Jekyll2018-02-17T19:53:37+00:00https://lgatto.github.io/~/Laurent Gatto's online homeLaurent GattoEngaging Researchers in Good Data Management2017-12-15T00:00:00+00:002017-12-15T00:00:00+00:00https://lgatto.github.io/engage-RDM-2017<p>Last months, I participated in the <em>Engaging Researchers in Good Data Management</em> meeting organised by the Office of Scholarly Communication, SPARC and Jisc (details <a href="https://www.eventbrite.co.uk/e/engaging-researchers-in-good-data-management-registration-37769325068">here</a>). This post and additional feedback are also available in <a href="https://unlockingresearch-blog.lib.cam.ac.uk/?p=1833">Engaging Researchers with Good Data Management: Perspectives from Engaged Individuals</a> on the University of Cambridge’s Office of Scholarly Communication blog.</p> <p>As a researcher who cherishes good and reproducible data analysis, I naturally view good data management as essential. I have been involved in research data management activities for a long time, acting as a local <a href="https://www.data.cam.ac.uk/data-champions-search?search_api_views_fulltext=Gatto">data champion</a> and participating in open research and open data events. I was interested in participating in this conference because it gathered data champions, stewards and alike from various British and European institutions (Cambridge, Lancaster, Delft), and I was curious to see what approaches were implemented and issues were addressed across institutions. Another aspect of data championship/stewardship I am interested in is the recognition these efforts offer (<a href="https://lgatto.github.io/DataChampions-Sept-2017">this post</a> touches on this a bit).</p> <p>Focusing on the presentations from Lancaster, Cambridge and Delft, it is clear that direct engagement from active researchers is essential to promote healthy data management. There needs to be an enthusiastic researcher, or somebody that has some experience in research, to engage with the research community about open data, reproducibility, transparency, security, …; a blunt top-down approach lead to limited engagement. This is also important due to the plurality of what researchers across disciplines consider to be data. An informal setting, ideally driven by researchers and, or in collaboration with librarians, focusing on conversations, use-cases, interviews, … (I am just quoting some successful activities cited during the conference) have been the most successful, and have sometime also lead to new collaborations.</p> <p>Despite the apparent relative success of these various data championing efforts and the support that the data champions get from their local libraries, these activities remain voluntary and come with little academic reward. Being a data champion is certainly an enriching activity for young researchers that value data, but is comes with relatively little credit and without any reward or recognition, suggesting that there is probably room for a professional approach to data stewardship.</p> <p>With this in mind, I was very interested to hear the approach that is currently in place at TU Delft, where data stewards hold a joint position (<strong>EDIT</strong> this is not correct, see Marta Teperek’s comment/correction below) at the Centre for Research Data and at their respective faculty. This defines research data stewardship as an established and official activity, allows the stewards to pursue a research activity, and, explicitly, links research data to research and researchers.</p> <p>I am wondering if this would be implemented more broadly to provide financial, professional and academic recognition to data stewards/champions, offer incentives (in particular for early-career researchers) to approach research data management professionally and seriously, make data management a more explicit activity that is part of research itself, and move towards a professionalisation of data management posts.</p>Laurent GattoLast months, I participated in the Engaging Researchers in Good Data Management meeting organised by the Office of Scholarly Communication, SPARC and Jisc (details here). This post and additional feedback are also available in Engaging Researchers with Good Data Management: Perspectives from Engaged Individuals on the University of Cambridge’s Office of Scholarly Communication blog.A discussion about Open Access2017-11-23T00:00:00+00:002017-11-23T00:00:00+00:00https://lgatto.github.io/OA-discussion-01<p>Last week, <a href="http://richardpoynder.co.uk/">Richard Poynder</a> (<a href="https://twitter.com/RickyPo">@RickyPo</a> on Twitter) organised an informal get together around open access (OA), that was attended by researchers, publishers and librarians. A broad range of points were discussed, but one aspect caught my attention in particular, which I wanted to write down.</p> <p>I will start with a comment by <a href="https://www.sheffield.ac.uk/is/staff/pinfield">Stephen Pinfield</a> (<a href="https://twitter.com/StephenPinfield">@StephenPinfield</a> on Twitter), who mentioned that many proponents of the green OA route (which I consider myself one of) see it as a way to disseminate research and not as a business model (which the golden OA route, the dominant model in the UK, certainly has become<sup id="fnref:1"><a href="#fn:1" class="footnote">1</a></sup>). The views of these green OA proponents are often based, rarely explicitly though, on author processing charge (APC), albeit very low ones.</p> <p>Later, we had a quick survey where all participants shared what they thought a fair APC should cost - this wasn’t meant to be an objective assessment (because a lot of what is said and felt related to OA is very subjective). The range of suggestions ranged from $5 (based on the arXiv model) to $3500. The reason for such a huge variance, and some (arguable very) high APCs comes from cost unrelated to publication. <a href="https://www.gen.cam.ac.uk/directory/sudhakaran-prabakaran">Sudhakaran Prabakaran</a> (<a href="https://twitter.com/wk181">@wk181</a> on Twitter), who has first hand experience with AAAS, explained that these costs include, for example, the news that are published in the journal Science; for eLife, represented by Emily Packer (<a href="https://twitter.com/PackerLEmily">@PackerLEmily</a> on Twitter), APCs of £2500 (based on <a href="https://elifesciences.org/inside-elife/b6365b76/setting-a-fee-for-publication">this post</a>, down from £3147 <a href="https://elifesciences.org/inside-elife/a058ec77/what-it-costs-to-publish">projected cost for 2016</a>), include the development of new publishing platforms (that are released as open source software, by the way).