path: root/tex/src/references.tex

%% Non-software BibTeX entries. The software-specific BibTeX entries are
%% stored in a `*.tex' file under the `tex/dependencies' directory.
%
%% [[[BibTeX 0.99d complains with the at-character, even when its in a
%%    comment line! So ::at:: is used instead in the email address]]].
%% Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad::at::akhlaghi.org>
%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
%% notice and this notice are preserved.  This file is offered as-is,
%% without any warranty.





@ARTICLE{peper20,
       author = {{Peper}, Marius and {Roukema}, Boudewijn F.},
        title = "{The role of the elaphrocentre in low surface brightness galaxy formation}",
      journal = {arXiv e-prints},
     keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies},
         year = 2020,
        month = oct,
          eid = {arXiv:2010.03742},
        pages = {arXiv:2010.03742},
archivePrefix = {arXiv},
       eprint = {2010.03742},
 primaryClass = {astro-ph.CO},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv201003742P},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{roukema20,
       author = {{Roukema}, Boudewijn F.},
        title = "{Anti-clustering in the national SARS-CoV-2 daily infection counts}",
      journal = {arXiv e-prints},
     keywords = {Quantitative Biology - Populations and Evolution, Physics - Physics and Society, Statistics - Methodology},
         year = 2020,
        month = jul,
          eid = {arXiv:2007.11779},
        pages = {arXiv:2007.11779},
archivePrefix = {arXiv},
       eprint = {2007.11779},
 primaryClass = {q-bio.PE},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv200711779R},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{aissi20,
     author = {Dylan A\"issi},
      title = {Review for Towards Long-term and Archivable Reproducibility},
       year = {2020},
    journal = {Authorea},
     volume = {n/a},
      pages = {n/a},
        doi = {10.22541/au.159724632.29528907},

}

@ARTICLE{mesnard20,
     author = {Olivier Mesnard and Lorena A. Barba},
      title = {Reproducible Workflow on a Public Cloud for Computational Fluid Dynamics},
       year = {2020},
    journal = {Computing in Science \& Engineering},
     volume = {22},
      pages = {102-116},
        doi = {10.1109/MCSE.2019.2941702},
}





@ARTICLE{dicosmo20,
       author = {{Di Cosmo}, Roberto and {Gruenpeter}, Morane and {Zacchiroli}, Stefano},
        title = "{Referencing Source Code Artifacts: a Separate Concern in Software Citation}",
      journal = {Computing in Science \& Engineering},
         year = 2020,
       volume = 22,
          eid = {arXiv:2001.08647},
        pages = {33},
archivePrefix = {arXiv},
       eprint = {2001.08647},
 primaryClass = {cs.DL},
          doi = {10.1109/MCSE.2019.2963148},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv200108647D},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{menke20,
     author = {Joe Menke and Martijn Roelandse and Burak Ozyurt and Maryann Martone and Anita Bandrowski},
      title = {Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods},
       year = {2020},
    journal = {bioRxiv},
     volume = {},
      pages = {2020.01.15.908111},
        doi = {10.1101/2020.01.15.908111},
}





@ARTICLE{nust20,
     author = {Daniel N\"ust and Vanessa Sochat and Ben Marwick and Stephen J. Eglen and Tim Head and Tony Hirst and Benjamin D. Evans},
      title = {Ten simple rules for writing Dockerfiles for reproducible data science},
       year = {2020},
    journal = {PLOS Computational Biology},
     volume = {16},
      pages = {e1008316},
        doi = {10.1371/journal.pcbi.1008316},
}





@ARTICLE{konkol20,
       author = {{Konkol}, Markus and {N{\"u}st}, Daniel and {Goulier}, Laura},
        title = "{Publishing computational research -- A review of infrastructures for reproducible and transparent scholarly communication}",
      journal = {arXiv},
         year = 2020,
        month = jan,
        pages = {2001.00484},
archivePrefix = {arXiv},
       eprint = {2001.00484},
 primaryClass = {cs.DL},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv200100484K},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{infante20,
       author = {{Infante-Sainz}, Ra{\'u}l and {Trujillo}, Ignacio and
         {Rom{\'a}n}, Javier},
        title = "{The Sloan Digital Sky Survey extended point spread functions}",
      journal = {Monthly Notices of the Royal Astronomical Society},
     keywords = {instrumentation: detectors, methods: data analysis, techniques: image processing, techniques: photometric, galaxies: haloes, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies},
         year = "2020",
        month = "Feb",
       volume = {491},
       number = {4},
        pages = {5317-5329},
          doi = {10.1093/mnras/stz3111},
archivePrefix = {arXiv},
       eprint = {1911.01430},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2020MNRAS.491.5317I},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{gibney20,
     author = {Elizabeth Gibney},
      title = {This AI researcher is trying to ward off a reproducibility crisis},
       year = {2020},
    journal = {Nature},
     volume = {577},
      pages = {14},
        doi = {10.1038/d41586-019-03895-5},
}





