# References

### ![](https://3600949599-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-L9tXFxt2NTQml3C-9jM%2F-LFretQnjqaet1JlATMG%2F-LFrezOb5WPPuJQA53pu%2Fmagnifying_glass.png?generation=1529942377935191\&alt=media)

### References

> *Note:* This bibliography is collaboratively maintained by the *Open Science Training Handbook* community at <https://www.zotero.org/groups/2114699/open\\_science\\_book/items/collectionKey/XIUNJBME>.

Balasegaram, Manica, Peter Kolb, John McKew, Jaykumar Menon, Piero Olliaro, Tomasz Sablinski, Zakir Thomas, Matthew H. Todd, Els Torreele, and John Wilbanks. ‘An Open Source Pharma Roadmap’. *PLOS Medicine* 14, no. 4 (18 April 2017): e1002276. [doi.org/10/gbrb4b](https://doi.org/10/gbrb4b)

Barba, Lorena A. ‘Terminologies for Reproducible Research’. *ArXiv:1802.03311 \[Cs]*, 9 February 2018. [arxiv.org/abs/1802.03311](http://arxiv.org/abs/1802.03311)

Barnes, Nick. ‘Publish Your Computer Code: It Is Good Enough’. *Nature* 467, no. 7317 (14 October 2010): 753–753. [doi.org/10/cj8t6n](https://doi.org/10/cj8t6n)

Björk, Bo-Christer, Patrik Welling, Mikael Laakso, Peter Majlender, Turid Hedlund, and Guðni Guðnason. ‘Open Access to the Scientific Journal Literature: Situation 2009’. *PLOS ONE* 5, no. 6 (23 June 2010): e11273. [doi.org/10/csjg36](https://doi.org/10/csjg36)

Blackmore, Paul, and Camille B. Kandiko. ‘Motivation in Academic Life: A Prestige Economy’. *Research in Post-Compulsory Education* 16, no. 4 (1 December 2011): 399–411. [doi.org/10/fqrkft](https://doi.org/10/fqrkft)

Buckheit, Jonathan B., and David L. Donoho. ‘WaveLab and Reproducible Research’. In *Wavelets and Statistics*, edited by Anestis Antoniadis and Georges Oppenheim, 103:55–81. New York, NY: Springer New York, 1995. [doi.org/10.1007/978-1-4612-2544-7\_5](https://doi.org/10.1007/978-1-4612-2544-7_5)

Candela, Leonardo, Donatella Castelli, and Pasquale Pagano (2013). Virtual Research Environments: An Overview and a Research Agenda. Data Science Journal. 12, pp.GRDI75–GRDI81. [doi.org/10.2481/dsj.GRDI-013](https://doi.org/10.2481/dsj.GRDI-013)

Christodoulou, Michail, Stefanos Kachrilas, Ahmed Dina, Andreas Bourdoumis, Junaid Masood, Noor Buchholz, and Athanasios Papatsoris. ‘How to Conduct a Successful Workshop: The Trainees’ Perspective’. *Arab Journal of Urology*, Teaching and Training in Urology, 12, no. 1 (1 March 2014): 12–14. [doi.org/10/gcbmkm](https://doi.org/10/gcbmkm)

Cobb, Matthew. ‘The Prehistory of Biology Preprints: A Forgotten Experiment from the 1960s’. PeerJ Inc., 22 August 2017. [doi.org/10.7287/peerj.preprints.3174v1](https://doi.org/10.7287/peerj.preprints.3174v1)

Crosas, Mercè. ‘Joint Declaration of Data Citation Principles - FINAL’. FORCE11, 30 October 2013. [force11.org/datacitationprinciples](https://www.force11.org/datacitationprinciples)

Dryden, Michael D. M., Ryan Fobel, Christian Fobel, and Aaron R. Wheeler. ‘Upon the Shoulders of Giants: Open-Source Hardware and Software in Analytical Chemistry’. *Analytical Chemistry* 89, no. 8 (18 April 2017): 4330–38. [doi.org/10/gc5sjm](https://doi.org/10/gc5sjm)

Goodman, Steven N., Daniele Fanelli, and John P. A. Ioannidis. ‘What Does Research Reproducibility Mean?’ *Science Translational Medicine* 8, no. 341 (1 June 2016): 341ps12-341ps12. [doi.org/10/gc5sjs](https://doi.org/10/gc5sjs)

Haklay, Muki. ‘Citizen Science and Policy: A European Perspective’. *Washington, DC*, February 2015, 76.

