draft.bib

@article{Munaf:2017,
  doi =          {10.1038/s41562-016-0021},
  url =          {https://doi.org/10.1038/s41562-016-0021},
  year =         2017,
  month =        {1},
  publisher =    {Springer Nature},
  volume =       1,
  number =       1,
  pages =        0021,
  author =       {Marcus R. Munaf{\`{o}} and Brian A. Nosek and Dorothy
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                  D. Chambers and Nathalie Percie du Sert and Uri Simonsohn and
                  Eric-Jan Wagenmakers and Jennifer J. Ware and John
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  title =        {A manifesto for reproducible science},
  journal =      {Nature Human Behaviour}
}

@article{Baker:2016,
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  volume =       533,
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  pages =        {452--454},
  author =       {Monya Baker},
  title =        {1, 500 scientists lift the lid on reproducibility},
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@ARTICLE{Smith:2017,
  author =       {{Smith}, A.~M and {E Niemeyer}, K. and {Katz}, D.~S and
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  title =        "{Journal of Open Source Software (JOSS): design and
                  first-year review}",
  journal =      {ArXiv e-prints},
  archivePrefix ="arXiv",
  eprint =       {1707.02264},
  primaryClass = "cs.DL",
  keywords =     {Computer Science - Digital Libraries, Computer Science -
                  Software Engineering},
  year =         2017,
  month =        7,
  adsurl =       {http://adsabs.harvard.edu/abs/2017arXiv170702264S},
}

@article{Manninen:2017,
  doi =          {10.3389/fninf.2017.00011},
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  year =         2017,
  month =        2,
  publisher =    {Frontiers Media {SA}},
  volume =       11,
  author =       {Tiina Manninen and Riikka Havela and Marja-Leena Linne},
  title =        {Reproducibility and Comparability of Computational Models for
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  journal =      {Frontiers in Neuroinformatics}
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@article{coudert:2017,
  author =       {Coudert, François-Xavier},
  title =        {Reproducible Research in Computational Chemistry of
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  pages =        {2615-2617},
  year =         2017,
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@article{donoho:2009,
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  doi =          {10.1109/MCSE.2009.15},
  ISSN =         {1521-9615},
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@misc{Mesnard:2016,
  Author =       {Mesnard, Olivier and Barba, Lorena A.},
  Date-Added =   {2016-07-02 20:29:25 +0000},
  Date-Modified ={2016-10-08 22:11:23 +0000},
  Howpublished = {Preprint on
                  \href{http://arxiv.org/abs/1605.04339}{arXiv:1605.04339}},
  Note =         {Accepted in \emph{Comput.\ Sci.\ Eng.}},
  Title =        {Reproducible and replicable {CFD}: it's harder than you
                  think},
  Year =         2016
}

@article{perkel:2016,
  doi =          {10.1038/538127a},
  year =         2016,
  volume =       538,
  number =       7623,
  pages =        {127--128},
  author =       {Jeffrey Perkel},
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@Article{nordlie:2009,
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@online{wilson:2016,
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  title       = {Software Carpentry: Lessons Learned},
  version     = {2},
  date        = {2016-01-28},
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  doi         = {10.12688/f1000research.3-62.v2}
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@Article{sandve:2013,
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@Article{halchenko:2015,
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  year =         2015,
  doi =          {10.1186/s13742-015-0072-7}
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@Article{janz:2015,
  author =       {Nicole Janz},
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  year =         2015,
  doi =          {10.1111/insp.12104}
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@Article{hinsen:2015,
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  number =       3,
  year =         2015,
  doi =          {10.1109/MCSE.2015.64},
}

@Inbook{crook:2013,
  author =       {Crook, Sharon M.  and Davison, Andrew P.  and Plesser, Hans
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  editor =       {Bower, M. James},
  chapter =      {Learning from the Past: Approaches for Reproducibility in
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  title =        {20 Years of Computational Neuroscience},
  year =         2013,
  publisher =    "Springer New York",
  address =      "New York, NY",
  pages =        "73--102",
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@Article{wilson:2014,
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@Article{topalidou:2015b,
  author =       {Meropi Topalidou and Nicolas P. Rougier},
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  journal =      {ReScience},
  year =         2015,
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@Article{stachelek:2016,
  author =       {Joseph Stachelek},
  title =        {{[Re]} Least-cost modelling on irregular landscape graphs},
  journal =      {ReScience},
  year =         2016,
  volume =       2,
  number =       1,
  doi =          {10.5281/zenodo.45852},
  url =          {https://github.com/ReScience-Archives/Stachelek-2016/}
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@Article{viejo:2016,
  author =       {Guillaume Viejo and Benoît Girard and Mehdi Khamassi},
  title =        {{[Re]} Speed/accuracy trade-off between the habitual and the
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  journal =      {ReScience},
  year =         2016,
  volume =       2,
  number =       1,
  doi =          {10.5281/zenodo.27944},
  url =
                  {https://github.com/ReScience-Archives/Viejo-Girard-Khamassi-2016}
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@Article{topalidou:2015a,
  author =       {Meropi Topalidou and Arthur Leblois and Thomas Boraud and
                  Nicolas P. Rougier},
  title =        {A Long Journey into Reproducible Computational Neuroscience},
  journal =      {Frontiers in Computational Neuroscience},
  year =         2015,
  volume =       9,
  number =       28,
  doi =          {10.3389/fncom.2015.00030},
}

