OPEN SCIENCE PUBLISHING: BEYOND OPEN ACCESS MAX PLANCK OPEN ACCESS AMBASSADORS CONFERENCE, 4 December 2014 Michaela Torkar Editorial Director, F1000 Research Ltd

PAINFUL PUBLISHING “…what is in the paper is fundamentally the responsibility of the authors, not of the reviewers. “ Nobel Laureate Robert Horvitz *from: J Biol 2009; 8: 1

PROBLEMS WITH TRADITIONAL PUBLISHING Extensive delays in publication Repeat refereeing of work for different journals Time and money wasted by authors restructuring manuscripts for different journals Anonymous pre-publication peer review conceals referee and editorial bias Lack of reproducibility of much published science Publication bias: much good science is never shared or published, e.g. negative/null results, small studies

PUBLISHING IS CHANGING – SOME EXAMPLES Saving peer reviewers time: journal cascade systems (e.g. Neuroscience Peer Review Consortium) Increasing transparency: open peer review (e.g. BMJ, BMC series) Focus on scientific validity, not perceived interest (e.g. PLOS ONE) Improved decision making: referee/editor discussions to reach a consensus view (e.g. eLife, Frontiers journals] Separating peer review from journals (e.g. PubPeer, Peerage of Science) Post-publication commenting (e.g. PubMed Commons, Publons) Preprint servers (e.g. PeerJ PrePrints, BiorXiv) Data journals (e.g. GigaScience, Scientific Data) Reproducibility (e.g. ScienceXchange) Open Science publishing: F1000Research; ScienceOpen

WHAT IS F1000RESEARCH? Scope: all research – big and small – across the life sciences and medicine Immediate publication Transparent refereeing No editorial bias All source data included Indexed in PubMed Open Science Publishing Platform

F1000RESEARCH IS PART OF FACULTY OF 1000 Faculty of 1000: > 5,000 expert scientists and clinical researchers globally (100 from Max-Planck Institutes) > 40 disciplines > 150,000 literature recommendations (F1000Prime) > 1,400 F1000 members are also F1000Research advisory board members

F1000RESEARCH: POST-PUBLICATION PEER REVIEW Author-driven process: F1000Research articles are published online after an in-house pre-refereeing check (copyedited and typeset) Peer review and revisions are carried out publicly Invited referees judge whether the work is scientifically sound Articles with sufficient positive referee reports are indexed in PubMed

TRANSPARENT PEER REVIEW Referee reports and author comments are visible to anyone... Referee names are visible Referee reports are citable with a DOI View count shows how many people read the referee report

REFEREE SCORES Approved Approved with reservations Not approved Articles with sufficient positive evaluations are indexed in PubMed, Scopus, and Embase Articles that haven’t yet reached this threshold can be revised and re-reviewed (no time limit) or Minimal requirements for indexing

VERSIONS: LIVING ARTICLES F1000Research articles can always be updated, even after being indexed. Amended papers have one of two possible labels: Authors amended their article in response to referee or community feedback Authors updated the article following minor developments (e.g. software updates) Especially useful for software tools, systematic reviews…: ensures article remains up-to-date; better reflects pace of research Each version is independently citable yet linked All versions indexed in PubMed, PubMed Central, etc (if article passed review) ‘Track’ option

VERSIONS Different versions of the article are tracked Referees can update the approval status Unique DOI for each version

ALL SOURCE DATA INCLUDED Data sharing improves reproducibility: “[W]e evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005– We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability.” All research articles published by F1000Research are accompanied by the source data on which the reported results are based Ioannidis, J. P. A. et al. Repeatability of published microarray gene expression analyses. Nature Genetics 41, 149–55 (2009)

EASY ACCESS TO DATA: DATA VIEWER WIDGETS Data sets within article are citable and downloadable. Data sets within article are citable and downloadable. DataVerse, Dryad etc are also developing such widgets

ASSESSMENT OF RESULTS: IN-ARTICLE DATA MANIPULATION

DYNAMIC FIGURES Simply data + code Creates opportunities to change the definition of a figure, and ultimately the journal article Colomb J and Brembs B. Sub-strains of Drosophila Canton-S differ markedly in their locomotor behavior [v1; ref status: indexed, F1000Research 2014, 3:176

VERSIONS: LIVING FIGURES Colomb J and Brembs B. Sub-strains of Drosophila Canton-S differ markedly in their locomotor behavior [v1; ref status: indexed, F1000Research 2014, 3:176 Other labs can attempt to replicate the study and then submit their data directly onto the figure in the article (with associated metadata). Provides a new way to show reproducibility attempts and could change fundamentally what an article is.

SUMMARY Open Access is increasingly solving the ‘access’ problem to new scientific discoveries, but several major problems with the traditional scientific publishing model persist Open Science publishing goes beyond open access: - insight gained during peer review is added value and part of the publication - data are included and methods described in detail, making it easier to reproduce findings - post-publication peer-review makes fast sharing of results possible and ‘versioning’ embraces opportunities offered by online publishing

THANK YOU! Michaela Torkar, PhD Editorial Director, F1000Research

ARTICLE TYPES ACCEPTED BY F1000RESEARCH Research ArticlesData Notes Opinion ArticlesSoftware Tools Reviews Research Notes Study ProtocolsCorrespondence Systematic ReviewsCase Reports Clinical Practice ArticlesObservation Articles Method Articles Single-Figure Posts

DETAILED PROTOCOLS FOR REPRODUCIBILITY Authors encouraged to link to specific reagents used (Resource Identification Initiative; Analysis code included and archived through Github and Zenodo Launched antibody validation Guest Editors Andrew Chalmers, Co-founder of CiteAb, University of Bath, UK Matt Helsby, Development Manager, CiteAb, Bath, UK Mei Leung, Peprotech EC Ltd, London, UK