bibliography.bib

@Misc{EuXFEL-datapolicy-2017,
  OPTkey =       {},
  OPTauthor =    {},
  title =     {European XFEL Scientific Data Policy},
  OPThowpublished = {},
  OPTmonth =     {},
  year =      {2017},
  OPTnote =      {},
  OPTannote =    {},
  URL = {https://www.xfel.eu/users/experiment_support/policies/scientific_data_policy/index_eng.html}
}

@article{Kluyver2016,
  title = {Jupyter Notebooks -- a publishing format for reproducible computational workflows},
  volume = {0},
  ISSN = {0000-0000},
  url = {http://doi.org/10.3233/978-1-61499-649-1-87},
  DOI = {10.3233/978-1-61499-649-1-87},
  number = {Positioning and Power in Academic Publishing: Players,  Agents and Agendas},
  journal = {Stand Alone},
  publisher = {IOS Press},
  author = {Kluyver, Thomas and Ragan-Kelley, Benjamin and Pérez, Fernando and Granger, Brian and Bussonnier, Matthias and Frederic, Jonathan and Kelley, Kyle and Hamrick, Jessica and Grout, Jason and Corlay, Sylvain and et al.},
  year = {2016},
  pages = {87–90}
}

@article{Soille2018,
  doi = {10.1016/j.future.2017.11.007},
  url = {https://doi.org/10.1016/j.future.2017.11.007},
  year  = {2018},
  month = {apr},
  publisher = {Elsevier {BV}},
  volume = {81},
  pages = {30--40},
  author = {P. Soille and A. Burger and D. De Marchi and P. Kempeneers and D. Rodriguez and V. Syrris and V. Vasilev},
  title = {A versatile data-intensive computing platform for information retrieval from big geospatial data},
  journal = {Future Generation Computer Systems}
}

@Article{Wang2016,
  author = { Wang, Z and Ma'ayan, A},
  title = {An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study [version 1; referees: 3 approved]},
  journal = {F1000Research},
  volume = {5},
  year = {2016},
  number = {1574},
  doi = {10.12688/f1000research.9110.1}
}

@article{Hughes2014,
 title = {A workflow for characterizing nanoparticle monolayers for biosensors: Machine learning on real and artificial SEM images},
 author = {Hughes, Adam and Liu, Zhaowen and Raftari, Maryam and Reeves, Mark E},
 year = 2014,
 month = dec,
 keywords = {Image Processing, Plasmonics, Biosensor, Gold Nanoparticles, Electron Microscopy, Microsopy, Ilastik, Reproducible Research, Segmentation, Bioengineering, IPython Notebook},
 abstract = {
        A persistent challenge in materials science is the characterization of a large ensemble of heterogeneous nanostructures in a set of images. This often leads to practices such as manual particle counting, and sampling bias of a favorable region of the “best” image. Herein, we present the open-source software, imaging criteria and workflow necessary to fully characterize an ensemble of SEM nanoparticle images. Such characterization is critical to nanoparticle biosensors, whose performance and characteristics are determined by the distribution of the underlying nanoparticle film. We utilize novel artificial SEM images to objectively compare commonly-found image processing methods through each stage of the workflow: acquistion, preprocessing, segmentation, labeling and object classification. Using the semi- supervised machine learning application, Ilastik, we demonstrate the decomposition of a nanoparticle image into particle subtypes relevant to our application: singles, dimers, flat aggregates and piles. We outline a workflow for characterizing and classifying nanoscale features on low-magnification images with thousands of nanoparticles. This work is accompanied by a repository of supplementary materials, including videos, a bank of real and artificial SEM images, and ten IPython Notebook tutorials to reproduce and extend the presented results.
      },
 volume = 2,
 pages = {e671v2},
 journal = {PeerJ PrePrints},
 issn = {2167-9843},
 url = {https://doi.org/10.7287/peerj.preprints.671v2},
 doi = {10.7287/peerj.preprints.671v2}
}

