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

Barba, Lorena A. ‘Terminologies for Reproducible Research’. ArXiv:1802.03311 [Cs], 9 February 2018. 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

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

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

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

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

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

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

Crosas, Mercè. ‘Joint Declaration of Data Citation Principles - FINAL’. FORCE11, 30 October 2013. 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

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

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

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

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

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

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

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

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

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

Luther J. The Stars Are Aligning for Preprints. The Scholarly Kitchen. 2017. [December 2018]. scholarlykitchen.sspnet.org

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

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

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

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

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

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

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

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

Picarra, Mafalda, and Alma Swan. ‘Monitoring Compliance with Open Access Policies’, December 2015. pasteur4oa.eu

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

‘Point of View: How Open Science Helps Researchers Succeed’, n.d. 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

Priem, Jason, D. Taraborelli, P. Groth, C. Neylon (2010). Altmetrics: A manifesto, 26 October 2010. 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

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

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

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

Scopatz, Anthony, and Kathryn D. Huff. Effective Computation in Physics: Field Guide to Research in Python. Sebastopol, CA: O’Reilly Media, 2015. PDF.pdf)

Sewell, Claire. ‘Research Data Management: Activity Cards’, 23 November 2017. 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

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

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

Soergel, David A. W. ‘Rampant Software Errors May Undermine Scientific Results [Version 2; Referees: 2 Approved]’. F1000Research 3 (2015): 303. 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

Stodden, Victoria. ‘The Scientific Method in Practice: Reproducibility in the Computational Sciences’. SSRN Electronic Journal, 2010. 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

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

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

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)

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

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

Wilson, Greg. ‘Software Carpentry: Lessons Learned [Version 2; Referees: 3 Approved]’. F1000Research 3 (2016): 62. doi.org/10/gc5sjr

Wilson, Greg, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, and Tracy K. Teal. ‘Good Enough Practices in Scientific Computing’. Edited by Francis Ouellette. PLOS Computational Biology 13, no. 6 (22 June 2017): e1005510. doi.org/10/gbkbwp

Wilson, Paul M., Mark Petticrew, Mike W. Calnan, and Irwin Nazareth. ‘Disseminating Research Findings: What Should Researchers Do? A Systematic Scoping Review of Conceptual Frameworks’. Implementation Science 5 (22 November 2010): 91. https://doi.org/10/cprfmr.

Wilson, Paul M, Mark Petticrew, Mike W Calnan, and Irwin Nazareth. ‘Disseminating Research Findings: What Should Researchers Do? A Systematic Scoping Review of Conceptual Frameworks’. Implementation Science 5, no. 1 (December 2010). https://doi.org/10/cprfmr.