Ince, Darrel C., Leslie Hatton, and John Graham-Cumming. ‘The Case for Open Computer Programs’. *Nature* 482, no. 7386 (22 February 2012): 485–88. [doi.org/10/hqg](https://doi.org/10/hqg)

Iskoujina, Zilia, and Joanne Roberts. ‘Knowledge Sharing in Open Source Software Communities: Motivations and Management’. *Journal of Knowledge Management* 19, no. 4 (13 July 2015): 791–813. [doi.org/10/f7htj8](https://doi.org/10/f7htj8)

Jahn, Najko, and Marco Tullney. ‘A Study of Institutional Spending on Open Access Publication Fees in Germany’. *PeerJ* 4 (9 August 2016): e2323. [doi.org/10/bnqm](https://doi.org/10/bnqm)

Jiménez, Rafael C., Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, et al. ‘Four Simple Recommendations to Encourage Best Practices in Research Software \[Version 1; Referees: 3 Approved]’. *F1000Research* 6 (13 June 2017): 876. [doi.org/10/gbp2wh](https://doi.org/10/gbp2wh)

Knowles, Malcolm S, Elwood F Holton, and Richard A Swanson. *The Adult Learner: The Definitive Classic in Adult Education and Human Resource Development.* Oxford: Butterworth-Heinemann, 2011.

Kreutzer, Till. ‘Validity of the Creative Commons Zero 1.0 Universal Public Do-Main Dedication and Its Usability for Bibliographic Metadata from the Perspective of German Copyright Law’, 2011. [PDF](https://www.rd-alliance.org/sites/default/files/cc0-analysis-kreuzer.pdf)

LEARN. *LEARN Toolkit of Best Practice for Research Data Management*. Edited by LEARN. Leaders Activating Research Networks (LEARN), 2017. [dx.doi.org/10.14324/000.learn.00](http://dx.doi.org/10.14324/000.learn.00)

Lionelli, Sabina. ‘Implementing Open Science: Strategies, Experiences and Models’. Thematic Report. Mutual Learning Exercise: Open Science – Altmetrics and Rewards. European Commission, n.d. [rio.jrc.ec.europa.eu](https://rio.jrc.ec.europa.eu/en/library/mle-open-science-altmetrics-and-rewards-%E2%80%93-implementing-open-science-strategies-experiences)

Lowndes, Julia S. Stewart, Benjamin D. Best, Courtney Scarborough, Jamie C. Afflerbach, Melanie R. Frazier, Casey C. O’Hara, Ning Jiang, and Benjamin S. Halpern. ‘Our Path to Better Science in Less Time Using Open Data Science Tools’. *Nature Ecology & Evolution* 1, no. 6 (23 May 2017): 0160. [doi.org/10/gc4jb3](https://doi.org/10/gc4jb3)

Luther J. The Stars Are Aligning for Preprints. The Scholarly Kitchen. 2017. \[December 2018]. [scholarlykitchen.sspnet.org](https://scholarlykitchen.sspnet.org/2017/04/18/stars-aligning-preprints)

Martinez-Torres, M.R., and M.C. Diaz-Fernandez. ‘Current Issues and Research Trends on Open-Source Software Communities’. *Technology Analysis & Strategic Management* 26, no. 1 (2 January 2014): 55–68. [doi.org/10/gc5sjj](https://doi.org/10/gc5sjj)

McKiernan, Erin C, Philip E Bourne, C Titus Brown, Stuart Buck, Amye Kenall, Jennifer Lin, Damon McDougall, et al. ‘How Open Science Helps Researchers Succeed’. *ELife* 5 (7 July 2016). [doi.org/10/gbqsng](https://doi.org/10/gbqsng)

McQuilton, Peter, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Milo Thurston, Allyson Lister, Eamonn Maguire, and Susanna-Assunta Sansone. ‘BioSharing: Curated and Crowd-Sourced Metadata Standards, Databases and Data Policies in the Life Sciences’. *Database* 2016 (1 January 2016). [doi.org/10/f8wzmc](https://doi.org/10/f8wzmc)

Morin, A., J. Urban, P. D. Adams, I. Foster, A. Sali, D. Baker, and P. Sliz. ‘Shining Light into Black Boxes’. *Science* 336, no. 6078 (13 April 2012): 159–60. [doi.org/10/m5t](https://doi.org/10/m5t)