@article{Baron2017,
  author = {Baron, Dalya and Poznanski, Dovi},
  title = {The weirdest SDSS galaxies: results from an outlier detection algorithm},
  journal = {Monthly Notices of the Royal Astronomical Society},
  volume = {465},
  number = {4},
  pages = {4530-4555},
  year = {2017},
  doi = {10.1093/mnras/stw3021},
  URL = {http://dx.doi.org/10.1093/mnras/stw3021},
}

@misc{Laken2015,
  Author = {Benjamin A. Laken},
  Title = {Reply to 'Influence of cosmic ray variability on the monsoon rainfall and temperature': a false-positive in the field of solar-terrestrial research},
  Year = {2015},
  Eprint = {arXiv:1502.00505},
}

@misc{Laken2015b,
  title={The cosmic ray flux and the Indian Summer Monsoon},
  url={https://figshare.com/articles/Comment_on_Badruddin_amp_Aslam_2014_/1299413/3},
  DOI={10.6084/m9.figshare.1299413.v3},
  abstractNote={
    The data, code, and figure outputs for my work re-examining the claims of Badruddin & Aslam (2015) , hereafter BA15, titled "Influence of cosmic ray variability on the monsoon rainfall and temperature", published in JASTP.

    This work reproducibly demonstrates the errors in BA15, and explains why their conclusions (of a solar link to the Indian monsoon intensity) are not supported by their analysis.

    Further notes and explanation are included in the iPython Notebook, and accompanying paper.
  },
  publisher={figshare},
  author={Laken, Benjamin},
  year={2015},
  month={Oct}
}

@Misc{IPython,
  OPTkey = 	 {},
  OPTauthor = 	 {},
  title = 	 {Interactive Python (IPython)},
  OPThowpublished = {},
  OPTmonth = 	 {},
  year = 	 {2019},
  note = 	 {\href{http://ipython.org}{http://ipython.org}},
  OPTannote = 	 {}
}

@Misc{Jupyter,
  OPTkey = 	 {},
  OPTauthor = 	 {},
  title = 	 {Project Jupyter},
  OPThowpublished = {},
  OPTmonth = 	 {},
  year = 	 {2019},
  note = 	 {\href{http://jupyter.org}{http://jupyter.org}},
  OPTannote = 	 {}
}

@Misc{Nbsphinx,
  title = 	 {Nbsphinx},
  url =      {https://nbsphinx.readthedocs.io/}
}

@Misc{nbval,
  title = 	 {nbval},
  url =      {https://github.com/computationalmodelling/nbval}
}

@Misc{nbdime,
  title = 	 {nbdime},
  url =      {https://nbdime.readthedocs.io/en/latest/}
}

@Misc{ipywidgets,
  title = 	 {ipywidgets},
  url =      {https://github.com/jupyter-widgets/ipywidgets}
}

@Misc{bqplot,
  title = 	 {bqplot},
  url =      {https://github.com/bloomberg/bqplot}
}

@Misc{ipyvolume,
  title = 	 {ipyvolume},
  url =      {https://github.com/maartenbreddels/ipyvolume}
}

@Misc{Voila,
  title = 	 {Voila},
  url =      {https://github.com/QuantStack/voila}
}

@Misc{K3D,
  title = 	 {K3D},
  url =      {https://github.com/K3D-tools/K3D-jupyter}
}

@Misc{Gryd,
  title = 	 {Gryd},
  url =      {https://gryd.us}
}

@Misc{OKpy,
  title = 	 {OK},
  url =      {https://okpy.org/}
}

@Misc{Colab,
  title = 	 {Colaboratory},
  url =      {https://colab.research.google.com/},
  publisher = {Google LLC}
}

@Misc{Cocalc,
  title = 	 {CoCalc},
  url =      {https://cocalc.com/},
  publisher = {SageMath, Inc.}
}

@Inproceedings{Corlay2017,
  title = 	 {Xeus: A framework for writing native Jupyter kernels},
  author =   {Sylvain Corlay and Johan Mabille},
  booktitle = {Jupytercon},
  year =     {2017},
  month =    "Aug",
  url =      {https://conferences.oreilly.com/jupyter/jup-ny-2017/public/schedule/detail/60038}
}

