bibliography.bib

@inproceedings{Forde2018ReproducibleRE,
  title={Reproducible Research Environments with Repo2Docker},
  author={Jessica Zosa Forde and Timothy Daniel Head and Chris Holdgraf and Yuvi Panda and Gladys Nalvarete and Benjamin Ragan-Kelley and Erik Sundell},
  url = {https://api.semanticscholar.org/CorpusID:49255709},
  year={2018}
}

@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 = {4},
  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={10}
}

@Misc{IPython,
  OPTkey = 	 {},
  author = 	 {{Interactive Python (IPython)}},
  OPThowpublished = {},
  OPTmonth = 	 {},
  year = 	 {2022},
  note = 	 {\href{http://ipython.org}{http://ipython.org}},
  OPTannote = 	 {}
}

@Misc{Jupyter,
  OPTkey = 	 {},
  author = 	 {{Project Jupyter}},
  OPTtitle = 	 {Project Jupyter},
  year = 	 {2022},
  url = 	 {http://jupyter.org},
}

@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{ReproducibilityRepositoryExample2022,
  author       = {{SOURCE team}},
  title        = {Example Repository for Reproducibility. Can be re-executed with Binder.},
  howpublished = {\url{https://github.com/fangohr/reproducibility-repository-example}},
  year         = {2022}
}



@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},
  OPThowpublished = {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},
}


@misc{GitHubRepoExampleAlbert2016,
  doi = {10.5281/ZENODO.60605},
  url = {https://zenodo.org/record/60605},
  author = {Albert,  Maximilian and Fangohr,  Hans and Metaxas,  Peter J.},
  keywords = {nanoparticle sensing,  magnetic nanoparticles,  finite element simulations,  micromagnetic simulations,  eigenmodes,  ferromagnetic resonance,  magnetic nanostructures},
  title = {Supplementary Data And Code For Paper: "Frequency-Based Nanoparticle Sensing Over Large Field Ranges Using The Ferromagnetic Resonances Of A Magnetic Nanodisc"},
  publisher = {Zenodo},
  year = {2016},
  copyright = {MIT License},
  note = {\url{https://github.com/maxalbert/paper-supplement-nanoparticle-sensing}}
}

@article{Beg2021,
  doi = {10.1109/mcse.2021.3052101},
  url = {https://doi.org/10.1109/mcse.2021.3052101},
  year = {2021},
  month = mar,
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  volume = {23},
  number = {2},
  pages = {36--46},
  author = {Marijan Beg and Juliette Taka and Thomas Kluyver and Alexander Konovalov and Min Ragan-Kelley and Nicolas M. Thiery and Hans Fangohr},
  title = {Using Jupyter for Reproducible Scientific Workflows},
  journal = {Computing in Science \& Engineering}
}


@article{Granger2021,
  doi = {10.1109/mcse.2021.3059263},
  url = {https://doi.org/10.1109/mcse.2021.3059263},
  year = {2021},
  month = mar,
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  volume = {23},
  number = {2},
  pages = {7--14},
  author = {Brian E. Granger and Fernando Perez},
  title = {Jupyter: Thinking and Storytelling With Code and Data},
  journal = {Computing in Science \& Engineering}
}

@article{Perkel2018,
  doi = {10.1038/d41586-018-07196-1},
  url = {https://doi.org/10.1038/d41586-018-07196-1},
  year  = {2018},
  month = {10},
  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-jupyter-binder,
  title        = {Photon and Neutron Open Science Cloud: European project (INFRAEOSC-04) for making FAIR data a reality in 6 ESFRI Research Infrastructures},
  year         = {2022},
  url          = {https://www.panosc.eu/services/data-analysis/},
  author = {{Photon and Neutron Open Science Cloud}},

}



@Misc{notebookcount,
  title        = {Estimate of Public Jupyter Notebooks on GitHub: Latest Report},
  year         = {2022},
  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,
  author={{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,
  author={{ACM Software System Award}},
  year={2017},
  OPTurl={https://awards.acm.org/software-system},
  url={https://awards.acm.org/software-system/award-winners?year=2017&award=149}
}