@ARTICLE{lofstead19,
     author = {Jay Lofstead and Joshua Baker and Andrew Younge},
      title = {Data Pallets: Containerizing Storage for Reproducibility and Traceability},
       year = {2019},
    journal = {High Performance Computing. ISC High Performance 2019},
     volume = {11887},
      pages = {1},
        doi = {10.1007/978-3-030-34356-9\_4},
}





@ARTICLE{clement19,
     author = {Cl\'ement-Fontaine, M\'elanie and Di Cosmo, Roberto and Guerry, Bastien and MOREAU, Patrick and Pellegrini, Fran\c cois},
      title = {Encouraging a wider usage of software derived from research},
       year = {2019},
    journal = {Archives ouvertes HAL},
     volume = {},
      pages = {\href{https://hal.archives-ouvertes.fr/hal-02545142}{hal-02545142}},
}





@ARTICLE{pimentel19,
     author = {{Jo\~ao Felipe} Pimentel and Leonardo Murta and Vanessa Braganholo and Juliana Freire},
      title = {A large-scale study about quality and reproducibility of jupyter notebooks},
       year = {2019},
    journal = {Proceedings of the 16th International Conference on Mining Software Repositories},
     volume = {1},
      pages = {507-517},
        doi = {10.1109/MSR.2019.00077},
}





@ARTICLE{miksa19a,
     author = {Tomasz Miksa and Paul Walk and Peter Neish},
      title = {RDA DMP Common Standard for Machine-actionable Data Management Plans},
       year = {2019},
    journal = {RDA},
      pages = {doi:10.15497/rda00039},
        doi = {10.15497/rda00039},
}





@ARTICLE{miksa19b,
     author = {Tomasz Miksa and Stephanie Simms and Daniel Mietchen and Sarah Jones},
      title = {Ten principles for machine-actionable data management plans},
       year = {2019},
    journal = {PLoS Computational Biology},
     volume = {15},
      pages = {e1006750},
        doi = {10.1371/journal.pcbi.1006750},
}





@ARTICLE{dicosmo19,
     author = {Roberto {Di Cosmo} and Francois Pellegrini},
      title = {Encouraging a wider usage of software derived from research},
       year = {2019},
    journal = {\doihref{https://www.ouvrirlascience.fr/wp-content/uploads/2020/02/Opportunity-Note\_software-derived-from-research\_EN.pdf}{Ouvrir la science}},
     volume = {},
      pages = {},
        doi = {},
}





@ARTICLE{perignon19,
     author = {Christophe P\'erignon and Kamel Gadouche and Christophe Hurlin and Roxane Silberman and Eric Debonnel},
      title = {Certify reproducibility with confidential data},
       year = {2019},
    journal = {Science},
     volume = {365},
      pages = {127},
        doi = {10.1126/science.aaw2825},
}





@ARTICLE{munafo19,
     author = {Marcus Munaf\'o},
      title = {Raising research quality will require collective action},
       year = {2019},
    journal = {Nature},
     volume = {576},
      pages = {183},
        doi = {10.1038/d41586-019-03750-7},
}





