From 2bfa3a043dcf394492a33bbcb16121dcb227b5ed Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Sat, 2 May 2020 04:38:55 +0100 Subject: First implementation of style in IEEEtran style The paper is no longer using LuaLaTeX, but raw LaTeX (that saves a DVI), it is so much faster! Initially I had used LuaLaTeX to use special fonts to resemble the CODATA Data Science Journal, but all that overhead is no longer necessary. Therefore I also removed the MANY extra LaTeX packages we were importing. The paper builds and is able to construct one of its images (the git-branching figure) with only 7 packages beyond the minimal TeX/LaTeX installation. Also in terms of processing it is so much faster. The text is just temporary now, and mainly just a place holder. With the next commit, I'll fill it with proper text. --- tex/img/icon-collaboration.eps | 159 ++++ tex/img/icon-collaboration.svg | 107 +++ tex/img/icon-complete.eps | 162 ++++ tex/img/icon-complete.svg | 2 + tex/img/icon-processing.eps | 212 +++++ tex/img/icon-processing.svg | 1 + tex/src/figure-branching.tex | 13 +- tex/src/preamble-pgfplots.tex | 22 +- tex/src/preamble-project.tex | 27 + tex/src/references.bib | 1772 ++++++++++++++++++++++++++++++++++++++++ tex/src/references.tex | 1772 ---------------------------------------- 11 files changed, 2463 insertions(+), 1786 deletions(-) create mode 100644 tex/img/icon-collaboration.eps create mode 100644 tex/img/icon-collaboration.svg create mode 100644 tex/img/icon-complete.eps create mode 100644 tex/img/icon-complete.svg create mode 100644 tex/img/icon-processing.eps create mode 100644 tex/img/icon-processing.svg create mode 100644 tex/src/preamble-project.tex create mode 100644 tex/src/references.bib delete mode 100644 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c 204 165.312 206.688 + 168 210 168 c 270 168 l 273.312 168 276 165.312 276 162 c 276 158.688 273.312 + 156 270 156 c h +270 156 m f +66 204 m 138 204 l 141.312 204 144 201.312 144 198 c 144 194.688 141.312 + 192 138 192 c 66 192 l 62.688 192 60 194.688 60 198 c 60 201.312 62.688 + 204 66 204 c h +66 204 m f +162 300 m 138 300 l 134.688 300 132 302.688 132 306 c 132 309.312 134.688 + 312 138 312 c 162 312 l 165.312 312 168 309.312 168 306 c 168 302.688 165.312 + 300 162 300 c h +162 300 m f +66 312 m 114 312 l 117.312 312 120 309.312 120 306 c 120 302.688 117.312 + 300 114 300 c 66 300 l 62.688 300 60 302.688 60 306 c 60 309.312 62.688 + 312 66 312 c h +66 312 m f +66 276 m 102 276 l 105.312 276 108 273.312 108 270 c 108 266.688 105.312 + 264 102 264 c 66 264 l 62.688 264 60 266.688 60 270 c 60 273.312 62.688 + 276 66 276 c h +66 276 m f +66 96 m 138 96 l 141.312 96 144 93.312 144 90 c 144 86.688 141.312 84 138 + 84 c 66 84 l 62.688 84 60 86.688 60 90 c 60 93.312 62.688 96 66 96 c h +66 96 m f +162 264 m 126 264 l 122.688 264 120 266.688 120 270 c 120 273.312 122.688 + 276 126 276 c 162 276 l 165.312 276 168 273.312 168 270 c 168 266.688 165.312 + 264 162 264 c h +162 264 m f +228.582 261.426 m 227.16 264.418 228.434 267.996 231.426 269.418 c 234.418 + 270.84 237.996 269.566 239.418 266.574 c 245.602 253.535 258.969 245.449 + 273.387 246.023 c 287.805 246.602 300.488 255.73 305.605 269.223 c 299.285 + 265.008 l 296.531 263.211 292.84 263.965 291.016 266.703 c 289.191 269.441 + 289.91 273.141 292.629 274.992 c 310.629 286.992 l 310.645 287 l 310.867 + 287.145 311.098 287.277 311.336 287.391 c 311.387 287.414 311.438 287.441 + 311.488 287.465 c 311.727 287.574 