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


@Misc{mybinder-archive,
  author={{MyBinder team}},
  title={MyBinder.org Events Archive},
  url={https://archive.analytics.mybinder.org},
  year={2022}
}

@article{Fangohr2020,
  doi = {10.18429/JACOW-ICALEPCS2019-TUCPR02},
  url = {https://jacow.org/icalepcs2019/doi/JACoW-ICALEPCS2019-TUCPR02.html},
  author = {Fangohr,  Hans and Beg,  Marijan and Bergemann,  Martin and Bondar,  Valerii and Brockhauser,  Sandor and Campbell,  Aidan and Carinan,  Cammille and Costa,  Raul and Dall'Antonia,  Fabio and Danilevski,  Cyril and E,  Juncheng and Ehsan,  Wajid and Esenov,  Sergey and Fabbri,  Riccardo and Fangohr,  Susanne and Fernandez-Del-Castillo,  Enol and Flucke,  Gero and Fortmann-Grote,  Carsten and Fulla Marsa,  Daniel and Giovanetti,  Gabriele and Goeries,  Dennis and G\"{o}tz,  Andrew and Hall,  Jamie and Hauf,  Steffen and Hickin,  David and Holm Rod,  Thomas and Jarosiewicz,  Tobiasz and Kamil,  Ebad and Karnevskiy,  Mikhail and Kieffer,  Jerome and Kirienko,  Yury and Klimovskaia,  Anna and Kluyver,  Thomas and Kuster,  Markus and Le Guyader,  Loïc and Madsen,  Anders and Maia,  Luis and Mamchyk,  Denys and Mercadier,  Laurent and Michelat,  Thomas and M\"{o}ller,  Johannes and Mohacsi,  Istvan and Parenti,  Andrea and Pellegrini,  Eric and Perrin,  Jean-Francois and Reiser,  Mario and Reppin,  Johannes and Rosca,  Robert and R\"{u}ck,  Denivy and R\"{u}ter,  Tonn and Santos,  Hugo and Schaffer,  Robert and Scherz,  Andreas and Schl\"{u}nzen,  Frank and Scholz,  Markus and Schuh,  Michael and Selknaes,  Jesper Rude and Silenzi,  Alessandro and Sipos,  Gergely and Spirzewski,  Michal and Sztuk,  Jolanta and Szuba,  Janusz and Taylor,  Jonathan and Trojanowski,  Sebastian and Wrona,  Krzysztof and Yaroslavtsev,  Alexander and Zhu,  Jun},
  keywords = {Accelerator Physics,  User Interfaces,  User Perspective,  and User Experience(UX)},
  language = {en},
  title = {Data Exploration and Analysis with Jupyter Notebooks},
  journal = {Proceedings of the 17th International Conference on Accelerator and Large Experimental Physics Control Systems},
  volume = {ICALEPCS2019},
  pages = {USA},
  publisher = {JACoW Publishing,  Geneva,  Switzerland},
  year = {2020},
  copyright = {Creative Commons Attribution 3.0 Unported}
}


@misc{Beg2019-blochpoint-data-repository,
  doi = {10.5281/ZENODO.2938933},
  url = {https://zenodo.org/record/2938933},
  author = {Beg,  Marijan and Pepper,  Ryan A. and Cortés-Ortuño,  David and Atie,  Bilal and {Marc-Antonio Bisotti} and Downing,  Gary and Kluyver,  Thomas and Hovorka,  Ondrej and Fangohr,  Hans},
  keywords = {micromagnetics,  Bloch point,  reproducibility,  computational science,  Binder,  Jupyter,  finmag,  computational magnetism},
  language = {en},
  title = {Stable and manipulable Bloch point -- supplementary data and code repository},
  publisher = {Zenodo},
  year = {2019},
  copyright = {BSD licenses (New and Simplified)},
  url = {https://github.com/reproducible-micromagnetics/2019-stable-and-manipulable-bloch-point}
}