@ARTICLE{jones19,
       author = {{Jones}, M.~G. and {Verdes-Montenegro}, L. and {Damas-Segovia}, A. and
         {Borthakur}, S. and {Yun}, M. and {del Olmo}, A. and {Perea}, J. and
         {Rom{\'a}n}, J. and {Luna}, S. and {Lopez Gutierrez}, D. and
         {Williams}, B. and {Vogt}, F.~P.~A. and {Garrido}, J. and
         {Sanchez}, S. and {Cannon}, J. and {Ram{\'\i}rez-Moreta}, P.},
        title = "{Evolution of compact groups from intermediate to final stages. A case study of the H I content of HCG 16}",
      journal = {Astronomy \& Astrophysics},
       eprint = {1910.03420},
     keywords = {galaxies: groups: individual: HCG 16, galaxies: interactions, galaxies: evolution, galaxies: ISM, radio lines: galaxies},
         year = "2019",
        month = "Dec",
       volume = {632},
          eid = {A78},
        pages = {A78},
          doi = {10.1051/0004-6361/201936349},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019A&A...632A..78J},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{banek19,
       author = {{Banek}, Christine and {Thornton}, Adam and {Economou}, Frossie and
         {Fausti}, Angelo and {Krughoff}, K. Simon and {Sick}, Jonathan},
        title = "{Why is the LSST Science Platform built on Kubernetes?}",
      journal = {Proceedings of ADASS XXIX},
       volume = {arXiv},
     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics},
         year = "2019",
        month = "Nov",
          eid = {arXiv:1911.06404},
        pages = {1911.06404},
archivePrefix = {arXiv},
       eprint = {1911.06404},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv191106404B},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{fineberg19,
     author = {Harvey V. Fineberg and David B. Allison and Lorena A. Barba and Dianne Chong and David L. Donoho and Juliana Freire and Gerald Gabrielse and Constantine Gatsonis and Edward Hall and Thomas H. Jordan and Dietram A. Scheufele and Victoria Stodden and Simine Vazire, Timothy D. Wilson and Wendy Wood and Jennifer Heimberg and Thomas Arrison and Michael Cohen and Michele Schwalbe and Adrienne Stith Butler and Barbara A. Wanchisen and Tina Winters and Rebecca Morgan and Thelma Cox and Lesley Webb and Garret Tyson and Erin Hammers Forstag},
      title = {Reproducibility and Replicability in Science},
    journal = {The National Academies Press},
       year = 2019,
      pages = {1-256},
        doi = {10.17226/25303},
}





@ARTICLE{akhlaghi19,
       author = {{Akhlaghi}, Mohammad},
        title = "{Carving out the low surface brightness universe with NoiseChisel}",
      journal = {IAU Symposium 355},
       volume = {\,},
     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies, Computer Science - Computer Vision and Pattern Recognition},
         year = "2019",
        month = "Sep",
          eid = {arXiv:1909.11230},
        pages = {},
archivePrefix = {arXiv},
       eprint = {1909.11230},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv190911230A},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{cribbs19,
     author = {Cribbs, AP and Luna-Valero, S and George, C and Sudbery, IM and Berlanga-Taylor, AJ and Sansom, SN and Smith, T and Ilott, NE and Johnson, J and Scaber, J and Brown, K and Sims, D and Heger, A},
      title = {CGAT-core: a python framework for building scalable, reproducible computational biology workflows [version 2; peer review: 1 approved, 1 approved with reservations]},
    journal = {F1000Research},
       year = 2019,
     volume = 8,
      pages = {377},
        doi = {10.12688/f1000research.18674.2},
}





@ARTICLE{kurtzer17,
     author = {Gregory M. Kurtzer and Vanessa Sochat and Michael W. Bauer},
      title = {Singularity: Scientific containers for mobility of compute},
    journal = {PLoS ONE},
       year = {2017},
     volume = {12},
      pages = {e0177459},
        doi = {10.1371/journal.pone.0177459},
}





@ARTICLE{meng17,
     author = {Haiyan Meng and Douglas Thain},
      title = {Facilitating the Reproducibility of Scientific Workflows with Execution Environment Specifications},
    journal = {Procedia Computer Science},
       year = {2017},
     volume = {108},
      pages = {705},
        doi = {10.1016/j.procs.2017.05.116},
}





@ARTICLE{tommaso17,
     author = {Paolo Di Tommaso and Maria Chatzou and Evan W Floden and Pablo Prieto Barja and Emilio Palumbo and Cedric Notredame},
      title = {Nextflow enables reproducible computational workflows},
    journal = {Nature Biotechnology},
       year = 2017,
     volume = 35,
      pages = 316,
        doi = {10.1038/nbt.3820},
}