311.969 287.668 312.219 287.746 c 312.258 + 287.758 312.301 287.766 312.34 287.777 c 312.551 287.832 312.762 287.879 + 312.973 287.914 c 313.051 287.93 313.125 287.941 313.199 287.949 c 313.434 + 287.98 313.672 287.996 313.906 288 c 313.957 288 l 313.957 288 313.984 +288 314 288 c 314.215 288 314.426 287.984 314.637 287.961 c 314.695 287.957 + 314.754 287.945 314.812 287.934 c 314.984 287.91 315.148 287.883 315.312 + 287.844 c 315.375 287.828 315.441 287.812 315.5 287.797 c 315.664 287.754 + 315.82 287.703 315.977 287.645 c 316.035 287.625 316.098 287.602 316.156 + 287.578 c 316.32 287.516 316.48 287.441 316.637 287.363 c 316.684 287.34 + 316.73 287.32 316.777 287.297 c 316.973 287.195 317.16 287.078 317.34 286.957 + c 317.395 286.922 317.445 286.879 317.5 286.84 c 317.625 286.746 317.75 + 286.648 317.871 286.547 c 317.934 286.492 317.996 286.434 318.059 286.375 + c 318.172 286.27 318.277 286.16 318.383 286.047 c 318.43 285.992 318.48 + 285.941 318.531 285.887 c 318.684 285.711 318.824 285.523 318.953 285.332 + c 330.953 267.332 l 332.77 264.574 332.02 260.871 329.273 259.039 c 326.527 + 257.207 322.816 257.938 320.969 260.676 c 317.281 266.211 l 310.871 247.816 + 293.984 235.121 274.535 234.07 c 255.086 233.023 236.934 243.832 228.586 + 261.43 c h +228.582 261.426 m f +320.574 306.582 m 319.137 305.898 317.488 305.812 315.988 306.348 c 314.488 + 306.879 313.262 307.988 312.582 309.426 c 306.398 322.465 293.031 330.551 + 278.613 329.977 c 264.195 329.398 251.512 320.27 246.395 306.777 c 252.715 + 310.992 l 255.469 312.789 259.16 312.035 260.984 309.297 c 262.809 306.559 + 262.09 302.859 259.371 301.008 c 241.371 289.008 l 241.352 288.996 241.328 + 288.984 241.309 288.969 c 241.164 288.875 241.016 288.785 240.863 288.703 + c 240.805 288.676 240.746 288.648 240.688 288.621 c 240.57 288.562 240.453 + 288.504 240.332 288.453 c 240.25 288.422 240.164 288.395 240.078 288.363 + c 239.98 288.328 239.883 288.289 239.781 288.258 c 239.676 288.23 239.562 + 288.203 239.457 288.176 c 239.375 288.156 239.297 288.133 239.215 288.117 + c 239.078 288.09 238.945 288.07 238.809 288.055 c 238.75 288.047 238.691 + 288.035 238.633 288.031 c 238.457 288.012 238.285 288.008 238.113 288.004 + c 238.09 288.004 238.066 288.004 238.039 288.004 c 238.031 288.004 l 237.832 + 288.004 237.629 288.016 237.434 288.035 c 237.344 288.043 237.258 288.062 + 237.168 288.074 c 237.066 288.09 236.961 288.102 236.859 288.121 c 236.719 + 288.148 236.582 288.188 236.445 288.227 c 236.395 288.238 236.344 288.25 + 236.297 288.262 c 236.168 288.301 236.043 288.352 235.922 288.398 c 235.863 + 288.418 235.805 288.438 235.75 288.461 c 235.641 288.504 235.543 288.555 + 235.438 288.605 c 235.363 288.641 235.289 288.676 235.215 288.715 c 235.137 + 288.754 235.055 288.805 234.977 288.852 c 234.898 288.898 234.797 288.957 + 234.707 289.016 c 234.648 289.055 234.594 289.102 234.535 289.145 c 234.434 + 289.219 234.332 289.285 234.234 289.367 c 234.188 289.406 234.145 289.449 + 234.098 289.488 c 234 289.578 233.898 289.664 233.805 289.758 c 233.711 + 289.852 233.633 289.941 233.551 290.035 c 233.508 290.086 233.457 290.133 + 233.414 290.184 c 233.285 290.34 233.164 290.504 233.055 290.672 c 233.055 + 290.676 l 221.055 308.676 l 220.16 310 219.832 311.625 220.141 313.191 +c 220.449 314.758 221.371 316.137 222.699 317.023 c 224.027 317.906 225.656 + 318.227 227.219 317.91 c 228.785 317.594 230.16 316.664 231.039 315.332 + c 234.727 309.797 l 241.137 328.191 258.023 340.887 277.473 341.934 c 296.922 + 342.984 315.074 332.176 323.422 314.578 c 324.105 313.141 324.191 311.488 + 323.656 309.988 c 323.121 308.488 322.012 307.262 320.574 306.582 c h +320.574 306.582 m f +Q Q +showpage +%%Trailer +end +%%EOF diff --git a/tex/img/icon-processing.svg b/tex/img/icon-processing.svg new file mode 100644 index 0000000..b75b312 --- /dev/null +++ b/tex/img/icon-processing.