@article{Beg2019-blochpoint-paper,
  doi = {10.1038/s41598-019-44462-2},
  url = {https://doi.org/10.1038/s41598-019-44462-2},
  year = {2019},
  month = may,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {9},
  number = {1},
  author = {Marijan Beg and Ryan A. Pepper and David Cort{\'{e}}s-Ortu{\~{n}}o and Bilal Atie and Marc-Antonio Bisotti and Gary Downing and Thomas Kluyver and Ondrej Hovorka and Hans Fangohr},
  title = {Stable and manipulable Bloch point},
  journal = {Scientific Reports}
}


@book{reproducibility-scoping-report,
  place = {LU},
  title = {Reproducibility of scientific results in the EU: scoping report.},
  url = {https://data.europa.eu/doi/10.2777/341654},
  DOI = {10.2777/341654},
  publisher = {Publications Office},
  author = {European Commission. Directorate General for Research and Innovation.},
  year = {2020}
}



@misc{Hettrick2014,
  doi = {10.5281/ZENODO.1183562},
  url = {https://zenodo.org/record/1183562},
  author = {Hettrick,  Simon},
  title = {Software In Research Survey},
  publisher = {Zenodo},
  year = {2018},
  copyright = {Open Access}
}



@Misc{OSCOVIDA2022,
  OPTkey =       {},
  author =    {Hans Fangohr and Robert Rosca and Yury Kirienko},
  title =     {Open Science COVID Analysis (OSCOVIDA)},
  url       = {https://oscovida.github.io},
  OPTmonth =     {},
  year =      {2022},
  OPTnote =      {},
  OPTannote =    {}
}

@misc{Fangohr2022,
  doi = {10.5281/ZENODO.5887400},
  url = {https://zenodo.org/record/5887400},
  author = {Hans Fangohr},
  title = {Introduction to Python for Computational Science and Engineering},
  publisher = {Github pages},
  howpublished = {\url{https://github.com/fangohr/introduction-to-python-for-computational-science-and-engineering/blob/master/Readme.md}},
  year = {2022},
  copyright = {Open Access}
}


@Book{Zeller2022,
  author =    {Andreas Zeller and Rahul Gopinath and Marcel Böhme and Gordon Fraser and Christian Holler},
  ALTeditor =    {},
  title =        {The Fuzzing Book},
  publisher =    {},
  year =         {2022},
  howpublished = {\url{https://www.fuzzingbook.org}},
  note = {\url{https://www.fuzzingbook.org}},
  OPTkey =       {},
  OPTvolume =    {},
  OPTnumber =    {},
  OPTseries =    {},
  OPTaddress =   {},
  OPTedition =   {},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}


@article{reana2019,
	author = {{Simko, Tibor} and {Heinrich, Lukas} and {Hirvonsalo, Harri} and {Kousidis, Dinos} and {Rodr\'{\i}guez, Diego}},
	title = {REANA: A System for Reusable Research Data Analyses},
	DOI= "10.1051/epjconf/201921406034",
	url= "https://doi.org/10.1051/epjconf/201921406034",
	journal = {EPJ Web Conf.},
	year = 2019,
	volume = 214,
	pages = "06034",
  howpublished = {https://reana.io}
}



@article{Liu2021,
  doi = {10.1007/s10586-021-03460-8},
  url = {https://doi.org/10.1007/s10586-021-03460-8},
  year = {2021},
  month = nov,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {25},
  number = {2},
  pages = {847--868},
  author = {Peini Liu and Jordi Guitart},
  title = {Performance characterization of containerization for {HPC} workloads on {InfiniBand} clusters: an empirical study},
  journal = {Cluster Computing}
}

@article{Gerhardt_2017,
	doi = {10.1088/1742-6596/898/8/082021},
	url = {https://doi.org/10.1088/1742-6596/898/8/082021},
	year = 2017,
	month = {10},
	publisher = {{IOP} Publishing},
	volume = {898},
	pages = {082021},
	author = {Lisa Gerhardt and Wahid Bhimji and Shane Canon and Markus Fasel and Doug Jacobsen and Mustafa Mustafa and Jeff Porter and Vakho Tsulaia},
	title = {Shifter: Containers for {HPC}},
	journal = {Journal of Physics: Conference Series},
	abstract = {Bringing HEP computing to HPC can be difficult. Software stacks are often very complicated with numerous dependencies that are difficult to get installed on an HPC system. To address this issue, NERSC has created Shifter, a framework that delivers Docker-like functionality to HPC. It works by extracting images from native formats and converting them to a common format that is optimally tuned for the HPC environment. We have used Shifter to deliver the CVMFS software stack for ALICE, ATLAS, and STAR on the supercomputers at NERSC. As well as enabling the distribution multi-TB sized CVMFS stacks to HPC, this approach also offers performance advantages. Software startup times are significantly reduced and load times scale with minimal variation to 1000s of nodes. We profile several successful examples of scientists using Shifter to make scientific analysis easily customizable and scalable. We will describe the Shifter framework and several efforts in HEP and NP to use Shifter to deliver their software on the Cori HPC system.}
}