</p> <p>I found it quite revealing; personally, I don’t want to pay for news and views as part of my APCs, but I might consider paying for them independently. Similarly, while I do believe that there is a need to a modern publishing platform, I am not convinced that my APCs should necessarily include such costs; or at least researchers should be able to decide how much they want to contribute to this. And let’s not forget that the money that pays for APCs comes from the funders (my previous sentence is misleading, as researchers don’t pay for APCs themselves).</p> <p>One comment and suggestion that I found particularly noteworthy was from <a href="http://www.econ.cam.ac.uk/people/cto/jrjg1">Rupert Gatti</a> (<a href="https://twitter.com/rupertgatti">@rupertgatti</a> on Twitter), co-founder <a href="https://www.openbookpublishers.com/">Open Book Publishers</a>. The publication of a hard-copy book at Open Book Publishers ranges between £3500 and $4500 (which is very low compared to the average costs of other mainstream publishers, peaking around 30K for small publisher and increasing for major players). Rupert made an important point in denouncing APCs, in that they explicitly separate research and its publication. This is certainly a major issue in the current climate: researchers <em>don’t pay</em> for APCs; the money comes straight from funders via their university library), and assume everything works behind the scenes, including licensing (and loosing the rights to their outputs). He suggested that if we embedded publishing into research, the cost would become essentially zero (in line with costs of pre-prints). While one could argue that publishing by third-party professionals has some benefits, if we consider that researchers do most of the fundamental work (from doing the research, writing and reviewing the research papers), one wonders if separating research and its dissemination at such a high cost is a reasonable solution.</p> <p>Finally, we also briefly discussed different publishing models, beyond the green and golden OA models that are currently mainstream.</p> <p><strong>Flipping</strong>, where publishers would flip to a fully OA model and would be paid by bulk deals. This is what I believe the current dominant golden OA model in the UK was meant to lead to.</p> <p><strong>Institutional publishing</strong>, which exists, but is rarely used as a means to comply to the OA mandate.</p> <p><strong>Funder-based publishing</strong>, such as what the <a href="https://wellcomeopenresearch.org/">Wellcome Trust</a>, the <a href="https://gatesopenresearch.org/">Gates Foundation</a>, … do through the <a href="https://f1000research.com/">F1000 publishing platform</a>. <a href="https://www.ubiquitypress.com/">Ubiquity Press</a> has a similar model, I believe.</p> <p>And there are probably more that I’m missing… (feel free to comment to expand the list).</p> <div class="footnotes"> <ol> <li id="fn:1"> <p>This is the model that was favoured in the UK. The Finch report envisioned that it would lead to a change in academic publishing (more on that later), which has arguably failed. OA has been hijacked by commercial publishers and there is currently little hope for a more fundamental revision of the publishing landscape. <a href="#fnref:1" class="reversefootnote">&#8617;</a></p> </li> </ol> </div>Laurent GattoLast week, Richard Poynder (@RickyPo on Twitter) organised an informal get together around open access (OA), that was attended by researchers, publishers and librarians. A broad range of points were discussed, but one aspect caught my attention in particular, which I wanted to write down.I won’t be Bullied Into Bad Science!2017-11-16T00:00:00+00:002017-11-16T00:00:00+00:00https://lgatto.github.io/BulliedIntoBadScience-OpenConCam<p>This is the content of my talk at <a href="http://www.opencon2017.org/lgatt0/opencon_2017_cambridge">OpenConCam</a>, the OpenCon satellite meeting in Cambridge, presented on the 16 November 2017. The slides are available <a href="https://rawgit.com/lgatto/2017_11_16_OpenConCam/master/slides.html">here</a>.</p> <!--more--> <h2 id="together-on-a-journey">Together on a journey</h2> <p>I am going to tell you about a long, still on-going journey. I’ll talk about my journey, but it applies to other, I know that. And when you are on a long journey, you meet many people, and some help and support on your journey. Before telling more about this journey, I would like to thank some people that are close to my heart when it comes to open science and open research. These are the people who <a href="http://www.openconcam.org/">helped organising this meeting</a>, and its predecessors; these are people who share the values I will be talking about; and there’s in particular the ever inspiring <a href="http://corinalogan.com/">Corina Logan</a>, who is the person who initiated the <a href="http://bulliedintobadscience.org/">#BulliedIntoBadScience</a> campaign.</p> <h2 id="yes-its-personal">Yes, it’s personal!</h2> <p>I do care a lot about my work as a researcher, very much indeed. I am a scientist doing research in the area of computational biology, more specifically in <a href="https://lgatto.github.io/cpu-spat-prot-2015/">spatial proteomics</a>. At the end of my degree (that was in biology), I was unable to imagine anything else I could do other than research. I never intended to do the kind of research I am doing now, but I wanted to understand the world around me by doing research. What has fascinated me since that time is the method of scientific investigation, a method to observe, define hypotheses, test them, and validate or invalidate them. That’s how we can understand the world that surrounds us.