = {Dynamic temperature selection for parallel-tempering in Markov chain Monte Carlo simulations},
  journal       = {Monthly Notices of the Royal Astronomical Society},
  year          = {2016},
  volume        = {455},
  pages = {1919-1937},
  doi           = {10.1093/mnras/stv2422},
}

@Misc{Nelson2018,
  author       = {Andrew Nelson and Stuart W. Prescott},
  title        = {Online reflectivity fitting with refnx},
  Xhowpublished = {https://mybinder.org/v2/gh/refnx/refnx-binder.git/master},
  year         = {2018},
  url          = {https://mybinder.org/v2/gh/refnx/refnx-binder.git/master},
}

@Article{Well2005,
  author  = {Ad van Well and H. Fredrikze},
  title   = {On the resolution and intensity of a time-of-flight neutron reflectometer},
  journal = {Physica B},
  year    = {2005},
  volume  = {357},
  pages   = {204-207},
  doi     = {10.1016/j.physb.2004.11.058},
}

@InCollection{Millman2014,
  chapter   = {Developing open source scientific practice},
  booktitle = {Implementing Reproducible Research},
  publisher = {Chapman \& Hall},
  year      = {2014},
  author    = {K. Jarrod Millman and Fernando Perez},
  editor    = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
}

@Article{Hughes2016,
  author  = {Arwel V. Hughes and Fillip Ciesielski and Antreas C. Kalli and Luke A. Clifton and Timothy R. Charlton and Mark S.P. Sansom and John R. P. Webster},
  title   = {On the interpretation of reflectivity data from lipid bilayers in terms of molecular-dynamics models},
  journal = {Acta Crystallographica D},
  year    = {2016},
  volume  = {72},
  pages   = {1226-1240},
  doi     = {10.1107/S2059798316016235},
}

@Comment{jabref-meta: databaseType:bibtex;}
