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      The Case for Open Preprints in Biology

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          Abstract

          Biologists should submit their preprints to open servers, a practice common in mathematics and physics, to open and accelerate the scientific process.

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          Git can facilitate greater reproducibility and increased transparency in science

          Karthik Ram (2013)
          Background Reproducibility is the hallmark of good science. Maintaining a high degree of transparency in scientific reporting is essential not just for gaining trust and credibility within the scientific community but also for facilitating the development of new ideas. Sharing data and computer code associated with publications is becoming increasingly common, motivated partly in response to data deposition requirements from journals and mandates from funders. Despite this increase in transparency, it is still difficult to reproduce or build upon the findings of most scientific publications without access to a more complete workflow. Findings Version control systems (VCS), which have long been used to maintain code repositories in the software industry, are now finding new applications in science. One such open source VCS, Git, provides a lightweight yet robust framework that is ideal for managing the full suite of research outputs such as datasets, statistical code, figures, lab notes, and manuscripts. For individual researchers, Git provides a powerful way to track and compare versions, retrace errors, explore new approaches in a structured manner, while maintaining a full audit trail. For larger collaborative efforts, Git and Git hosting services make it possible for everyone to work asynchronously and merge their contributions at any time, all the while maintaining a complete authorship trail. In this paper I provide an overview of Git along with use-cases that highlight how this tool can be leveraged to make science more reproducible and transparent, foster new collaborations, and support novel uses.
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            ArXiv at 20.

            Paul Ginsparg (2011)
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              Academia's obsession with quantity.

              Joern Fischer, Euan G. Ritchie, Jan Hanspach (2012)
              Article 0 comments Cited 37 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): PLoS Biol
                Journal ID (iso-abbrev): PLoS Biol
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosbiol
                Title: PLoS Biology
                Publisher: Public Library of Science (San Francisco, USA )
                ISSN (Print): 1544-9173
                ISSN (Electronic): 1545-7885
                Publication date Collection: May 2013
                Publication date (Print): May 2013
                Publication date (Electronic): 14 May 2013
                Volume: 11
                Issue: 5
                Electronic Location Identifier: e1001563
                Affiliations
                [1 ]Theoretical Ecosystem Ecology laboratory, Université du Québec à Rimouski, Rimouski, Quebec, Canada
                [2 ]Quebec Center for Biodiversity Science, McGill University, Montreal, Quebec, Canada
                [3 ]Department of Biology, Utah State University, Logan, Utah, United States of America
                [4 ]Ecology, Evolution and Organismic Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
                [5 ]Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America
                [6 ]International Network for Next-Generation Ecology
                Author notes

                I have read the journal's policy and have the following conflicts: Ethan White is an academic editor for PeerJ and Timothée Poisot is a member of the figshare advisors program.

                The Perspective section provides experts with a forum to comment on topical or controversial issues of broad interest.

                Article
                Publisher ID: PBIOLOGY-D-12-04204
                DOI: 10.1371/journal.pbio.1001563
                PMC ID: 3653830
                PubMed ID: 23690752
                SO-VID: 0c4b9e98-df08-480c-a6ee-c9c53b5b9059
                Copyright statement: Copyright @ 2013
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Page count
                Pages: 5
                Funding
                PDP is supported by an Alexander Graham Bell scholarship from the National Sciences and Engineering Council of Canada ( http://www.nserc-crsng.gc.ca/). EPW is supported by a CAREER Award from the National Science Foundation (DEB-0953694, http://www.nsf.gov/). JJA is supported by NSF DEB-0614166 and NSF DEB-0919018 ( http://www.nsf.gov/). TP is supported by a FQRNT-MELS post-doctoral scholarship ( http://www.fqrnt.gouv.qc.ca/). KR is supported by NSF DEB-1021553 ( http://www.nsf.gov/). DG is funded by a Discovery Grant from the National Sciences and Engineering Council of Canada and by the Canada Research Chair program ( http://www.nserc-crsng.gc.ca/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Perspective
                Subject: Biology

                ScienceOpen disciplines: Life sciences
                Data availability:
                ScienceOpen disciplines: Life sciences

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