</p> <p>What are some of the features that make this scientific investigation such a universally powerful paradigm? The science that I am passionate about is characterised by:</p> <ul> <li><strong>Trust</strong> - I need to trust you to stand on your shoulders.</li> <li><strong>Reproducibility</strong> - it’s not only your shoulders I will stand on.</li> <li><strong>Openness</strong> - I need to know what I am going to stand on. And I want <strong>everybody</strong> to be able to know.</li> </ul> <p>I didn’t realise this as a young PhD student, when initiating my journey. Nobody actually ever taught me that these concepts are among the very foundations that make science what it is, i.e. that we can stand on the shoulders of the giants that preceded us, and that, maybe, others will be able to stand on my shoulders, one day. This is the kind of science that I am passionate about, that I feel I can continue doing until the very end.</p> <h2 id="so-what-is-this-talk-about">So what is this talk about?</h2> <p>It is about the science that <strong>we</strong> are passionate about, it’s about the science that we can trust.</p> <p>But that is not always the science that is practised.</p> <p>This is a quote shared with us by one of the ECR signatories of the <strong>#BulliedIntoBadScience</strong> campaign.</p> <blockquote> <p>I have been constantly harassed by superiors to modify data in order to provide better agreement with known experimental values in order to make the paper look better for publishing in prestigious journals.</p> </blockquote> <p>We all have constraints in our work, in our lives. We don’t live and work in an ivory tower. Things can be hard at time. Things are certainly harder for many than there are for me. We have to live with these constraints, and we have to do our research with these in mind.</p> <p>But there are some compromises that we won’t make. We want to pursue our research following our values, following the principles that prompted us and guided us along the way.</p> <h2 id="the-campaign">The campaign</h2> <blockquote> <p>The <a href="http://BulliedIntoBadScience.org/">Bullied Into Bad Science</a> campaign is an initiative by early career researchers (ECRs) for early career researchers who aim for a fairer, more open and ethical research and publication environment.</p> </blockquote> <p>Because science and academia are not necessarily aligned. Because a good researcher and a successful researcher are not the same thing. With this campaign, we want to lead individuals and institutions in adopting open practices to improve research rigour. We want a good researcher and a successful academic to realign.</p> <h2 id="some-background">Some background</h2> <p>The <strong>#BulliedIntoBadScience</strong> campaign didn’t come out of the blue, but is the result of efforts that didn’t lead to satisfactory outcomes. Efforts that often lead to disappointment and frustrations.</p> <p>We have already written about the background behind the campaign, such as for example in this PLoS ECR <a href="http://blogs.plos.org/thestudentblog/2017/09/01/bullied-into-going-national-early-career-researchers-are-taking-initiative/">post</a>. Here, I want to provide a short summary to give you an idea of why this campaign exists.</p> <h2 id="success">Success?</h2> <p>It is difficult to say whether the campaign has been successful so far. Success is relative anyway. But here are a couple of points that we could consider indicators of success, or lack thereof.</p> <ul> <li> <p><a href="http://corinalogan.com/">Corina</a> just won a Shuttleworth Foundation Flash Grant for <strong>#BulliedIntoBadScience</strong>! <strong>WIN</strong></p> </li> <li> <p>Numbers: There are at this moment <strong>140 ECRs</strong> that have signed the campaign and <strong>73 non-ECRs</strong> (senior academics, people outside academia) that officially support it - unsure what they really mean.</p> </li> <li> <p>Feedback: we only got postive and supportive feedback so far - <strong>WIN</strong></p> </li> <li> <p>In Cambridge, there hasn’t been any change as a result of the campaign - <strong>FAIL</strong>. (But that doesn’t matter, as long as others benefit. It never was meant to be a Cambridge thing anyway) …</p> </li> <li> <p>… as for Cambridge signing the Declaration on Research Assessment (DORA): “No way on God’s earth” - <strong>FAIL</strong></p> </li> </ul> <h2 id="continuing-the-fight">Continuing the fight</h2> <ul> <li> <p>Approach prominent academics directly, because we need to show that those in charge also care, so that ECRs don’t feel intimidated to raise their voice.</p> </li> <li> <p>We have submitted evidence to the UK Parliament Science and Technology Committee inquiry on <a href="https://www.parliament.uk/business/committees/committees-a-z/commons-select/science-and-technology-committee/inquiries/parliament-2017/research-integrity-17-19/">Research Integrity</a> in the name of the campaign.</p> </li> <li> <p>An update to our web page is immindent, including translations (we are looking for more translators!), and we want to write regular blog posts.</p> </li> <li> <p>We want to discuss the signature of DORA at the <a href="https://www.governance.cam.ac.uk/governance/key-bodies/RH-Senate/Pages/default.aspx">Regent House</a> at the University of Cambridge?</p> </li> </ul> <h2 id="everyday-struggle">Everyday struggle</h2> <ul> <li> <p>And what about my <strong>day job</strong>? Why do <em>ECRs</em> need to fight for <strong>better</strong>, <strong>open</strong> and more <strong>trustworthy</strong> research?</p> </li> <li> <p>What’s the impact of being an open activist on my academic <strong>career</strong>? <strong>Good, IMHO!</strong> (see <a href="https://lgatto.github.io/EPFL-open-science/">here</a> for more details)</p> </li> <li> <p>There is so much work, and so little time. There are too many fights to pick - <strong>pick the battles that matter most to you</strong>.</p> </li> <li> <p>There are multiple ways to fight any battle, and often several are needed in parallel: <strong>official</strong> procedure and <strong>community</strong> efforts.