@ARTICLE{brinckman17,
     author = {Adam Brinckman and Kyle Chard and Niall Gaffney and Mihael Hategan and Matthew B. Jones and Kacper Kowalik and Sivakumar Kulasekaran and Bertram Ludäscher and Bryce D. Mecum and Jarek Nabrzyski and Victoria Stodden and Ian J. Taylor and Matthew J. Turk and Kandace Turner},
      title = {Computing environments for reproducibility: Capturing the ``Whole Tale''},
    journal = {Future Generation Computer Systems},
       year = 2017,
     volume = 94,
      pages = 854,
        doi = {10.1016/j.future.2017.12.029},
}





@ARTICLE{uhse19,
       author = {Uhse, Simon and Pflug, Florian G. and {von Haeseler}, Arndt and Djamei, Armin},
        title = {Insertion Pool Sequencing for Insertional Mutant Analysis in Complex Host‐Microbe Interactions},
      journal = {Current Protocols in Plant Biology},
       volume = {4},
         year = "2019",
        month = "July",
        pages = {e20097},
          doi = {10.1002/cppb.20097},
}





@ARTICLE{alliez19,
       author = {{Alliez}, Pierre and {Di Cosmo}, Roberto and {Guedj}, Benjamin and
         {Girault}, Alain and {Hacid}, Mohand-Said and {Legrand}, Arnaud and
         {Rougier}, Nicolas P.},
        title = "{Attributing and Referencing (Research) Software: Best Practices and Outlook from Inria}",
      journal = {Computing in Science \& Engineering},
       volume = {22},
     keywords = {Computer Science - Digital Libraries, Computer Science - Software Engineering},
         year = "2019",
        month = "May",
        pages = {39-52},
archivePrefix = {arXiv},
       eprint = {1905.11123},
 primaryClass = {cs.DL},
          doi = {10.1109/MCSE.2019.2949413},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv190511123A},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{kneller19,
       author = {Kneller,Gerald R. and Hinsen,Konrad},
        title = {Memory effects in a random walk description of protein structure ensembles},
      journal = {The Journal of Chemical Physics},
       volume = {150},
         year = {2019},
        pages = {064911},
          doi = {10.1063/1.5054887},
}





@ARTICLE{oliveira18,
       author = {Lu\'is Oliveira and David Wilkinson and Daniel Moss\'e and Bruce Robert Childers},
        title = {Supporting Long-term Reproducible Software Execution},
      journal = {Proceedings of the First International Workshop on Practical Reproducible Evaluation of Computer Systems (P-RECS'18)},
       volume = {1},
         year = {2018},
        pages = {6},
          doi = {10.1145/3214239.3214245},
}





@ARTICLE{rule19,
       author = {{Rule}, Adam and {Birmingham}, Amanda and {Zuniga}, Cristal and
                 {Altintas}, Ilkay and {Huang}, Shih-Cheng and {Knight}, Rob and
                 {Moshiri}, Niema and {Nguyen}, Mai H. and {Brin Rosenthal},
                 Sara and {P{\'e}rez}, Fernando and {Rose}, Peter W.},
        title = {Ten Simple Rules for Reproducible Research in Jupyter Notebooks},
      journal = {PLOS Computational Biology},
       volume = {15},
         year = 2019,
        month = jul,
        pages = {e1007007},
archivePrefix = {arXiv},
       eprint = {1810.08055},
          doi = {10.1371/journal.pcbi.1007007},
}





@article{tange18,
       author = {Tange, Ole},
        title = {GNU Parallel 2018},
      Journal = {Zenodo},
       volume = {1146014},
        pages = {\href{https://doi.org/10.5281/zenodo.1146014}{DOI:10.5281/zenodo.1146014}},
         year = 2018,
         ISBN = {9781387509881},
          doi = {10.5281/zenodo.1146014},
          url = {https://doi.org/10.5281/zenodo.1146014}
}





@ARTICLE{rule18,
       author = {Adam Rule and Aur\'elien Tabard and {James D.} Hollan},
        title = {Exploration and Explanation in Computational Notebooks},
      journal = {Proceedings of the 2018 CHI Conference on Human Factors in Computing Systems},
       volume = {1},
         year = {2018},
        pages = {30},
          doi = {10.1145/3173574.3173606},
}