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/tex/src/figure-branching.tex b/tex/src/figure-branching.tex index a917987..52a6303 100644 --- a/tex/src/figure-branching.tex +++ b/tex/src/figure-branching.tex @@ -27,6 +27,11 @@ + + + + + \begin{tikzpicture} %% Just for a reference (so the image size always remains fixed). It also @@ -71,13 +76,13 @@ \branchcommit{red!60!green}{4.5cm}{5cm}{f69e1f4} \branchcommit{red!60!green}{4.5cm}{6cm}{716b56b} \node[inner sep=0pt] at (3.92cm,5.55cm) - {\includegraphics[width=6.5mm]{tex/img/icon-collaboration.pdf}}; + {\includegraphics[width=6.5mm]{tex/img/icon-collaboration.eps}}; %% Paper being processed icon. The white rectangle over it is to blend it %% into the background. \node[anchor=south,inner sep=0pt] at (3.92cm,6.7cm) - {\includegraphics[width=1cm]{tex/img/icon-processing.pdf}}; - \draw[white, fill=white, opacity=0.7] (3.42cm,6.7) rectangle (5cm,7.7cm); + {\includegraphics[width=1cm]{tex/img/icon-processing.eps}}; + \draw[white, fill=white, opacity=0.7] (3.42cm,6.7) rectangle (5cm,7.8cm); %% Description of this scenario: \draw [rounded corners, fill=black!10!white] (3.1cm,0) rectangle (7.5cm,1.25cm); @@ -131,7 +136,7 @@ %% Project commits. \branchcommit{red!60!green}{11cm}{2.5cm}{4483a81} \branchcommit{red!60!green}{11cm}{4.5cm}{\projectversion} - \node[anchor=south, inner sep=0pt, color=white] at (11.05cm,4.8cm) {\includegraphics[width=1cm]{tex/img/icon-complete.pdf}}; + \node[anchor=south, inner sep=0pt, color=white] at (11.05cm,4.8cm) {\includegraphics[width=1cm]{tex/img/icon-complete.eps}}; %% Derivate project commits. \branchcommit{purple!60!yellow}{12.5cm}{5cm}{b177c7e} diff --git a/tex/src/preamble-pgfplots.tex b/tex/src/preamble-pgfplots.tex index 0a7b5d5..eabdeb7 100644 --- a/tex/src/preamble-pgfplots.tex +++ b/tex/src/preamble-pgfplots.tex @@ -84,7 +84,7 @@ \tikzsetnextfilename{#1}% \input{tex/src/#1.tex}% \else - \includegraphics[width=\linewidth]{tex/tikz/#1.pdf} + \includegraphics[width=\linewidth]{tex/tikz/#1.eps} \fi } @@ -92,15 +92,17 @@ -%% Uncomment the following lines for EPS and PS images. Note that you still -%% have to use the `pdflatex' executable and also add a `[dvips]' option to -%% graphicx. - -%% \tikzset{external/system call={rm -f "\image".eps "\image".ps -%% "\image".dvi; latex \tikzexternalcheckshellescape -halt-on-error -%% -interaction=batchmode -jobname "\image" "\texsource"; -%% dvips -o "\image".ps "\image".dvi; -%% ps2eps "\image.ps"}} +%% Uncomment the following lines for TiKZ external images to be saved as +%% EPS and PS images. +\tikzset{ + external/system call={ + rm -f "\image".eps "\image".ps "\image".dvi; + latex \tikzexternalcheckshellescape -halt-on-error + -interaction=batchmode -jobname "\image" "\texsource"; + dvips -o "\image".ps "\image".dvi; + ps2eps "\image.ps" + } +} diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex new file mode 100644 index 0000000..c4d7feb --- /dev/null +++ b/tex/src/preamble-project.tex @@ -0,0 +1,27 @@ +%% Import graphics +\usepackage{graphicx} + +%% IEEEtran V1.6 and later pre-defines the format of the cite.sty package +%% \cite{} output to follow that of the IEEE. +\usepackage{cite} + +%% For the `\url' command. +\usepackage{url} + +% correct bad hyphenation here +\hyphenation{op-tical net-works semi-conduc-tor} + +%% To use colors. +\usepackage{xcolor} + +%% To have links. +\usepackage[ + colorlinks, + urlcolor=gray, + citecolor=gray, + linkcolor=gray, + linktocpage]{hyperref} +\renewcommand\UrlFont{\rmfamily} + +%% To have typewriter font +\usepackage{courier} diff --git a/tex/src/references.bib b/tex/src/references.bib new file mode 100644 index 0000000..e19ec16 --- /dev/null +++ b/tex/src/references.bib @@ -0,0 +1,1772 @@ +@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{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{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}, + 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{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}, + 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. 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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}, + doi = {10.17226/25303}, +} + + + + + +@ARTICLE{akhlaghi19, + author = {{Akhlaghi}, Mohammad}, + title = "{Carving out the low surface brightness universe with NoiseChisel}", + journal = {IAU Symposium 355}, + volume = {arXiv}, + 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 = {1909.11230}, +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{brinckman19, +author = "Adam Brinckman and Kyle Chard and Niall Gaffney and Mihael Hategan and Matthew B. 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Turk and Kandace Turner", + title = {Computing environments for reproducibility: Capturing the ``Whole Tale''}, + journal = {Future Generation Computer Systems}, + year = 2019, + 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}, +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{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, + author = {Gabriel Becker and Cory Barr and Robert Gentleman and Michael Lawrence}, + title = {Enhancing Reproducibility and Collaboration via Management of R Package Cohorts}, + journal = {Journal of Statistical Software, Articles}, + volume = {82}, + pages = 1, + 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}, + title = "{Modern Python at the Large Synoptic Survey Telescope}", + journal = {ADASS 27}, + year = "2017", + 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}, + journal={SIAM {R}eview}, + volume={59}, + number={1}, + pages={65}, + year={2017}, + archivePrefix={arXiv}, + eprint={1411.1607}, + publisher={SIAM}, + doi={10.1137/141000671}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2014arXiv1411.1607B}, +} + + + + + +@ARTICLE{melson17, + author = {{Melsen}, L.A. and {Torfs}, P.J.J.F and {Uijlenhoet}, R. and {Teuling}, A.J.}, + title = {Comment on “Most computational hydrology is not reproducible, so is it really science?” by Christopher Hutton et al.}, + journal = {Water Resources Research}, + volume = 53, + pages = {2568}, + year = {2017}, + doi = {10.1002/2016WR020208}, +} + + + + + +@ARTICLE{munafo17, + author = {{Munaf\'o}, M.R. and {Nosek}, B.A. and {Bishop}, D.V.M. and {Button}, K.S. and {Chambers}, C.D. and {Percie du Sert}, N. and {Simonsohn}, U. and {Wagenmakers}, E.J. and {Ware}, J.J. {Ioannidis}, J.P.A.