</p> </li> </ul> <h2 id="its-not-only-personal">It’s not only personal</h2> <p>I started this presentation by sharing my experience, and highlighting how the current unethical research environment affected me. But it’s not about me, of course. It would be too easy for those, who don’t have ethical research high on their agenda, to dismiss everything in a blink of an eye.</p> <p>There is of course a community of ECR - PhD students, postdocs, tenure-tracked researchers, … - on whose shoulders I stand at this very moment. These are those who do the research, the all too often silent working force that drive research every single day. These are the researchers who have signed or support this campaign. And there are many more that haven’t yet.</p> <h2 id="final-word">Final word</h2> <p>If there’s one thing that is important to remember, it’s that</p> <blockquote> <p>No researcher is too junior to fix science!</p> </blockquote> <p>(find the reference <a href="https://www.nature.com/news/no-researcher-is-too-junior-to-fix-science-1.21928">here</a>)</p> <p>But while no researcher is too young, some certainly are more vulnerable than others. It is thus even more important that the more privileged ones (and that certainly counts me: white, male, from a prestigious institution) make themselves heard so that, together</p> <blockquote> <p>We won’t be <strong>#BulliedIntoBadScience</strong>!</p> </blockquote>Laurent GattoThis is the content of my talk at OpenConCam, the OpenCon satellite meeting in Cambridge, presented on the 16 November 2017. The slides are available here.An early career researcher’s view on modern and open scholarship2017-09-24T00:00:00+00:002017-09-24T00:00:00+00:00https://lgatto.github.io/EPFL-open-science<p>This post constitutes my talk at the <a href="https://osip2017.epfl.ch/">OPEN SCIENCE IN PRACTICE 2017</a> summer school in Lausanne, on the 25 September 2017. The slides used during the presentation are available <a href="http://bit.ly/20170925OpenScienceEPFL">here</a>.</p> <aside class="sidebar__right"> <nav class="toc"> <header><h4 class="nav__title"><i class="fa fa-file-text"></i> On This Page</h4></header> <ul class="toc__menu" id="markdown-toc"> <li><a href="#introduction" id="markdown-toc-introduction">Introduction</a> <ul> <li><a href="#who" id="markdown-toc-who">Who?</a></li> </ul> </li> <li><a href="#what-is-open-researchscience" id="markdown-toc-what-is-open-researchscience">What is Open Research/Science</a></li> <li><a href="#open-vs-closed" id="markdown-toc-open-vs-closed">Open vs. closed?</a></li> <li><a href="#why-isnt-it-open" id="markdown-toc-why-isnt-it-open">Why isn’t it open?</a></li> <li><a href="#go-open" id="markdown-toc-go-open">Go OPEN!</a> <ul> <li><a href="#funders-requirements" id="markdown-toc-funders-requirements">Funders’ requirements</a></li> <li><a href="#acceptance-of-open-practice-pre-prints" id="markdown-toc-acceptance-of-open-practice-pre-prints">Acceptance of open practice: pre-prints</a></li> <li><a href="#open-science-evaluation-criteria" id="markdown-toc-open-science-evaluation-criteria">Open science evaluation criteria</a></li> <li><a href="#open-as-a-career-boost" id="markdown-toc-open-as-a-career-boost">Open as a career boost</a></li> <li><a href="#reproducible-research" id="markdown-toc-reproducible-research">Reproducible research</a></li> <li><a href="#we-still-need-more" id="markdown-toc-we-still-need-more">We still need more</a></li> </ul> </li> <li><a href="#what-can-we-do" id="markdown-toc-what-can-we-do">What can we do?</a> <ul> <li><a href="#build-openness-at-the-core-your-research" id="markdown-toc-build-openness-at-the-core-your-research">Build openness at the core your research</a></li> <li><a href="#promoting-open-research-through-peer-review" id="markdown-toc-promoting-open-research-through-peer-review">Promoting open research through peer review</a></li> <li><a href="#be-reproducible" id="markdown-toc-be-reproducible">Be reproducible!</a></li> <li><a href="#promoting-open-researchscience" id="markdown-toc-promoting-open-researchscience">Promoting open research/science</a></li> </ul> </li> <li><a href="#what-can-institutions-and-senior-academics-do" id="markdown-toc-what-can-institutions-and-senior-academics-do">What can institutions and senior academics do?</a></li> <li><a href="#inclusivity-open-science-and-open-science" id="markdown-toc-inclusivity-open-science-and-open-science">Inclusivity: open science and open science</a></li> <li><a href="#conclusions" id="markdown-toc-conclusions">Conclusions</a></li> </ul> </nav> </aside> <p>Here’s a <a href="https://www.youtube.com/watch?v=AUoKV38HtcU">video</a> of a shorter version of this talk, presented in the evening at the EPFL library.</p> <p><strong>Abstract:</strong> If <em>research is the by-product of researchers getting promoted</em> (a quote by <a href="https://en.wikipedia.org/wiki/David_W._Barron">David Barron, Professor of Computer Science</a>, Prof. Leslie Carr, personal communication), then shouldn’t we, early career researchers (ECRs), focus on promotion and being docile academic citizens rather than aiming for the more noble cause of pursuing research to understand the world that surrounds us, and disseminate our findings using modern channels? Indeed, <a href="https://lgatto.github.io/open-research-project/">I have already argued</a> that a critical point that is failing us, is the academic promotion of open research and open researcher, as a way to promote a more rigorous and sound research process and tackle the reproducibility crisis. In this talk, I will present the case for open scholarship from an early career researcher’s perspective, pointing out that being an open researcher is not only the <em>right</em> thing to do, but is also the <em>best</em> thing to do.</p> <h2 id="introduction">Introduction</h2> <p>I am going to refer to the protagonists of this talk as <em>we</em>, we all. While I will focus specifically on early career researchers <sup id="fnref:1"><a href="#fn:1" class="footnote">1</a></sup> (ECRs), I really want to be inclusive, and use ‘we’. The reason is that open research is not only a concern for ECRs - that’s only the main theme of my talk - is concerns us all. In particular, we, ECRs, need <em>more</em> support from senior/established academics, librarians, funders, … Together, each of us in own quality, we need to drive change for a better, more open research environment.