@ARTICLE{plesser18,
       author = {Hans E. Plesser},
        title = {Reproducibility vs. Replicability: A Brief History of a Confused Terminology},
      journal = {Frontiers in Neuroinformatics},
       volume = {11},
         year = {2018},
        pages = {76},
          doi = {10.3389/fninf.2017.00076},
}





@ARTICLE{zhang18,
       author = {{Zhang}, Zhi-Yu and {Romano}, D. and {Ivison}, R.~J. and
         {Papadopoulos}, Padelis P. and {Matteucci}, F.},
        title = "{Stellar populations dominated by massive stars in dusty starburst galaxies across cosmic time}",
      journal = {Nature},
     keywords = {Astrophysics - Astrophysics of Galaxies},
         year = "2018",
        month = "Jun",
       volume = {558},
       number = {7709},
        pages = {260},
          doi = {10.1038/s41586-018-0196-x},
archivePrefix = {arXiv},
       eprint = {1806.01280},
 primaryClass = {astro-ph.GA},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2018Natur.558..260Z},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{smart18,
       author = {{Smart}, A.G.},
        title = {The war over supercooled water},
      journal = {Physics Today},
       volume = {Aug},
         year = "2018",
        pages = {DOI:10.1063/PT.6.1.20180822a},
          doi = {10.1063/PT.6.1.20180822a},
}





@ARTICLE{kaiser18,
       author = {{Kaiser}, J.},
        title = {Plan to replicate 50 high-impact cancer papers shrinks to just 18},
      journal = {Science},
       volume = {Jul},
         year = "2018",
        pages = {31},
          doi = {10.1126/science.aau9619},
}





@ARTICLE{dicosmo18,
       author = {{Di Cosmo}, Roberto and {Gruenpeter}, Morane and {Zacchiroli}, Stefano},
        title = {Identifiers for Digital Objects: The case of software source code preservation},
      journal = {Proceedings of iPRES 2018},
         year = "2018",
        pages = {204.4},
          doi = {10.17605/osf.io/kde56},
}





@ARTICLE{gruning18,
       author = {Gr\"uning, Bj\"orn and Chilton, John and K\"oster, Johannes and Dale, Ryan and Soranzo, Nicola and {van den Beek}, Marius and Goecks, Jeremy and Backofen, Rolf and Nekrutenko, Anton and Taylor, James},
        title = {Practical Computational Reproducibility in the Life Sciences},
      journal = {Cell Systems},
       volume = 6,
         year = "2018",
        pages = {631. bioRxiv:\href{https://www.biorxiv.org/content/10.1101/200683v2}{200683}},
          doi = {10.1016/j.cels.2018.03.014},
}





@ARTICLE{allen18,
       author = {{Allen}, Alice and {Teuben}, Peter J. and {Ryan}, P. Wesley},
        title = "{Schroedinger's Code: A Preliminary Study on Research Source Code Availability and Link Persistence in Astrophysics}",
      journal = {The Astrophysical Journal Supplement Series},
     keywords = {methods: numerical, Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Digital Libraries},
         year = "2018",
        month = "May",
       volume = {236},
       number = {1},
          eid = {10},
        pages = {10},
          doi = {10.3847/1538-4365/aab764},
archivePrefix = {arXiv},
       eprint = {1801.02094},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2018ApJS..236...10A},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{burrell18,
       author = {{Burrell}, A.G. and {Halford}, A. and {Klenzing}, J. and {Stoneback}, R.A. and {Morley}, S.K. and {Annex}, A.M. and {Laundal}, K.M. and {Kellerman}, A.C. and {Stansby}, D. and {Ma}, J.},
        title = {Snakes on a Spaceship—An Overview of Python in Heliophysics},
      journal = {Journal of Geophysical Research: Space Physics},
       volume = {123},
         year = "2018",
        pages = {384},
          doi = {10.1029/2018JA025877},
}





@article{stodden18,
	author = {{Stodden}, V. and {Seiler}, J. and {Ma}, Z.},
	title = {An empirical analysis of journal policy effectiveness for computational reproducibility},
	volume = {115},
	number = {11},
	pages = {2584},
	year = {2018},
	doi = {10.1073/pnas.1708290115},
	issn = {0027-8424},
	URL = {https://www.pnas.org/content/115/11/2584},
	journal = {Proceedings of the National Academy of Sciences}
}