@Inproceedings{Hamrick2016,
 author = {Hamrick, Jessica B.},
 title = {Creating and Grading IPython/Jupyter Notebook Assignments with NbGrader},
 booktitle = {Proceedings of the 47th ACM Technical Symposium on Computing Science Education},
 series = {SIGCSE '16},
 year = {2016},
 isbn = {978-1-4503-3685-7},
 location = {Memphis, Tennessee, USA},
 pages = {242--242},
 numpages = {1},
 url = {http://doi.acm.org/10.1145/2839509.2850507},
 doi = {10.1145/2839509.2850507},
 acmid = {2850507},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {autograding, ipython, jupyter, notebook assignments},
}

@Article{Vassilev2012,
  author = {Vassilev, Vassil and Canal, Philippe and Naumann, Axel and Russo, Paul},
  year = {2012},
  month = {05},
  title = {Cling – The New Interactive Interpreter for ROOT 6},
  volume = {396},
  number = {5},
  pages = {052071},
  journal = {Journal of Physics: Conference Series},
  publisher = {{IOP} Publishing},
  doi = {10.1088/1742-6596/396/5/052071}
}

@Misc{GEEJupyterLeaflet2017,
  author       = {Tyler Allen Erickson and Brian Granger and Jason Grout and Sylvain Corlay},
  title        = {Interacting with Petabytes of Earth Science Data using Jupyter Notebooks, IPython Widgets and Google Earth Engine},
  month        = "Dec",
  year         = {2017},
  journal      = {AGU Fall Meeting Abstracts}
}

@Misc{Pangeo2018,
  author       = {Joseph Hamman and Matthew Rocklin and Ryan Abernathy},
  title        = {Pangeo: A Big-data Ecosystem for Scalable Earth System Science},
  month        = "Apr",
  year         = {2018},
  volume       = {20},
  series       = {EGU General Assembly Conference Abstracts},
  pages        = {12146},
  adsurl       = {http://adsabs.harvard.edu/abs/2018EGUGA..2012146H},
  adsnote      = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{Chauvin2017,
  doi = {10.1016/j.ejmp.2017.09.081},
  year  = {2017},
  month = {oct},
  publisher = {Elsevier {BV}},
  volume = {42},
  pages = {32--33},
  author = {Maxime Chauvin and Damian Borys and Francesca Botta and Pawel
    Bzowski and Marco A. Coca P{\'{e}}rez and Marta Cremonesi and
      J{\'{e}}r{\'{e}}mie Dabin and Ana M. Denis-Bacelar and Aur{\'{e}}lie
      Desbr{\'{e}}e and Ziad El Bitar and Nadia Falzone and Ludovic Ferrer and
      Didier Franck and Nico Lanconelli and Andrea Mairani and Alessandra
      Malaroda and Kamil Matusik and Erin McKay and Massimiliano Pacilio and
      Justyna Pieter and Andrew P. Robinson and Jos{\'{e}} L. Rodr{\'{\i}}guez
      and Lara Struelens and Leonel A. Torres Aroches and Alex Vergara Gil and
      Manuel Bardi{\`{e}}s},
  title = {A collaborative effort to produce reference dosimetric data with
    Monte Carlo simulation software},
  journal = {Physica Medica}
}

@article{ICRP2009ICRPPhantoms,
  title = {{ICRP Publication 110. Adult Reference Computational Phantoms}},
  year = {2009},
  journal = {Annals of the ICRP},
  author = {{ICRP}},
  number = {2},
  month = {4},
  pages = {1--164},
  volume = {39},
  isbn = {978-0-7020-4186-0},
  doi = {10.1016/j.icrp.2009.07.004},
  issn = {0146-6453},
  pmid = {16168243},
  arxivId = {arXiv:1011.1669v3},
  keywords = {Computational phantoms, Reference Female, Reference Male, Voxel models}
}

@Article{Bodei2009,
  author="Bodei, L.
    and Ferone, D.
    and Grana, C. M.
    and Cremonesi, M.
    and Signore, A.
    and Dierckx, R. A.
    and Paganelli, G.",
  title="Peptide receptor therapies in neuroendocrine tumors",
  journal="Journal of Endocrinological Investigation",
  year="2009",
  month="Apr",
  day="01",
  volume="32",
  number="4",
  pages="360--369",
  issn="1720-8386",
  doi="10.1007/BF03345728"
}