</p> <p>It is also important to highlight that <strong>open is not a replacement of good research</strong>. I have heard too often that open access is synonym of lesser publication. This is clearly nonsense, and the result of ignorance or the sole desire to harm those that publish on open access venues. We need to work hard to do the best research, and share it openly. As I will argue later, I would even claim that <strong>open is a gateway to better research</strong>. So let’s not give anyone an opportunity to be confused.</p> <p>I also tend to refer to <em>open research</em> rather than <em>open science</em> as to not explicitly exclude non-STEM field. And while my views will however resonate with scientists primarily, I believe many of the discussions below should also apply to other communities.</p> <h3 id="who">Who?</h3> <p>A few words about myself to offer some context on my view on modern and open scholarship:</p> <p>I am <a href="https://lgatto.github.io/">Laurent Gatto</a>, an <strong>early career researcher</strong> at the University of Cambridge, UK. I am a Senior Research Associate (<strong>non-established research staff</strong>) in the department of Biochemistry and a <a href="https://www.sysbiol.cam.ac.uk/Investigators/laurent-gatto">principal investigator in the Cambridge Systems Biology Centre</a>.</p> <p>My research focuses on the <strong>reproducible</strong> analysis and interpretation of high-throughput biological <strong>data</strong> and the development of statistical machine learning methods and <strong>research software</strong>.</p> <p>I am a <strong>open scholar</strong> and make a point of being vocal about it.</p> <h2 id="what-is-open-researchscience">What is Open Research/Science</h2> <p>Any research output should be</p> <ul> <li>Free to read/access: no barriers to access knowledge</li> <li>Free to re-use (data, software, text and data mining, …)</li> </ul> <p>But also</p> <ul> <li>Free to publish (or how the golden OA movement excludes the global south and benefits commercial/hybrid predatory publishers<sup id="fnref:2"><a href="#fn:2" class="footnote">2</a></sup>. See also the <a href="http://rsnr.royalsocietypublishing.org/content/70/4/403">pay-to-publish model</a>).</li> </ul> <p>Open research/science should also be</p> <ul> <li>Inclusive</li> </ul> <p>More on this below.</p> <h2 id="open-vs-closed">Open vs. closed?</h2> <p>Let’s first reflect on the nature of science, and whether there really should be anything like <em>explicitly</em> open science.</p> <p>In 1942, Robert Merton introduced his four <a href="https://en.wikipedia.org/wiki/Mertonian_norms">Mertonian norms of Science</a> (pdf: <a href="http://www.collier.sts.vt.edu/5424/pdfs/merton_1973.pdf">The Sociology of Science</a>, a set of institutional imperatives taken to represent the ethos of modern science.</p> <ul> <li><strong>universalism</strong>: scientific validity is independent of the sociopolitical status/personal attributes of its participants</li> <li><strong>communalism</strong>: all scientists should have common ownership of scientific goods (intellectual property), to promote collective collaboration; secrecy is the opposite of this norm.</li> <li><strong>disinterestedness</strong>: scientific institutions act for the benefit of a common scientific enterprise, rather than for the personal gain of individuals within them</li> <li><strong>organised scepticism</strong>: scientific claims should be exposed to critical scrutiny before being accepted: both in methodology and institutional codes of conduct.</li> </ul> <p>Are these imperatives in line with current practice? Status of researchers and their institutions has major influence on their incomes and outputs, and ownership, IP and secrecy are part of research business at the highest level. Personal gain is not unheard of in science (see <a href="https://www.repository.cam.ac.uk/handle/1810/267263">Danny Kingsley’s recent key note talks at COASP9</a> for examples of financial rewards for publishing in certain venues). Finally, scepticism is organised and controlled by an elite and validated by commercial publishers. On the other hand, the imperatives are line with principles promoted by open science.</p> <p>More recently, in 2015, Mick Watson asked the question more directly: <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0669-2">When will <em>open science</em> become simply <em>science</em>?</a>.</p> <p><img src="/images/doi-13059-015-0669-2.png" alt="When will ‘open science’ become simply ‘science’?" /></p> <p>I claim that <strong>open is a gateway to more trustworthy research</strong>.</p> <ul> <li>Open research is research that enables reproducible and repeatable research.</li> <li>Open research is transparent and honest research.</li> <li>Open research is research that we can build upon.</li> </ul> <p>Open is better, and we should always aim for the better, not the worse.</p> <p>But then,</p> <blockquote> <p>Why would anyone not want to do open research?</p> </blockquote> <p>Note that nobody ever claimed (as far as I know, anyway) to do <em>closed science</em>. And there’s no black-and-white situation between open and non-open/closed. There is always a degree of how far one wants, or can, promote the most open possible research.</p> <h2 id="why-isnt-it-open">Why isn’t it open?</h2> <p>Incentives in for open career progression aren’t there (yet? - see below). On the contrary…</p> <blockquote> <p>If <em>research is the by-product of researchers getting promoted</em> (a quote by <a href="https://en.wikipedia.org/wiki/David_W._Barron">David Barron, Professor of Computer Science</a>, Prof. Leslie Carr, personal communication), then shouldn’t we, early career researchers (ECRs), focus on promotion and being docile academic citizens rather than aiming for the more noble cause of pursuing research to understand the world that surrounds us, and disseminate our findings using modern channels?</p> </blockquote> <p>In my opinion, barriers are not technological, but rather socio-cultural and political.