}, + title = {A manifesto for reproducible science}, + journal = {Nature Human Behaviour}, + volume = 1, + pages = {21}, + year = {2017}, + doi = {10.1038/s41562-016-0021}, +} + + + + + +@ARTICLE{jimenez17, + title={The popper convention: Making reproducible systems evaluation practical}, + author = {{Jimenez}, I. and {Sevilla}, M. and {Watkins}, N. and {Maltzahn}, C. and {Lofstead}, J. and {Mohror}, K. and {Arpaci-Dusseau}, A. and {Arpaci-Dusseau}, R.}, + journal = {IEEE IPDPSW}, + pages = {1561}, + year = {2017}, + doi = {10.1109/IPDPSW.2017.157}, +} + + + + + +@ARTICLE{bacon17, + author = {{Bacon}, Roland and {Conseil}, Simon and {Mary}, David and + {Brinchmann}, Jarle and {Shepherd}, Martin and {Akhlaghi}, Mohammad and + {Weilbacher}, Peter M. and {Piqueras}, Laure and {Wisotzki}, Lutz and + {Lagattuta}, David and {Epinat}, Benoit and {Guerou}, Adrien and + {Inami}, Hanae and {Cantalupo}, Sebastiano and + {Courbot}, Jean Baptiste and {Contini}, Thierry and {Richard}, Johan and + {Maseda}, Michael and {Bouwens}, Rychard and {Bouch{\'e}}, Nicolas and + {Kollatschny}, Wolfram and {Schaye}, Joop and {Marino}, Raffaella Anna and + {Pello}, Roser and {Herenz}, Christian and {Guiderdoni}, Bruno and + {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}, + year = "2017", + month = "Nov", + volume = {608}, + eid = {A1}, + pages = {A1}, + doi = {10.1051/0004-6361/201730833}, +archivePrefix = {arXiv}, + eprint = {1710.03002}, + primaryClass = {astro-ph.GA}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2017A\&A...608A...1B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@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}, + title = {Key components of data publishing: using current best practices to develop a reference model for data publishing}, + journal = {International Journal on Digital Libraries}, + volume = {18}, + year = {2017}, + pages = {77}, + doi = {10.1007/s00799-016-0178-2}, +} + + + + + +@ARTICLE{smith16, + author = {Arfon M. Smith and Daniel S. Katz and Kyle E. Niemeyer}, + title = {Software citation principles}, + journal = {PeerJ Computer Science}, + volume = {2}, + year = {2016}, + pages = {e86}, + doi = {10.7717/peerj-cs.86}, +} + + + + + +@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}, + pages = {177}, + doi = {10.1186/s13059-016-1044-7}, +} + + + + + +@ARTICLE{hinsen16, + author = {Konrad Hinsen}, + title = {Scientific notations for the digital era}, + journal = {The Self Journal of Science}, + year = {2016}, + pages = {1: arXiv:\href{https://arxiv.org/abs/1605.02960}{1605.02960}}, +} + + + + + +@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}", + journal = {Positioning and Power in Academic Publishing: Players, Agents and Agendas}, + year = {2016}, + pages = {87}, + doi = {10.3233/978-1-61499-649-1-87}, +} + + + + + +@ARTICLE{baker16, + author = {{Baker}, M.}, + title = "{Is there a reproducibility crisis?}", + journal = {Nature}, + volume = {533}, + year = "2016", + month = "May", + pages = {452}, + doi = {10.1038/533452a}, +} + + + + + +@ARTICLE{wilkinson16, + author = { {Wilkinson}, M.D and {Dumontier}, M. and {Aalbersberg}, I.J. and {Appleton}, G. and {Axton}, M. and {Baak}, A. and {Blomberg}, N. and {Boiten}, J. and {da Silva Santos}, L.B and {Bourne}, P.E. and {Bouwman}, J. and {Brookes}, A.J. and {Clark}, T. and {Crosas}, M. and {Dillo}, I. and {Dumon}, O. and {Edmunds}, S. and {Evelo}, C. and {Finkers}, R. and {Gonzalez-Beltran}, A. and {Gray}, A.J.G. and {Groth}, P. and {Goble}, C. and {Grethe}, Jeffrey S. and {Heringa}, J. and {’t Hoen}, P.A.C and {Hooft}, R. and {Kuhn}, T. and {Kok}, R. and {Kok}, J. and {Lusher}, S. and {Martone}, M. and {Mons}, A. and {Packer}, A. and {Persson}, B. and {Rocca-Serra}, P. and {Roos}, M. and {van Schaik}, R. and {Sansone}, S. and {Schultes}, E. and {Sengstag}, T. and {Slater}, T. and {Strawn}, G. and {Swertz}, M. and {Thompson}, M. and {van der Lei}, J. and {van Mulligen}, E. and {Velterop}, J. and {Waagmeester}, A. and {Wittenburg}, P. and {Wolstencroft}, K. and {Zhao}, J. and {Mons}, B.