@misc{binder-workshops,
  author = {{Binder-supported Workshops}},
  title = {Over 60 requests from organisers of workshops to increase mybinder.org resources temporarily for their workshop deliveries},
  % howpublished = {\url{https://github.com/jupyterhub/mybinder.org-deploy/issues?q=is%3Aissue+label%3Aimpact+is%3Aclosed},
  % Couldn't get the above URL to work within the bibliography
  howpublished = {\url{https://tinyurl.com/mr36bfzu}},
  year = {2022},
}


@misc{interactive-documentation,
  % author = {{Discretised field documentation}},
  title = {Example of "Discretised field" software documentation that allows interactive testing of the software in browser (through the "launch Binder" button)},
  howpublished = {\url{https://ubermag.github.io/documentation/notebooks/discretisedfield/field-matplotlib-visualisation.html}},
  year = {2022},
}






@InProceedings{Fangohr:ICALEPCS2017-TUCPA01,
  author       = {H. Fangohr and others},
  title        = {{D}ata {A}nalysis {S}upport in {K}arabo at {E}uropean {XFEL}},
  booktitle    = {Proc. of International Conference on Accelerator and Large Experimental Control Systems (ICALEPCS'17),
                  Barcelona, Spain, 8-13 October 2017},
  pages        = {245--252},
  paper        = {TUCPA01},
  language     = {english},
  keywords     = {ion, data-analysis, experiment, FEL, controls},
  venue        = {Barcelona, Spain},
  series       = {International Conference on Accelerator and Large Experimental Control Systems},
  number       = {16},
  publisher    = {JACoW},
  address      = {Geneva, Switzerland},
  OPTmonth        = {1},
  year         = {2018},
  isbn         = {978-3-95450-193-9},
  doi          = {https://doi.org/10.18429/JACoW-ICALEPCS2017-TUCPA01},
  url          = {http://jacow.org/icalepcs2017/papers/tucpa01.pdf},
  note         = {https://doi.org/10.18429/JACoW-ICALEPCS2017-TUCPA01},
}


@misc{nbval-arxiv,
  doi = {10.48550/ARXIV.2001.04808},
  url = {https://arxiv.org/abs/2001.04808},
  author = {Fangohr, Hans and Fauske, Vidar and Kluyver, Thomas and Albert, Maximilian and Laslett, Oliver and Cortes-Ortuno, David and Beg, Marijan and Ragan-Kelly, Min},
  keywords = {Software Engineering (cs.SE), FOS: Computer and information sciences, FOS: Computer and information sciences},
  title = {Testing with Jupyter notebooks: NoteBook VALidation (nbval) plug-in for pytest},
  publisher = {arXiv},
  year = {2020},
  howpublished = {\url{https://github.com/computationalmodelling/nbval}},
  copyright = {arXiv.org perpetual, non-exclusive license}
}


@misc {repo2docker-checker2020,
	title = {Measuring notebook reproducibility with repo2docker},
	year = {2020},
	month = {10},
	address = {JupyterCon},
	keywords = {jupyter, reproducibility},
  author = {Vilde Dille Øvreeide and Benjamin Ragan-Kelley},
  doi = {10.6084/m9.figshare.19604239.v1}
}