@book{loevinger1991mird,
  title={MIRD Primer for Absorbed Dose Calculations},
  author={Loevinger, R. and Budinger, T.F. and Watson, E.E.},
  isbn={9780932004383},
  lccn={91004858},
  year={1991},
  publisher={Society of Nuclear Medicine}
}

@article{CortsOrtuo2018,
  doi = {10.1088/1367-2630/aaea1c},
  url = {https://doi.org/10.1088/1367-2630/aaea1c},
  year  = {2018},
  month = {nov},
  publisher = {{IOP} Publishing},
  volume = {20},
  number = {11},
  pages = {113015},
  author = {David Cort{\'{e}}s-Ortu{\~{n}}o and Marijan Beg and Vanessa Nehruji
    and Leoni Breth and Ryan Pepper and Thomas Kluyver and Gary Downing and
      Thorsten Hesjedal and Peter Hatton and Tom Lancaster and Riccardo Hertel
      and Ondrej Hovorka and Hans Fangohr},
  title = {Proposal for a micromagnetic standard problem for materials with Dzyaloshinskii{\textendash}Moriya interaction},
  journal = {New Journal of Physics}
}


@Misc{GitHubRepoExampleCortes2018,
  author       = {David Cort{\'e}s-Ortu{\~n}o and Marijan Beg and Vanessa Nehruji and Leoni Breth and Ryan Pepper and Thomas Kluyver and Gary Downing and Thorsten Hesjedal and Peter Hatton and Tom Lancaster and Riccardo Hertel and Ondrej Hovorka and Hans Fangohr},
  title        = {Data set for: Proposal for a micromagnetic standard problem for materials with {Dzyaloshinskii-Moriya} interaction},
  howpublished = {Zenodo doi:10.5281/zenodo.1174311. GitHub: https://github.com/fangohr/paper-supplement-standard-problem-dmi},
  month        = apr,
  year         = {2018},
  doi          = {10.5281/zenodo.1174311},
  url          = {https://doi.org/10.5281/zenodo.1174311},
}


@article{Perkel2018,
  doi = {10.1038/d41586-018-07196-1},
  url = {https://doi.org/10.1038/d41586-018-07196-1},
  year  = {2018},
  month = {oct},
  publisher = {Springer Nature America,  Inc},
  volume = {563},
  number = {7729},
  pages = {145--146},
  author = {Jeffrey M. Perkel},
  title = {Why Jupyter is data scientists' computational notebook of choice},
  journal = {Nature}
}


@Misc{panosc,
  title        = {Photon and Neutron Open Science Cloud: European project (financed by the INFRAEOSC-04 call) for making FAIR data a reality in 6 ESFRI Research Infrastructures},
  year         = {2018},
  url          = {https://panosc-eu.github.io}
}



@Misc{notebookcount,
  title        = {Estimate of Public Jupyter Notebooks on GitHub: Latest Report}, 
  year         = {2019},
  author       = {Peter Parente},
  url          = {https://github.com/parente/nbestimate}
}

@Report{ODK_D4.16,
  author= {Odile Benassy and Nicolas M. Thiéry},
  title={Exploratory support for semantic-aware interactive widgets on mathematical objects},
  howpublished={European Infrastructure Project OpenDreamKit \#676541; report for Deliverable D
  4.16},
  year=2018,
  month={08},
  url={https://github.com/OpenDreamKit/OpenDreamKit/raw/master/WP4/D4.16/report-final.pdf}
}


@article{januszewski2010accelerating,
  title={Accelerating numerical solution of stochastic differential equations with CUDA},
  author={Januszewski, Michal and Kostur, Marcin},
  journal={Computer Physics Communications},
  volume={181},
  number={1},
  pages={183--188},
  year={2010},
  publisher={North-Holland}
}

@article{spiechowicz2015gpu,
  title={GPU accelerated Monte Carlo simulation of Brownian motors dynamics with CUDA},
  author={Spiechowicz, J and Kostur, Marcin and Machura, Lukasz},
  journal={Computer Physics Communications},
  volume={191},
  pages={140--149},
  year={2015},
  publisher={North-Holland}
}