}, + title = "{The FAIR Guiding Principles for scientific data management and stewardship}", + journal = {Scientific Data}, + year = 2016, + month = mar, + volume = 3, + pages = {160018}, + doi = {10.1038/sdata.2016.18}, +} + + + + +@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?}, + journal = {Water Resources Research}, + year = {2016}, + volume = 52, + pages = {7548}, + doi = {10.1002/2016WR019285}, +} + + + + + +@ARTICLE{topalidou16, + author = {{Topalidou}, M. and {Leblois}, A. and {Boraud}, T. and {Rougier}, N.P.}, + title = {A long journey into reproducible computational neuroscience}, + journal = {Frontiers in Computational Neuroscience}, + year = {2016}, + volume = 9, + pages = {30}, + doi = {10.3389/fncom.2015.00030}, +} + + + + + +@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}, + title = {Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance}, + journal = {Earth and Space Science}, + year = 2016, + volume = 3, + pages = {388}, + doi = {10.1002/2015EA000136}, +} + + + + + +@ARTICLE{romine15, + author = {Charles H. Romine}, + title = {Secure Hash Standard (SHS)}, + journal = {Federal Information processing standards publication}, + volume = {180}, + pages = {4}, + year = {2015}, + doi = {10.6028/NIST.FIPS.180-4}, +} + + + + + +@ARTICLE{horvath15, + author = {Steve Horvath}, + title = {Erratum to: DNA methylation age of human tissues and cell types}, + journal = {Genome Biology}, + volume = {16}, + pages = {96}, + year = {2015}, + doi = {10.1186/s13059-015-0649-6}, +} + + + + + +@ARTICLE{chang15, + author = {Andrew C. Chang and Phillip Li}, + title = {Is Economics Research Replicable? Sixty Published Papers from Thirteen Journals Say ``Usually Not''}, + journal = {Finance and Economics Discussion Series 2015-083}, + year = {2015}, + pages = {1}, + doi = {10.17016/FEDS.2015.083}, +} + + + + + +@ARTICLE{schaffer15, + author = {Jonathan Schaffer}, + title = {What Not to Multiply Without Necessity}, + journal = {Australasian Journal of Philosophy}, + volume = {93}, + pages = {644}, + year = {2015}, + doi = {10.1080/00048402.2014.992447}, +} + + + + + +@ARTICLE{clarkso15, + author = "Chris Clarkson and Mike Smith and Ben Marwick and Richard Fullagar and Lynley A. Wallis and Patrick Faulkner and Tiina Manne and Elspeth Hayes and Richard G. Roberts and Zenobia Jacobs and Xavier Carah and Kelsey M. Lowe and Jacqueline Matthews and S. Anna Florin", + title = {The archaeology, chronology and stratigraphy of Madjedbebe (Malakunanja II): A site in northern Australia with early occupation}, + journal = {Journal of Human Evolution}, + year = 2015, + volume = 83, + pages = 46, + doi = {10.1016/j.jhevol.2015.03.014}, +} + + + + + +@ARTICLE{meng15, + author = {Haiyan Meng and Rupa Kommineni and Quan Pham and Robert Gardner and Tanu Malik and Douglas Thain}, + title = {An invariant framework for conducting reproducible computational science}, + journal = {Journal of Computational Science}, + year = 2015, + volume = 9, + pages = 137, + doi = {10.1016/j.jocs.2015.04.012}, +} + + + + + +@ARTICLE{gamblin15, + author = {Gamblin, Todd and LeGendre, Matthew and Collette, Michael R. and Lee, Gregory L. and Moody, Adam and {de Supinski}, Bronis R. and Futral, Scott}, + title = {The Spack package manager: bringing order to HPC software chaos}, + journal = {IEEE SC15}, + year = 2015, + volume = 1, + pages = {1}, + doi = {10.1145/2807591.2807623}, +} + + + + +@ARTICLE{akhlaghi15, + author = {{Akhlaghi}, M. and {Ichikawa}, T.