@article {fanelli18,
	author = {{Fanelli}, D.},
	title = {Opinion: Is science really facing a reproducibility crisis, and do we need it to?},
	volume = {115},
	number = {11},
	pages = {2628},
	year = {2018},
	doi = {10.1073/pnas.1708272114},
	publisher = {National Academy of Sciences},
	issn = {0027-8424},
	URL = {https://www.pnas.org/content/115/11/2628},
	journal = {Proceedings of the National Academy of Sciences}
}






@ARTICLE{lewis18,
       author = {{Lewis}, L.M. and {Edwards}, M.C. and {Meyers}, Z.R. and {Conover Talbot}, C. and {Hao}, H. and {Blum}, D. },
        title = "{Replication Study: Transcriptional amplification in tumor cells with elevated c-Myc}",
      journal = {eLife},
       volume = {7},
         year = "2018",
        month = "January",
        pages = {e30274},
          doi = {10.7554/eLife.30274},
}





@ARTICLE{akhlaghi18b,
       author = {{Akhlaghi}, Mohammad and {Bacon}, Roland and {Inami}, Hanae},
        title = "{MUSE HUDF survey I \& II, Sections 7.3 \& 3.4: photometry for objects with no prior broad-band segmentation map}",
      journal = {Zenodo},
        pages = {DOI:10.5281/zenodo.1164774},
         year = "2018",
        month = "February",
          doi = {10.5281/zenodo.1164774},
}





@ARTICLE{akhlaghi18a,
       author = {{Akhlaghi}, Mohammad and {Bacon}, Roland},
        title = "{MUSE HUDF survey I, Section 4: data and reproduction pipeline for photometry and astrometry}",
      journal = {Zenodo},
        pages = {DOI:10.5281/zenodo.1163746},
         year = "2018",
        month = "January",
          doi = {10.5281/zenodo.1163746},
}





@ARTICLE{leek17,
     author = {Jeffrey T. Leek and Leah R. Jager},
      title = {Is Most Published Research Really False?},
    journal = {Annual Review of Statistics and Its Application},
     volume = {4},
       year = {2017},
      pages = {109},
        doi = {10.1146/annurev-statistics-060116-054104},
}





@ARTICLE{reich17,
     author = {Michael Reich and Thorin Tabor and Ted Liefeld and Helga Thorvaldsdóttir and Barbara Hill and Pablo Tamayo and Jill P. Mesirov},
      title = {The GenePattern Notebook Environment},
    journal = {Cell Systems},
       year = {2017},
     volume = {5},
      pages = {149},
        doi = {10.1016/j.cels.2017.07.003},
}





@ARTICLE{becker17,
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        title = {Enhancing Reproducibility and Collaboration via Management of R Package Cohorts},
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         year = "2017",
archivePrefix = {arXiv},
       eprint = {1501.02284},
          doi = {10.18637/jss.v082.i01},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2015arXiv150102284B},
}





@ARTICLE{jenness17,
       author = {{Jenness}, Tim},
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      journal = {ADASS 27},
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        month = "Dec",
          eid = {arXiv:1712.00461},
        pages = {arXiv:1712.00461},
archivePrefix = {arXiv},
       eprint = {1712.00461},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2017arXiv171200461J},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@article{bezanson17,
    title={Julia: A fresh approach to numerical computing},
    author={Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B},
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    number={1},
    pages={65},
    year={2017},
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    eprint={1411.1607},
    publisher={SIAM},
    doi={10.1137/141000671},
    adsurl = {https://ui.adsabs.harvard.edu/abs/2014arXiv1411.1607B},
}





@ARTICLE{melson17,
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@ARTICLE{munafo17,
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        title = {A manifesto for reproducible science},
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}





@ARTICLE{jimenez17,
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}





@ARTICLE{bacon17,
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         {Carollo}, Marcella},
        title = "{The MUSE Hubble Ultra Deep Field Survey. I. Survey description, data reduction, and source detection}",
      journal = {Astronomy \& Astrophysics},
     keywords = {galaxies: distances and redshifts, galaxies: high-redshift, cosmology: observations, methods: data analysis, techniques: imaging spectroscopy, galaxies: formation, Astrophysics - Astrophysics of Galaxies},
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        month = "Nov",
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       adsurl = {https://ui.adsabs.harvard.edu/abs/2017A\&A...608A...1B},
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}