Munafò, Marcus R., Brian A. Nosek, Dorothy V. M. Bishop, Katherine S. Button, Christopher D. Chambers, Nathalie Percie du Sert, Uri Simonsohn, Eric-Jan Wagenmakers, Jennifer J. Ware, and John P. A. Ioannidis. ‘A Manifesto for Reproducible Science’. *Nature Human Behaviour* 1, no. 1 (January 2017): 0021. [doi.org/10/bw28](https://doi.org/10/bw28)

Niemeyer, Kyle E., Arfon M. Smith, and Daniel S. Katz. ‘The Challenge and Promise of Software Citation for Credit, Identification, Discovery, and Reuse’. *Journal of Data and Information Quality* 7, no. 4 (6 October 2016): 1–5. [doi.org/10/gc5sjd](https://doi.org/10/gc5sjd)

Oishi, Jeffrey S., Benjamin P. Brown, Keaton J. Burns, Daniel Lecoanet, and Geoffrey M. Vasil. ‘Perspectives on Reproducibility and Sustainability of Open-Source Scientific Software from Seven Years of the Dedalus Project’. arXiv:1801.08200 \[astro-ph.IM], 24 January 2018. [arxiv.org/abs/1801.08200](http://arxiv.org/abs/1801.08200)

Pavelin, Katrina, Sangya Pundir, and Jennifer A. Cham. ‘Ten Simple Rules for Running Interactive Workshops’. *PLOS Computational Biology* 10, no. 2 (27 February 2014): e1003485. [doi.org/10/gc5sjq](https://doi.org/10/gc5sjq)

Picarra, Mafalda, and Alma Swan. ‘Monitoring Compliance with Open Access Policies’, December 2015. [pasteur4oa.eu](http://pasteur4oa.eu/resources/162#.WoL40Z_iZhF)

Piwowar, Heather, Jason Priem, Vincent Larivière, Juan Pablo Alperin, Lisa Matthias, Bree Norlander, Ashley Farley, Jevin West, and Stefanie Haustein. ‘The State of OA: A Large-Scale Analysis of the Prevalence and Impact of Open Access Articles’. *PeerJ* 6 (13 February 2018): e4375. [doi.org/10/ckh5](https://doi.org/10/ckh5)

‘Point of View: How Open Science Helps Researchers Succeed’, n.d. [doi.org/10/gc5sjc](https://doi.org/10/gc5sjc)

Pontika, Nancy, Petr Knoth, Matteo Cancellieri, and Samuel Pearce. ‘Fostering Open Science to Research Using a Taxonomy and an ELearning Portal’. In *Proceedings of the 15th International Conference on Knowledge Technologies and Data-Driven Business*, 11:1–11:8. I-KNOW ’15. New York, NY, USA: ACM, 2015. [doi.org/10.1145/2809563.2809571](https://doi.org/10.1145/2809563.2809571)

Priem, Jason, D. Taraborelli, P. Groth, C. Neylon (2010). Altmetrics: A manifesto, 26 October 2010. [altmetrics.org/manifesto](http://altmetrics.org/manifesto)

Prins, Pjotr, Joep de Ligt, Artem Tarasov, Ritsert C Jansen, Edwin Cuppen, and Philip E Bourne. ‘Toward Effective Software Solutions for Big Biology’. *Nature Biotechnology* 33, no. 7 (July 2015): 686–87. [doi.org/10/f3mn4p](https://doi.org/10/f3mn4p)

Ross-Hellauer, Tony. ‘What Is Open Peer Review? A Systematic Review \[Version 2; Referees: 4 Approved]’. *F1000Research* 6 (31 August 2017): 588. [doi.org/10/gc5sjh](https://doi.org/10/gc5sjh)

Sandve, Geir Kjetil, Anton Nekrutenko, James Taylor, and Eivind Hovig. ‘Ten Simple Rules for Reproducible Computational Research’. Edited by Philip E. Bourne. *PLoS Computational Biology* 9, no. 10 (24 October 2013): e1003285. [doi.org/10/pjb](https://doi.org/10/pjb)

Scacchi, Walt. ‘The Future of Research in Free/Open Source Software Development’. In *Proceedings of the FSE/SDP Workshop on Future of Software Engineering Research - FoSER’10*, 315. Santa Fe, New Mexico, USA: ACM Press, 2010. [doi.org/10.1145/1882362.1882427](https://doi.org/10.1145/1882362.1882427)