}, + title = "{Noise-based Detection and Segmentation of Nebulous Objects}", + journal = {The Astrophysical Journal Supplement Series}, + archivePrefix = "arXiv", + eprint = {1505.01664}, + primaryClass = "astro-ph.IM", + keywords = {galaxies: irregular, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric}, + year = 2015, + month = sep, + volume = 220, + eid = {1}, + pages = {1}, + doi = {10.1088/0067-0049/220/1/1}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A}, + 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}, + journal = {Euro-Par}, + volume = {9523}, + keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Operating Systems, Computer Science - Software Engineering}, + year = {2015}, + month = {Jun}, + eid = {arXiv:1506.02822}, + pages = {arXiv:1506.02822}, +archivePrefix = {arXiv}, + eprint = {1506.02822}, + primaryClass = {cs.DC}, + doi = {10.1007/978-3-319-27308-2_47}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2015arXiv150602822C}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{hinsen15, + author = {{Hinsen}, K.}, + title = {ActivePapers: a platform for publishing and archiving computer-aided research}, + journal = {F1000Research}, + year = 2015, + volume = 3, + pages = {289}, + doi = {10.12688/f1000research.5773.3}, +} + + + + + +@ARTICLE{belhajjame15, + author = {{Belhajjame}, K. and {Zhao}, Z. and {Garijo}, D. and {Gamble}, M. and {Hettne}, K. and {Palma}, R. and {Mina}, E. and {Corcho}, O. and {Gómez-Pérez}, J.M. and {Bechhofer}, S. and {Klyne}, G. and {Goble}, C}, + title = "{Using a suite of ontologies for preserving workflow-centric research objects}", + journal = {Journal of Web Semantics}, + year = 2015, + volume = 32, + pages = {16}, + doi = {10.1016/j.websem.2015.01.003}, +} + + + + + +@ARTICLE{bechhofer13, + author = {{Bechhofer}, S. and {Buchan}, I. and {De Roure}, D. and {Missier}, P. and {Ainsworth}, J. and {Bhagat}, J. and Couch, P. and Cruickshank, D. and {Delderfield}, M and Dunlop, I. and {Gamble}, M. and {Michaelides}, D. and {Owen}, S. and {Newman}, D. and {Sufi}, S. and {Goble}, C}, + title = "{Why linked data is not enough for scientists}", + journal = {Future Generation Computer Systems}, + year = 2013, + volume = 29, + pages = {599}, + doi = {10.1016/j.future.2011.08.004}, +} + + + + + +@ARTICLE{peng15, + author = {{Peng}, R.D.}, + title = {The reproducibility crisis in science: A statistical counterattack}, + journal = {Significance}, + year = 2015, + month = jun, + volume = 12, + pages = {30}, + doi = {10.1111/j.1740-9713.2015.00827.x}, +} + + + + + +@ARTICLE{katz14, + author = {Daniel S. Katz}, + title = {Transitive Credit as a Means to Address Social and Technological Concerns Stemming from Citation and Attribution of Digital Products}, + journal = {Journal of Open Research Software}, + year = {2014}, + volume = {2}, + pages = {e20}, + doi = {10.5334/jors.be}, +} + + + + + +@ARTICLE{herndon14, + author = {Thomas Herndon and Michael Ash and Robert Pollin}, + title = {Does high public debt consistently stifle economic growth? 