</p> <ul> <li>Systemic control and inertia</li> <li>Vested interests by people in charge</li> <li>Abuse of power dynamics</li> <li>Fear of being scooped (<strong>update</strong> - an editorial in PLoS Biology on <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005203"><em>The importance of being second</em></a> and, and how they prefer to focus on <em>complementary research</em>, recognising its important role in reproducibility of science.)</li> <li>Fear of not being credited</li> <li>Fear of errors and public humiliation, risk for reputation</li> <li>Fear of information overload</li> <li>…</li> <li>Fear of becoming less competitive in a over-competitive market!</li> </ul> <p>While it is important to identify why open can look dangerous to some, I don’t want to spent too much time discussing these points. See Jon Tennant’s recent presentation about <a href="https://doi.org/10.6084/m9.figshare.5383711.v1."><em>Barriers to Open Science for junior researchers</em></a> on figshare for more details.</p> <p>The important message at this point is that, many if not all of these fears are only <em>perceived</em> risks. Let’s move on to why ECRs should seriously consider being open researchers.</p> <h2 id="go-open">Go OPEN!</h2> <p>Open science/research is particularly important for ECRs. Open research practices are here, and won’t go away. It is clear that they will increase in the near future. If <em>you</em>, as an ECR, want to be a competitive researcher in the coming years (and you’ll need to be), you’ll need to be well versed in open research practices.</p> <p>Here, I give some reasons and examples supporting my claims.</p> <h3 id="funders-requirements">Funders’ requirements</h3> <ul> <li>CC-BY open access publication (golden or green) with limited embargo period. In the UK, Wellcome Trust and all RCUK funders.</li> <li>Requirement for a data management plan (see <a href="https://riojournal.com/articles.php?id=11624">here</a> for one of mine)</li> <li>Open data mandatory for H2020 grants and many national applications.</li> <li>The Wellcome Trust recently <a href="https://wellcome.ac.uk/news/our-new-policy-sharing-research-data-what-it-means-you">expanded it’s data management plan</a> to any research outputs (software, antibodies, cell lines, …) (July 2017).</li> </ul> <h3 id="acceptance-of-open-practice-pre-prints">Acceptance of open practice: pre-prints</h3> <ul> <li><a href="https://wellcome.ac.uk/news/we-now-accept-preprints-grant-applications">Wellcome Trust</a> (Jan 2017) and the <a href="https://www.mrc.ac.uk/research/policies-and-guidance-for-researchers/preprints/">Medical Research Council (MRC)</a> (April 2017) accept pre-prints in grant applications.</li> <li>NIH <a href="https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-050.html">encourages submission of pre-prints</a> and cite them (March 2017).</li> </ul> <h3 id="open-science-evaluation-criteria">Open science evaluation criteria</h3> <p>The EU’s <a href="https://cdn1.euraxess.org/sites/default/files/policy_library/os-rewards-wgreport-final_integrated_0.pdf">Evaluation of Research Careers fully acknowledging Open Science Practice</a> defines an Open Science Career Assessment Matrix (OS-CAM):</p> <p><img src="/images/2017-09-21-eu-os-cam.png" alt="Open Science Career Assessment Matrix (OS-CAM)" /></p> <p><a href="https://cos.io/blog/are-reproducibility-and-open-science-starting-matter-tenure-and-promotion-review/">Reproducibility and open science are starting to matter in tenure and promotion</a> July 14th, 2017, Brian Nosek</p> <blockquote> <p>In any case, my experience with <strong>promotion review requests</strong> this summer suggests that change is occurring, particularly in assigning <strong>scholarly value to open science</strong> contributions and behavior, and it’s great to see.</p> </blockquote> <h3 id="open-as-a-career-boost">Open as a career boost</h3> <p>The majority concluded that there is a <strong>significant citation advantage for Open Access articles</strong>.</p> <p><img src="https://f1000researchdata.s3.amazonaws.com/manuscripts/10376/4f98c19e-717b-4d16-87c5-aaf0602e1ff8_figure2.gif" alt="Citation advantage" /></p> <p>From Tennant JP, Waldner F, Jacques DC et al. <a href="https://f1000research.com/articles/5-632/"><em>The academic, economic and societal impacts of Open Access: an evidence-based review</em></a>. F1000Research 2016, 5:632 (doi:10.12688/f1000research.8460.3)</p> <p><strong>Open access articles get more citations</strong> The relative citation rate (OA: non-OA) in 19 fields of research. This rate is defined as the mean citation rate of OA articles divided by the mean citation rate of non-OA articles.</p> <p><img src="https://iiif.elifesciences.org/lax:16800/elife-16800-fig1-v2.tif/full/1076,/0/default.jpg" alt="Open access articles get more citations." /></p> <p>From Erin C McKiernan et al. <a href="https://elifesciences.org/articles/16800"><em>Point of View: How open science helps researchers succeed</em></a> eLife 2016;5:e16800 (doi:10.7554/eLife.16800)</p> <p><strong>Data availability is associated with citation benefit.</strong></p> <p><img src="https://dfzljdn9uc3pi.cloudfront.net/2013/175/1/fig-1-1x.jpg" alt=" Citation density for papers with and without publicly available microarray data, by year of study publication" /></p> <p>From Piwowar HA, Vision TJ. (2013) <a href="https://peerj.com/articles/175/"><em>Data reuse and the open data citation advantage</em></a>. PeerJ 1:e175 https://doi.org/10.7717/peerj.175</p> <p>See also <a href="http://whyopenresearch.org/"><strong>Why Open Research</strong></a>.</p> <h3 id="reproducible-research">Reproducible research</h3> <p>Who hasn’t hear of the reproducibility crisis? A major underlying factor of the lack of reproducibility is the lack of openness (voluntary or accidental):</p> <ul> <li>Is the data available and re-usable?</li> <li>Is the software available usable?</li> <li>Is the method described in enough details?</li> <li>…</li> </ul> <p>(More about reproducible research below)</p> <p>Institutions should worry about research being reproducible and trustworthy, and some argue for it.