@ARTICLE{austin17,
       author = {{Claire C.} Austin and Theodora Bloom and Sünje Dallmeier-Tiessen and {Varsha K.} Khodiyar and Fiona Murphy and Amy Nurnberger and Lisa Raymond and Martina Stockhause and Jonathan Tedds and Mary Vardigan and Angus Whyte},
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}





@ARTICLE{chirigati16,
       author = {Chirigati, Fernando and Rampin, R{\'e}mi and Shasha, Dennis and Freire, Juliana},
        title = {ReproZip: Computational Reproducibility With Ease},
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       volume = {2},
         year = {2016},
        pages = {2085},
          doi = {10.1145/2882903.2899401},
}





@ARTICLE{smith16,
       author = {Arfon M. Smith and Daniel S. Katz and Kyle E. Niemeyer},
        title = {Software citation principles},
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}





@ARTICLE{ziemann16,
       author = {Mark Ziemann and Yotam Eren and Assam El-Osta},
        title = {Gene name errors are widespread in the scientific literature},
      journal = {Genome Biology},
       volume = {17},
         year = {2016},
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}





@ARTICLE{hinsen16,
       author = {Konrad Hinsen},
        title = {Scientific notations for the digital era},
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}





@ARTICLE{kluyver16,
       author = {Thomas Kluyver and Benjamin Ragan-Kelley and Fernando Pérez 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 Damián Avila and Safia Abdalla and Carol Willing},
        title = "{Jupyter Notebooks – a publishing format for reproducible computational workflows}",
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}





@ARTICLE{baker16,
       author = {{Baker}, M.},
        title = "{Is there a reproducibility crisis?}",
      journal = {Nature},
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@ARTICLE{wilkinson16,
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@ARTICLE{hutton16,
     author = {{Hutton}, C. and {Wagener}, T. and {Freer}, J. and {Han}, D. and {Duffy}, C. and {Arheimer}, B.},
      title = {Most computational hydrology is not reproducible, so is it really science?},
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@ARTICLE{topalidou16,
     author = {{Topalidou}, M. and {Leblois}, A. and {Boraud}, T. and {Rougier}, N.P.},
      title = {A long journey into reproducible computational neuroscience},
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@ARTICLE{gil16,
     author = {{Gil}, Yolanda and {David}, C.H. and {Demir}, I. and {Essawy}, B.T. and {Fulweiler}, R.W. and {Goodall}, J.L. and {Karlstrom}, L. and {Lee}, H. and {Mills}, H.J. and {Oh}, J. and {Pierce}, S.A. and {Pope}, A. and {Tzeng}, M.W. and {Villamizar}, S.R. and {Yu}, X},
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@ARTICLE{romine15,
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@ARTICLE{horvath15,
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@ARTICLE{chang15,
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@ARTICLE{schaffer15,
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@ARTICLE{clarkso15,
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}





@ARTICLE{meng15b,
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}





@ARTICLE{meng15,
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}





@ARTICLE{gamblin15,
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@ARTICLE{akhlaghi15,
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    adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{courtes15,
       author = {{Court{\'e}s}, Ludovic and {Wurmus}, Ricardo},
        title = {Reproducible and User-Controlled Software Environments in HPC with Guix},
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archivePrefix = {arXiv},
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       adsurl = {https://ui.adsabs.harvard.edu/abs/2015arXiv150602822C},
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}





@ARTICLE{hinsen15,
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@ARTICLE{belhajjame15,
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@ARTICLE{bechhofer13,
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@ARTICLE{peng15,
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@ARTICLE{dolfi14,
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@ARTICLE{katz14,
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@ARTICLE{herndon14,
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@ARTICLE{easterbrook14,
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@ARTICLE{fomel13,
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@ARTICLE{sandve13,
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@ARTICLE{malik13,
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@ARTICLE{koster12,
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@ARTICLE{gronenschild12,
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@ARTICLE{pham12,
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@ARTICLE{davison12,
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@ARTICLE{zhao12,
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@ARTICLE{vangorp11,
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@ARTICLE{hinsen11,
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@ARTICLE{limare11,
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@ARTICLE{gavish11,
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@ARTICLE{gabriel11,
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@ARTICLE{nowakowski11,
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@ARTICLE{peng11,
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@ARTICLE{gil10,
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@ARTICLE{pence10,
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