@misc {JupyterHub-for-education-2016,
	title = {JupyterHub: Deploying Jupyter Notebooks for students and researchers},
	howpublished = {PyData London},
	year = {2016},
	type = {Tutorial},
	abstract = {The Jupyter Notebook is an interactive web-based tool for interactive programming and writing code-centric documents. Being a web-based environment, the notebook server can be run remotely, not just on your local machine. JupyterHub is a multi-user server, aimed at helping research groups and instructors host notebook servers for their users or students. By default, JupyterHub uses the local system users and PAM authentication, but it can be customized to use any authentication system, including GitHub, CILogon, Shibboleth, and more. The way single-user servers are spawned can also be customized to use services such as Docker, Kubernetes, or HPC cluster queuing systems. The tutorial will cover a basic deployment of JupyterHub on a single machine, then extending it to use docker and GitHub authentication, as well as general best practices for JupyterHub deployment.},
	keywords = {jupyter, jupyterhub, notebook},
	url = {http://pydata.org/london2016/schedule/presentation/59/},
	author = {Ragan-Kelley, Benjamin and Kelley, Kyle and Kluyver, Thomas}
}

@article{woillez2016,
  title = {A {{HMM-based}} Model to Geolocate Pelagic Fish from High-Resolution Individual Temperature and Depth Histories: {{European}} Sea Bass as a Case Study},
  shorttitle = {A {{HMM-based}} Model to Geolocate Pelagic Fish from High-Resolution Individual Temperature and Depth Histories},
  author = {Woillez, Mathieu and Fablet, Ronan and Ngo, Tran-Thanh and Lalire, Maxime and Lazure, Pascal and de Pontual, Hélène},
  options = {useprefix=true},
  date = {2016-02},
  journaltitle = {Ecological Modelling},
  shortjournal = {Ecological Modelling},
  volume = {321},
  pages = {10--22},
  issn = {03043800},
  doi = {10.1016/j.ecolmodel.2015.10.024},
  langid = {english},
  keywords = {bargip}
}

@article{maze2020,
  title = {Argopy: {{A Python}} Library for {{Argo}} Ocean Data Analysis},
  shorttitle = {Argopy},
  author = {Maze, Guillaume and Balem, Kevin},
  date = {2020-09-01},
  journaltitle = {Journal of Open Source Software},
  shortjournal = {JOSS},
  volume = {5},
  number = {53},
  pages = {2425},
  issn = {2475-9066},
  doi = {10.21105/joss.02425}
}

@incollection{odaka2020,
  title = {The {{Pangeo Ecosystem}}: {{Interactive Computing Tools}} for the {{Geosciences}}: {{Benchmarking}} on {{HPC}}},
  shorttitle = {The {{Pangeo Ecosystem}}},
  booktitle = {Tools and {{Techniques}} for {{High Performance Computing}}},
  author = {Odaka, Tina Erica and Banihirwe, Anderson and Eynard-Bontemps, Guillaume and Ponte, Aurelien and Maze, Guillaume and Paul, Kevin and Baker, Jared and Abernathey, Ryan},
  editor = {Juckeland, Guido and Chandrasekaran, Sunita},
  date = {2020},
  series = {Communications in {{Computer}} and {{Information Science}}},
  volume = {1190},
  pages = {190--204},
  publisher = {{Springer International Publishing}},
  location = {{Cham}},
  doi = {10.1007/978-3-030-44728-1_12},
  isbn = {978-3-030-44728-1},
  langid = {english}
}

@article{Afgan2018,
  doi = {10.1093/nar/gky379},
  url = {https://doi.org/10.1093/nar/gky379},
  year = {2018},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {46},
  number = {W1},
  pages = {W537--W544},
  author = {Enis Afgan and Dannon Baker and B{\'{e}}r{\'{e}}nice Batut and Marius van~den~Beek and Dave Bouvier and Martin {\v{C}}ech and John Chilton and Dave Clements and Nate Coraor and Bj\"{o}rn A Gr\"{u}ning and Aysam Guerler and Jennifer Hillman-Jackson and Saskia Hiltemann and Vahid Jalili and Helena Rasche and Nicola Soranzo and Jeremy Goecks and James Taylor and Anton Nekrutenko and Daniel Blankenberg},
  title = {The Galaxy platform for accessible,  reproducible and collaborative biomedical analyses: 2018 update},
  journal = {Nucleic Acids Research}
}

