John Inglis is the co-founder of bioRxiv<\/em><\/a>, the preprint service for the life sciences based at Cold Spring Harbor Laboratory (CSHL).\u00a0 He is also the founding Executive Director and Publisher of Cold Spring Harbor Laboratory Press in New York, a not-for-profit publisher of journals, books, and online media in molecular and cellular biology. He spoke about bioRxiv<\/em> at three years old.<\/p>\n First a definition. John defined a preprint as \u201ca complete but unpublished manuscript yet to be certified by peer review\u201d. The definition is all about what it\u2019s not (i.e. peer-reviewed) but the key to preprints is all about the speed of dissemination of research results.<\/p>\n Preprints are currently distributed\u00a0under two models. In the first, a manuscript is submitted to a journal which makes it available as a reprint and then puts it into a peer review process. \u00a0The journal publishes those preprints that pass peer review. \u00a0The business model is that of the journal – i.e. it is funded by APCs (article processing charges). An example of this model is F1000Research<\/em>. In the second model manuscripts are submitted to a service dedicated to preprints. There is no fee and no peer review as part of the service. The service is supported by institutions and foundations. An example of this model is arXiv, supported by Cornell University and others. It gets 100,000 submissions p.a.<\/p>\n John explained that CSHL is committed to science communication so bioRxiv<\/em> was a natural extension to its activities.<\/p>\n Modelled on the arXiv, it is a dedicated, publisher-neutral service. The time seemed right to launch it in 2013 as there was a new enthusiasm for openness, a greater acceptance of digital resources and practices, and increased posting to the quantitative biology section on the arXiv showed that some biologists at least were ready for preprints.<\/p>\n In building bioRxiv<\/em>\u00a0the founders aimed for a simple, reliable submission system, and wanted to ensure that authors would have total control over their content (using a variety of licenses).<\/p>\n John Inglis is always careful to talk about\u00a0bioRxiv<\/em>\u00a0 in terms of ‘posting’ and ‘distribution’ rather than publishing. There is no peer review component of the service.<\/p>\n Manuscripts submitted to biorXiv<\/em> are allocated to one of 26 subject categories then checked for scope and format, and subjected to a plagiarism check. Some basic\u00a0checks are made to confirm that the submission is scientific in nature, is a report of research (rather than just a hypothesis) and\u00a0whether there are human health implications. In the latter case some further screening is needed.<\/p>\n If all checks are passed then a few hours later it will be posted on the website. The author can post revisions at any time.\u00a0biorXiv<\/em> gets information out there very quickly.<\/p>\n In its first three years bioRxiv<\/em> has posted 6200 manuscripts. \u00a0Disappointingly not many of them are confirmatory or contradictory results. \u00a025% of them have been revised at least once. There are more submissions in biology than in health.<\/p>\n Submissions come from 2900 institutions, across 82 countries. Submissions are increasing, currently standing at 450 per month.<\/p>\n Authors seem to like it. Transmission of research results is very rapid. They get useful\u00a0feedback and their preprints are read. 11% of the preprints receive comments and there have been many blogposts and tweets about bioRxiv<\/em> preprints – 93k tweets in the past 12 months.<\/p>\n Institutions and funders are starting to accept preprints as evidence of productivity. Both NIH and Wellcome are considering their policies on\u00a0accepting\u00a0preprints in grant applications. Rockefeller University has accepted preprints as part of a CV. EMBO accepts preprints on CVs for fellowship applications. Many journals will consider preprints for publication as papers, including\u00a0Nature<\/em>, Science<\/em> and Cell<\/em>.\u00a0\u00a0PLOS Genetics<\/em> has appointed editors specifically to search bioRxiv for potential manuscripts to publish in the journal. \u00a0CSHL has undertaken a good deal of advocacy with learned societies and publishers.\u00a0Several publishers now offer a\u00a0\u201csubmit your manuscript to bioRxiv<\/em>\u201d button as part of their\u00a0submission process.<\/p>\n It\u2019s time to start sending your\u00a0manuscripts to bioRxiv<\/a>!<\/p>\n Wellcome Open Research<\/strong><\/p>\n Robert Kiley is Head of Digital Services at the Wellcome Library and is currently acting as Wellcome’s Open Research Development Lead, responsible for developing a new open research strategy for the Wellcome Trust. Over the past decade Robert has played a leading role in the implementation of the Trust\u2019s open access policy and overseeing the development of the Europe PubMed Central repository. He is also the Trust\u2019s point of contact for eLife<\/em>.\u00a0He spoke about the Trust\u2019s latest publishing initiative: Wellcome Open Research<\/a>.<\/p>\n Just as with bioRxiv,<\/em>\u00a0the purpose of WOR is to make research communication faster, and more transparent.