</p> <p><a href="https://www.nature.com/news/faculty-promotion-must-assess-reproducibility-1.22596"><img src="/images/2017-09-22-promotion-rr.png" alt="Faculty promotion must assess reproducibility" /></a></p> <h3 id="we-still-need-more">We still need more</h3> <p>But, let’s face it, in practice, it is currently still relatively easy to brush over many of these requirements. In addition, the incentives are still inconsequential compared to the (perceived) risks. Maybe we need more threads when not being open.</p> <h2 id="what-can-we-do">What can we do?</h2> <h3 id="build-openness-at-the-core-your-research">Build openness at the core your research</h3> <p>Many aspects of open research, and arguable the most important ones, can’t be implemented as an afterthought. You won’t be able to share data that you don’t have anymore, or can’t find. You won’t want to share poor data or ugly code (half-backed, un-annotated, without any documentation), because you’ll look like a fool. You won’t be able to reproduce any results if your don’t make your research repeatable.</p> <p>In that respect, I want to briefly talk about the <em>SpatialMap</em> project, which aims at producing a visualisation and data sharing platform for <a href="https://lgatto.github.io/cpu-spat-prot-2015/">spatial proteomics</a>. I decided to promote and drive it as openly as possible in the frame of the <a href="http://osc.cam.ac.uk/open-research/open-research-pilot-project">Open Research Pilot Project</a>. The ORPP is a joint project by the <a href="http://osc.cam.ac.uk/">Office of Scholarly Communication</a> at the University of Cambridge and the <a href="https://wellcome.ac.uk/what-we-do/our-work/open-research">Wellcome Trust Open research team</a>. From the official page, the pilot project looks at:</p> <ul> <li>the support research groups’ need in order to make all aspects of their research open,</li> <li>why they want to do this,</li> <li>how it benefits them,</li> <li>how it improves the research process</li> <li>what barriers there might be that prevent the sharing of their research.</li> </ul> <p>Four research groups from Cambridge have been selected to participate. The project proceeds through meetings with all participants (every 6 months), discussions between the research groups and their recognised OSC collaborator, blog posts and occasional emails on a dedicate mailing list. (<a href="https://lgatto.github.io/open-research-project/">Here</a> are some early thoughts about the project itself.)</p> <p>Here are the reasons why the <em>SpatialMap</em> project is an open project:</p> <ol> <li> <p>The <em>SpatialMap</em> project in itself is about opening up spatial proteomics data by facilitating data sharing and providing tools to further the comprehension of the data. One aim is to allow users to use the <em>SpatialMap</em> web portal to upload, share, explore and discuss their data privately with collaborators in a first instance (few researchers share their data before publication), then make the data available to reviewer, and finally, once reviewed, make it public at the push of a button. The incentive for early utilisation of the platform is to provide interactive data visualisation and integration with other tools and sharing of the data with close collaborators.</p> </li> <li> <p>The project is developed completely openly in a public <a href="https://github.com/SpatialMap/SpatialMapDev">GitHub repository</a><sup id="fnref:3"><a href="#fn:3" class="footnote">3</a></sup>. Absolutely all code and contributions are publicly available. Anyone can collaborate, or even <em>fork</em> the project and build their own.</p> </li> <li> <p>I publicly announced the <em>SpatialMap</em> project in a <a href="https://lgatto.github.io/spatialmap-proposal/">blog post</a>. The blog post was written as a legitimate grant application (albeit a little bit shorter and sticking to the most important parts).</p> </li> </ol> <p>Note that I do not have any dedicated funding for this project. The progress so far was the result of a masters student visiting my group. Given that the project is not trivial, I am considering applying for dedicated funding to support the project.</p> <h3 id="promoting-open-research-through-peer-review">Promoting open research through peer review</h3> <p>This section is based on my <a href="https://rawgit.com/lgatto/2017-03-30-OSC-peerreview/master/slides.html">The role of peer-reviewers in <del>checking supporting information</del> promoting open science</a> talk.</p> <p>As an open researcher, I think it is important to apply and promote the importance of data and good data management on a day-to-day basis (see for example Marta Teperek’s 2017 <a href="http://doi.org/10.5281/zenodo.897785">Data Management: Why would I bother?</a> slides), but also to express this ethic in our academic capacity, such as peer review. My responsibility as a reviewer is to</p> <ul> <li>Accept sound/valid research and provide constructive comments</li> </ul> <p>and hence</p> <ul> <li>Focus firstly on the validity of the research by inspecting the data, software and method. If the methods and/or data fail, the rest is meaningless.</li> </ul> <p>I don’t see novelty, relevance, news-worthiness as my business as a reviewer. These factors are not the prime qualities of thorough research, but rather characteristics of flashy news.</p> <p>Here are some aspects that are easy enough to check, and go a long way to verify the availability and validity and of the data</p> <ol> <li> <p><strong>Availability</strong>: Are the data/software/methods accessible and understandable in a way that would allow an informed researcher in the same or close field to reproduce and/or verify the results underlying the claims? Note that this doesn’t mean that as a reviewer, I will necessarily try to repeat the whole analysis (that would be too time consuming indeed). But, conversely, a submission without data/software will be reviewed (and rejected, or more appropriately send back for completion) in matters of minutes. Are the data available in a public repository that guarantees that it will remain accessible, such as a subject-specific or, if none is available, a generic repository (such as <a href="https://zenodo.org/">zenodo</a> or <a href="https://figshare.com/">figshare</a>, …), an institutional repository (we have <a href="https://www.repository.cam.ac.uk/">Apollo</a> at the University of Cambridge), or, but less desirable, supplementary information or a personal webpage<sup id="fnref:4"><a href="#fn:4" class="footnote">4</a></sup>.