@InProceedings{collberg:2015,
  author =       {Christian Collberg and Todd Proebsting and Alex M Warren},
  title =        {Repeatability and Benefaction in Computer Systems Research —
                  A Study and a Modest Proposal},
  year =         2015,
}

@InProceedings{collberg:2014,
  author =       {Christian Collberg and Todd Proebsting and Gina Moraila and
                  Akash Shankaran and Zuoming Shi and Alex M Warren},
  title =        {Measuring Reproducibility in Computer Systems Research},
  year =         2014,
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@Article{iqbal:2016,
  author =       {Shareen A. Iqbal and Joshua D. Wallach and Muin J. Khoury and
                  Sheri D. Schully and John P. A. Ioannidis},
  title =        {Reproducible Research Practices and Transparency across the
                  Biomedical Literature},
  journal =      {PLoS Biology},
  year =         2016,
  volume =       14,
  number =       1,
  doi =          {10.1371/journal.pbio.1002333},
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@Article{nosek:2015,
  author =       {{Open Science Collaboration}},
  title =        {Estimating the reproducibility of psychological science},
  journal =      {Science},
  year =         2015,
  volume =       349,
  doi =          {10.1126/science.aac4716},
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@Article{ioannidis:2005,
  author =       {John P. A. Ioannidis},
  title =        {Why Most Published Research Findings Are False},
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  doi =          {10.1371/journal.pmed.0020124},
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@Book{kitzes:2017,
  address =      {Oakland, CA, USA},
  title =        {The {{Practice}} of {{Reproducible Research}}: {{Case
                  Studies}} and {{Lessons}} from the {{Data}}-{{Intensive
                  Sciences}}},
  language =     {English},
  timestamp =    {2017-03-24T12:54:18Z},
  publisher =    {{University of California Press}},
  editor =       {Kitzes, Justin and Turek, Daniel and Deniz, Fatma},
  year =         2017,
  keywords =     {reproducible research},
}

@InProceedings{murta:2015,
  title =        {{noWorkflow}: Capturing and Analyzing Provenance of Scripts},
  author =       {Leonardo Murta and Vanessa Braganholo and Fernando Chirigati
                  and David Koop and Juliana Freire},
  booktitle =    {Provenance and Annotation of Data and Processes},
  volume =       8628,
  series =       {Lecture Notes in Computer Science},
  pages =        {71--83},
  publisher =    {Springer International Publishing},
  year =         2015
}

@InProceedings{guo:2011,
  author =       {Philip J. Guo and Dawson Engler},
  title =        {{CDE}: Using System Call Interposition to Automatically
                  Create Portable Software Packages},
  booktitle =    {Proceedings of the 2011 USENIX Annual Technical Conference},
  series =       {USENIX'11},
  year =         2011,
  location =     {Portland, OR},
  url =          {http://dl.acm.org/citation.cfm?id=2002181.2002202},
  acmid =        2002202,
  publisher =    {USENIX Association},
  address =      {Berkeley, CA, USA}
}

@Article{davison:2012,
  author =       {Andrew P. Davison},
  doi =          {10.1109/MCSE.2012.41},
  journal =      {Computing in Science and Engineering},
  month =        7,
  pages =        {48--56},
  title =        {Automated capture of experiment context for easier
                  reproducibility in computational research},
  volume =       14,
  year =         2012
}

@InProceedings{Courtes:2015,
  author =       {Ludovic Courtès and Ricardo Wurmus},
  title =        {Reproducible and User-Controlled Software Environments in
                  {HPC} with {Guix}},
  doi =          {10.1007/978-3-319-27308-2_47},
  booktitle =    {{Euro-Par} 2015: {P}arallel {P}rocessing {W}orkshops},
  series =       {Lecture Notes in Computer Science, vol 9523},
  editor =       {Sascha Hunold and Alexandru Costan and Domingo Giménez and Alexandru Iosup and Laura Ricci and María Engracia Gómez Requena and Vittorio Scarano and Ana Lucia Varbanescu and Stephen L. Scott and Stefan Lankes and Josef Weidendorfer and Michael Alexander},
  year =         {2015},
  publisher =    {Springer, Cham},
}

@misc{conda,
  author = {{Anaconda Inc.}},
  title = {Conda},
  year = {2017},
  Howpublished = {\url{https://conda.io/}},
}

@misc{docker,
  author = {{Docker Inc.}},
  title = {Docker},
  year = {2017},
  Howpublished = {\url{https://www.docker.com/}},
}

@book{JVM,
author = {Lindholm, Tim and Yellin, Frank},
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year = {1999},
isbn = {0201432943},
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}