Scopatz, Anthony, and Kathryn D. Huff. *Effective Computation in Physics: Field Guide to Research in Python*. Sebastopol, CA: O’Reilly Media, 2015. [PDF](http://lilith.fisica.ufmg.br/~dickman/transfers/comp/textos/Effective%20Computation%20in%20Physics%20\(Python\).pdf)

Sewell, Claire. ‘Research Data Management: Activity Cards’, 23 November 2017. [doi.org/10.17863/CAM.10074](https://doi.org/10.17863/CAM.10074)

Shamir, Lior, John F. Wallin, Alice Allen, Bruce Berriman, Peter Teuben, Robert J. Nemiroff, Jessica Mink, Robert J. Hanisch, and Kimberly DuPrie. ‘Practices in Source Code Sharing in Astrophysics’. *Astronomy and Computing* 1 (February 2013): 54–58. [doi.org/10/gc5sjk](https://doi.org/10/gc5sjk)

Smith, Arfon M., Daniel S. Katz, Kyle E. Niemeyer, and FORCE11 Software Citation Working Group. ‘Software Citation Principles’. *PeerJ Computer Science* 2 (19 September 2016): e86. [doi.org/10/bw3g](https://doi.org/10/bw3g)

Smith, Arfon M., Kyle E. Niemeyer, Daniel S. Katz, Lorena A. Barba, George Githinji, Melissa Gymrek, Kathryn D. Huff, et al. ‘Journal of Open Source Software (JOSS): Design and First-Year Review’. *PeerJ Computer Science* 4 (12 February 2018): e147. [doi.org/10/gc5sjf](https://doi.org/10/gc5sjf)

Soergel, David A. W. ‘Rampant Software Errors May Undermine Scientific Results \[Version 2; Referees: 2 Approved]’. *F1000Research* 3 (2015): 303. [doi.org/10/gc5sjg](https://doi.org/10/gc5sjg)

Steinmacher, Igor, Marco Aurelio Graciotto Silva, Marco Aurelio Gerosa, and David F. Redmiles. ‘A Systematic Literature Review on the Barriers Faced by Newcomers to Open Source Software Projects’. *Information and Software Technology* 59 (March 2015): 67–85. [doi.org/10/f6z643](https://doi.org/10/f6z643)

Stodden, Victoria. ‘The Scientific Method in Practice: Reproducibility in the Computational Sciences’. *SSRN Electronic Journal*, 2010. [doi.org/10/fzmph2](https://doi.org/10/fzmph2)

Union, Publications Office of the European. ‘Evaluation of Research Careers Fully Acknowledging Open Science Practices : Rewards, Incentives and/or Recognition for Researchers Practicing Open Science.’ Website, 14 November 2017. [publications.europa.eu](https://publications.europa.eu/en/publication-detail/-/publication/47a3a330-c9cb-11e7-8e69-01aa75ed71a1/language-en)

Vandewalle, Patrick. ‘Code Sharing Is Associated with Research Impact in Image Processing’. *Computing in Science & Engineering* 14, no. 4 (July 2012): 42–47. [doi.org/10/gc5sjp](https://doi.org/10/gc5sjp)

Vicente-Saez, Ruben, and Clara Martinez-Fuentes. ‘Open Science Now: A Systematic Literature Review for an Integrated Definition’. *Journal of Business Research*, January 2018. [doi.org/10/gc5sjb](https://doi.org/10/gc5sjb)

Wicherts, Jelte M., Coosje L. S. Veldkamp, Hilde E. M. Augusteijn, Marjan Bakker, Robbie C. M. van Aert, and Marcel A. L. M. van Assen. ‘Degrees of Freedom in Planning, Running, Analyzing, and Reporting Psychological Studies: A Checklist to Avoid p-Hacking’. *Frontiers in Psychology* 7 (2016): 1832. [doi.org/10/gc5sjn)](https://doi.org/10/gc5sjn)

Wilkinson, Mark D., Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al. ‘The FAIR Guiding Principles for Scientific Data Management and Stewardship’. *Scientific Data*, 15 March 2016. [doi.org/10/bdd4](https://doi.org/10/bdd4)

Wilsdon, James, Judit Bar-Ilan, Robert Frodeman, Elisabeth Lex, Isabella Peters, Paul Wouters (2017). Next-generation metrics: Responsible metrics and evaluation for open science. Directorate-General for Research and Innovation.European Commission Expert Group on Altmetrics. [PDF](https://ec.europa.eu/research/openscience/pdf/report.pdf)

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