<\/p>\n WOR is fast, inclusive (you can publish everything – not just standard research narratives), open, reproducible (data is published alongside the article), transparent (it uses open peer review), and easy (the costs are met directly by Wellcome). The only drawback is that it is only available for outputs from Wellcome-funded researchers.<\/p>\n In early submissions, they have seen a range of publication types and a range of researchers from senior to junior. Submissions have come from a range of institutions.<\/p>\n The open peer review process allows for one of three decisions from each reviewer: approved; approved with reservations; not approved. If a preprint gets two ‘approved\u2019\u00a0decisions then it is indexed in PubMed and deposited in ePMC.\u00a0The is the same process used by F1000Research<\/em><\/a>, which provides publishing services for WOR.<\/p>\n Wellcome hope to attract a range of outputs from a range of researchers. They hope that other funders will in due course emulate their\u00a0initiative.<\/p>\n Open science\u00a0workflows<\/strong><\/p>\n Bianca Kramer and Jeroen Bosman are subject specialist librarians from Utrecht University who have considerable expertise in\u00a0scholarly communication and research workflow tools. Together they\u00a0led the global survey in Innovations in Scholarly Communication. Their talk,\u00a0Open Science workflows: Tools and practices to make your research more open, reproducible and efficient<\/em>\u00a0promised us a glimpse of the future.<\/p>\n One of the slides from Bianca Kramer and Jeroen Bosman’s talk<\/p><\/div>\n They started by showing some diagrams of research workflows – nice well-behaved cycles with boxes and arrows. But life is not so\u00a0simple. To make the workflow more\u00a0realistic Jeroen added cycles within cycles, put in some dead ends and some repeats. By the end it looked more like a game of snakes and ladders.<\/p>\n We then learnt a little about\u00a0the survey of tools that Bianca and Jeroen had made, and how they had categorised different tools as either:<\/p>\n Lest we become too focused on technology and tools though they emphasised that research workflows are less about tools<\/strong> and more about work practices and people<\/strong>.<\/p>\n Bianca and Jeroen are nothing if not\u00a0practical and they are happiest when considering reality instead of abstractions. \u00a0The\u00a0remainder of their presentation was in the form of a workshop, an endeavour to define a set of work practices\u00a0that\u00a0would constitute an open science\u00a0workflow, and tools\u00a0that would\u00a0support it.<\/p>\n The scale\u00a0of their ambition for the\u00a0workshop, and the amount of preparation they had\u00a0done, astounded me. There were three or stages to this exercise.<\/p>\n The final result of Bianca Kramer and Jeroen Bosman’s workshop<\/p><\/div>\n Each seat had a small paper button with the name of a research tool on it. \u00a0We were first invited to review the tool on our own seat, consider its usage and\u00a0application in open research, and then to discuss this with our neighbour. Around the periphery of the room a number of research practices had been arranged, grouped according to the different stages of the\u00a0research cycle. We were next asked to affix our paper button to an\u00a0appropriate research practice. Finally, we were each asked to move one of the research\u00a0practices that we considered to be part of an open science\u00a0workflow and place it in a new area\u00a0at the back of the room, together with any tool\u00a0we thought would help\u00a0with the\u00a0practice. \u00a0This back wall filled up with open research practices and tools.<\/p>\n As a participant it was quite challenging to grasp all of this, and a bit mind-boggling to assimilate everything that was on the back wall. I suspect that Bianca and Jeroen, who live and breathe this stuff, had a clearer picture than anyone else n the room. It certainly stimulated us to focus on the role that tools can play in open research practices, and on what an open research practice is. I liked the way too that the whole process of the workshop was open and transparent. \u00a0Everyone in the room had a sense of the task we\u2019d been set and of how the solution to it was emerging – we could see it on the walls. This really was a great model for open research.<\/p>\n Bianca and Jeroen’s mixture of openness and outreach is a great combination.<\/p>\n You can read their own account of the workshop <\/a>on their blog.<\/p>\n And that was Open Research London, Oct 2016. We’re planning the next one already – expect it to be Jan or Feb 2017. Hope to see you there! Find out more about Open Research London on the website<\/a>\u00a0or follow it on Twitter<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":" I was very relieved that the\u00a0Open Research London (ORL) meeting on 19 October 2016 went well. Jon Tennant, Ross Mounce and Liz Ing-Simmons established ORL\u00a0in Jan 2015 but it faded away after a couple of meetings. \u00a0I’d been thinking for … Continue reading ![\"\"](\"http:\/\/biorxiv.org\/sites\/default\/files\/bioRxiv_logo.png\"){kind=logo}
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