@article{Mlder2021,
  doi = {10.12688/f1000research.29032.2},
  url = {https://doi.org/10.12688/f1000research.29032.2},
  year = {2021},
  month = apr,
  publisher = {F1000 Research Ltd},
  volume = {10},
  pages = {33},
  author = {Felix M\"{o}lder and Kim Philipp Jablonski and Brice Letcher and Michael B. Hall and Christopher H. Tomkins-Tinch and Vanessa Sochat and Jan Forster and Soohyun Lee and Sven O. Twardziok and Alexander Kanitz and Andreas Wilm and Manuel Holtgrewe and Sven Rahmann and Sven Nahnsen and Johannes K\"{o}ster},
  title = {Sustainable data analysis with Snakemake},
  journal = {F1000Research}
}

@inproceedings{CharlieCloud2017,
  author = {Priedhorsky, Reid and Randles, Tim},
  title = {Charliecloud: Unprivileged Containers for User-Defined Software Stacks in HPC},
  year = {2017},
  isbn = {9781450351140},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3126908.3126925},
  doi = {10.1145/3126908.3126925},
  abstract = {Supercomputing centers are seeing increasing demand for user-defined software stacks (UDSS), instead of or in addition to the stack provided by the center. These UDSS support user needs such as complex dependencies or build requirements, externally required configurations, portability, and consistency. The challenge for centers is to provide these services in a usable manner while minimizing the risks: security, support burden, missing functionality, and performance. We present Charliecloud, which uses the Linux user and mount namespaces to run industry-standard Docker containers with no privileged operations or daemons on center resources. Our simple approach avoids most security risks while maintaining access to the performance and functionality already on offer, doing so in just 800 lines of code. Charliecloud promises to bring an industry-standard UDSS user workflow to existing, minimally altered HPC resources.},
  booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
  articleno = {36},
  numpages = {10},
  keywords = {user environments, least privilege, containers},
  location = {Denver, Colorado},
  series = {SC '17}
}

@article{Singularity2017,
    doi = {10.1371/journal.pone.0177459},
    author = {Kurtzer, Gregory M. AND Sochat, Vanessa AND Bauer, Michael W.},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    title = {Singularity: Scientific containers for mobility of compute},
    year = {2017},
    month = {05},
    volume = {12},
    url = {https://doi.org/10.1371/journal.pone.0177459},
    pages = {1-20},
    abstract = {Here we present Singularity, software developed to bring containers and reproducibility to scientific computing. Using Singularity containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms. Singularity is an open source initiative that harnesses the expertise of system and software engineers and researchers alike, and integrates seamlessly into common workflows for both of these groups. As its primary use case, Singularity brings mobility of computing to both users and HPC centers, providing a secure means to capture and distribute software and compute environments. This ability to create and deploy reproducible environments across these centers, a previously unmet need, makes Singularity a game changing development for computational science.},
    number = {5}
}

@article{Seland2020,
  doi = {10.5194/gmd-13-6165-2020},
  url = {https://doi.org/10.5194/gmd-13-6165-2020},
  year = {2020},
  month = dec,
  publisher = {Copernicus {GmbH}},
  volume = {13},
  number = {12},
  pages = {6165--6200},
  author = {{\O}yvind Seland and Mats Bentsen and Dirk Olivi{\'{e}} and Thomas Toniazzo and Ada Gjermundsen and Lise Seland Graff and Jens Boldingh Debernard and Alok Kumar Gupta and Yan-Chun He and Alf Kirkev{\aa}g and J\"{o}rg Schwinger and Jerry Tjiputra and Kjetil Schanke Aas and Ingo Bethke and Yuanchao Fan and Jan Griesfeller and Alf Grini and Chuncheng Guo and Mehmet Ilicak and Inger Helene Hafsahl Karset and Oskar Landgren and Johan Liakka and Kine Onsum Moseid and Aleksi Nummelin and Clemens Spensberger and Hui Tang and Zhongshi Zhang and Christoph Heinze and Trond Iversen and Michael Schulz},
  title = {Overview of the Norwegian Earth System Model ({NorESM}2) and key climate response of {CMIP}6 {DECK},  historical,  and scenario simulations},
  journal = {Geoscientific Model Development}
}