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Jacobs and Ron Mengelers and Nico Rozendaal and Jim van Os and Machteld Marcelis}, + title = {The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements}, + journal = {PLoS ONE}, + volume = {7}, + year = {2012}, + pages = {e38234}, + doi = {10.1371/journal.pone.0038234}, +} + + + + + +@ARTICLE{pham12, + author = {Quan Pham and Tanu Malik and Ian Foster and Roberto {Di Lauro} and Raffaele Montella}, + title = {SOLE: Linking Research Papers with Science Objects}, + journal = {Provenance and Annotation of Data and Processes (IPAW)}, + year = {2012}, + pages = {203}, + doi = {10.1007/978-3-642-34222-6_16}, +} + + + + + +@ARTICLE{davison12, + author = {Andrew Davison}, + title = {Automated Capture of Experiment Context for Easier Reproducibility in Computational Research}, + journal = {Computing in Science \& Engineering}, + volume = {14}, + year = {2012}, + pages = {48}, + doi = {10.1109/MCSE.2012.41}, +} + + + + + +@ARTICLE{zhao12, + author = {Jun Zhao and Jose Manuel Gomez-Perez and Khalid Belhajjame and Graham Klyne and Esteban Garcia-Cuesta and Aleix Garrido and Kristina Hettne and Marco Roos and David {De Roure} and Carole Goble}, + title = {Why workflows break — Understanding and combating decay in Taverna workflows}, + journal = {IEEE 8th International Conference on E-Science}, + year = {2012}, + pages = {1}, + doi = {10.1109/eScience.2012.6404482}, +} + + + + +@ARTICLE{vangorp11, + author = {Pieter {Van Gorp} and Steffen Mazanek}, + title = {SHARE: a web portal for creating and sharing executable research}, + journal = {Procedia Computer Science}, + year = 2011, + volume = 4, + pages = {589}, + doi = {10.1016/j.procs.2011.04.062}, +} + + + + + +@ARTICLE{hinsen11, + author = {{Hinsen}, Konrad}, + title = {A data and code model for reproducible research and executable papers}, + journal = {Procedia Computer Science}, + year = 2011, + volume = 4, + pages = {579}, + doi = {10.1016/j.procs.2011.04.061}, +} + + + + + +@ARTICLE{limare11, + author = {Nicolas Limare and Jean-Michel Morel}, + title = {The IPOL Initiative: Publishing and Testing Algorithms on Line for +Reproducible Research in Image Processing}, + journal = {Procedia Computer Science}, + year = 2011, + volume = 4, + pages = {716}, + doi = {10.1016/j.procs.2011.04.075}, +} + + + + + +@ARTICLE{gavish11, + author = {Matan Gavish and David L. 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Tague}, + title = {UNIX Time-Sharing System: Forward}, + journal = {\doihref{https://archive.org/details/bstj57-6-1899/mode/2up}{Bell System Technical Journal}}, + year = {1978}, + volume = {57}, + pages = {6, ark:/13960/t0gt6xf72}, + doi = {}, +} + + + + + +@ARTICLE{anscombe73, + author = {{Anscombe}, F.J.}, + title = {Graphs in Statistical Analysis}, + journal = {The American Statistician}, + year = {1973}, + volume = {27}, + pages = {17}, + doi = {10.1080/00031305.1973.10478966}, +} + + + + + +@ARTICLE{roberts69, + author = {{Roberts}, K.V.}, + title = {The publication of scientific fortran programs}, + journal = {Computer Physics Communications}, + year = {1969}, + volume = {1}, + pages = {1}, + doi = {10.1016/0010-4655(69)90011-3}, +} diff --git a/tex/src/references.tex b/tex/src/references.tex deleted file mode 100644 index e19ec16..0000000 --- a/tex/src/references.tex +++ /dev/null @@ -1,1772 +0,0 @@ -@ARTICLE{clement19, - author = {Cl\'ement-Fontaine, M\'elanie and Di Cosmo, Roberto and Guerry, Bastien and MOREAU, Patrick and Pellegrini, Fran\c cois}, - 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