@article{januszewski2014sailfish,
  title={Sailfish: A flexible multi-GPU implementation of the lattice Boltzmann method},
  author={Januszewski, Michal and Kostur, Marcin},
  journal={Computer Physics Communications},
  volume={185},
  number={9},
  pages={2350--2368},
  year={2014},
  publisher={North-Holland}
}

@misc{lsst2017scienceplatform,
  title={LSST Science Platform Vision Document},
  author={Juric, Mario and Ciardi, David and Dubois-Felsmann, Gregory},
  year={2017},
  url={https://ls.st/LSE-319}
}

@misc{ivoa,
  title = 	 {IVOA},
  url =      {http://ivoa.net/}
}

@misc{datapolicy-euxfel,
  title={Scientific Data Policy of European X-Ray Free-Electron Laser Facility GmbH},
  year={2017},
  url={https://www.xfel.eu/users/experiment_support/policies/scientific_data_policy/index_eng.html}
}

@misc{datapolicy-uio,
  title =     {University of Oslo Policies and guidelines for research data management},
  year =      {2017},
  URL = {https://www.uio.no/english/for-employees/support/research/research-data-management/policies-and-guidelines/}
}



@InProceedings{binder,
  author    = { {P}roject {J}upyter and {M}atthias {B}ussonnier and {J}essica {F}orde and {J}eremy {F}reeman and {B}rian {G}ranger and {T}im {H}ead and {C}hris {H}oldgraf and {K}yle {K}elley and {G}ladys {N}alvarte and {A}ndrew {O}sheroff and {M} {P}acer and {Y}uvi {P}anda and {F}ernando {P}erez and {B}enjamin {R}agan-{K}elley and {C}arol {W}illing },
  title     = { {B}inder 2.0 - {R}eproducible, interactive, sharable environments for science at scale },
  booktitle = { {P}roceedings of the 17th {P}ython in {S}cience {C}onference },
  pages     = { 113 - 120 },
  year      = { 2018 },
  editor    = { {F}atih {A}kici and {D}avid {L}ippa and {D}illon {N}iederhut and {M} {P}acer },
  doi       = { 10.25080/Majora-4af1f417-011 }
}

@InProceedings{repo2docker,
  title={Reproducible research environments with repo2docker},
  author={Forde, Jessica and Head, Tim and Holdgraf, Chris and Panda, Yuvi and Nalvarte, Gladys and Ragan-Kelley, Benjamin and Sundell, Erik},
  year={2018},
  booktitle = { ICML 2018 RML Proceedings },
}

@Misc{columbia-nytimes,
  title={How We Got Published in The New York Times},
  year={2018},
  author={Mark Hansen},
  url={https://journalism.columbia.edu/nyt-twitter-story}
}

@Misc{latimes-datadesk,
  title={LA Times Data Desk Jupyter Notebooks},
  year={2018},
  url={https://github.com/datadesk/notebooks}
}

@Article{data-journalism,
  title={The Rise of Transparent Data Journalism – The BuzzFeed Tennis Match Fixing Data Analysis Notebook},
  author={Tony Hirst},
  year={2016},
  url={https://blog.ouseful.info/2016/01/18/the-rise-of-transparent-data-journalism-the-buzzfeed-tennis-match-fixing-data-analysis-notebook/}
}

@Misc{jupyter-grant,
  title={Project Jupyter: Computational Narratives as the Engine of Collaborative Data Science},
  author={Fernando P\'erez and Brian Granger},
  year={2015},
  url={http://archive.ipython.org/JupyterGrantNarrative-2015.pdf}
}


@Misc{binder-billing,
  title={mybinder.org billing data},
  year={2018},
  url={https://github.com/jupyterhub/binder-billing}
}

@Misc{acm-award,
  title={ACM Software System Award},
  year={2017},
  url={https://awards.acm.org/software-system}
}

@Misc{ligo-open-science,
  title={Gravitational Wave Open Science Center},
  url={https://www.gw-openscience.org/about/}
}

@Misc{mybinder-archive,
  title={MyBinder.org Events Archive},
  url={https://archive.analytics.mybinder.org}
}