</p> </li> <li> <p><strong>Meta-data</strong>: It’s of course not enough to provide a wild dump of the data/software/…, but these need to be appropriately documented. Personally, I recommend an <code class="highlighter-rouge">README</code> file in every top project directory to summarise the project, the data, …</p> </li> <li> <p><strong>Do numbers match?</strong>: The first thing when reproducing someone’s analysis is to match the data files to the experimental design. That is one of the first things I check when reviewing a paper. For example if the experimental design says there are 2 groups, each with 3 replicates, I expect to find 6 (or a multiple thereof) data files or data columns in the data matrix. Along these lines, I also look at the file names (of column names in the data matrix) for a consistent naming convention, that allows to match the files (columns) to the experimental groups and replicates.</p> </li> <li> <p><strong>What data, what format</strong>: Is the data readable with standard and open/free software? Are the raw and processed available, and have the authors described how to get from one to the other?</p> </li> <li> <p><strong>License</strong>: Is the data shared in a way that allows users to re-use it. Under what conditions? Is the research output shared under a valid license?</p> </li> </ol> <p>Make sure that the data adhere to the <strong><a href="http://www.nature.com/articles/sdata201618">FAIR</a> principles</strong>:</p> <blockquote> <p>Findable and Accessible and Interoperable and Reusable</p> </blockquote> <p>Note that SI are not FAIR, not discoverable, not structured, voluntary, used to bury stuff. A personal web page is likely to disappear in the near future.</p> <p>As a quick note, my <em>ideal</em> review system would be one where</p> <ol> <li> <p>Submit your data to a repository, where it get’s checked (by specialists, data scientists, data curators) for quality, annotation, meta-data.</p> </li> <li> <p>Submit your research with a link to the peer reviewed data. First review the intro and methods, then only the results (to avoid positive results bias).</p> </li> </ol> <p>When talking about open research and peer review, one logical extension is <strong>open peer review</strong>. While I personally value open peer review and practice it when possible, it can be a difficult issue for ECRs, exposing them unnecessarily when reviewing work from prominent peers. It also can reinforce an already unwelcoming environment for underrepresented minorities. See more about this in the <em>Inclusivity: open science and open science</em> section below.</p> <h3 id="be-reproducible">Be reproducible!</h3> <p><a href="https://doi.org/10.1186/s13059-015-0850-7"><img src="/images/2017-09-22-selfish-rr.png" alt="Five selfish reasons to work reproducibly" /></a></p> <blockquote> <p>And so, my fellow scientists: ask not what you can do for reproducibility; ask what reproducibility can do for you!</p> </blockquote> <p>Florian Markowetz.. Five selfish reasons to work reproducibly, Genome Biology 2015 16:274 https://doi.org/10.1186/s13059-015-0850-7</p> <ol> <li> <p><strong>Reproducibility helps to avoid disaster</strong>: a project is more than a beautiful result. You need to record in detail how you got there. Starting to work reproducibly early on will save you time later. I had cases where a collaborator told me they preferred the results on the very first plots they received, that I couldn’t recover a couple of month later. But because my work was reproducible and I had tracked it over time (using git and GitHub), I was able, after a little bit of data analysis forensics, to identify why these first, preliminary plots weren’t consistent with later results (and it as a simple, but very relevant bug in the code). Imagine if my collaborators had just used these first plots for publication, or to decide to perform further experiments.</p> </li> <li> <p><strong>Reproducibility makes it easier to write papers</strong>: Transparency in your analysis makes writing papers much easier. In dynamic documents (using <a href="http://rmarkdown.rstudio.com/">rmarkdown</a>, <a href="https://jupyter.org/">juypter notebook</a> and other similar tools), all results are automatically update when the data are changed. You can be confident your numbers, figures and tables are up-to-date.</p> </li> <li><strong>Reproducibility helps reviewers see it your way</strong>: a reproducible document will tick many of the boxes enumerated above. You will make me very happy reviewer if I can review a paper that is reproducible.</li> <li><strong>Reproducibility enables continuity of your work:</strong> quoting Florian, “In my own group, I don’t even discuss results with students if they are not documented well. No proof of reproducibility, no result!”.</li> <li><strong>Reproducibility helps to build your reputation:</strong> publishing reproducible research will build you the reputation of being an honest and careful researcher. In addition, should there ever be a problem with a paper, a reproducible analysis will allow to track the error and show that you reported everything in good faith.</li> </ol> <h3 id="promoting-open-researchscience">Promoting open research/science</h3> <p>If you want, as an ECR, you can also promote open research/science. Most of the open science supporters are young researchers that want to improve a system they find unhealthy, unfair and does not support good scientific practice.</p> <p><a href="https://www.nature.com/news/no-researcher-is-too-junior-to-fix-science-1.21928"><img src="/images/2017-09-21-fix-science.png" alt="No researcher is too junior to fix science" /></a></p> <p>Promoting open science, especially when done in an constructive way, might also give you an online presence that can be helpful in raising you profile as a researcher.</p> <p>Open science practice is also a valuable and transferable skill. Good data management and reproducible research might not always be skills that are appreciated in academia, but in many other fields (for example anything related to data science), they are absolutely essential. Science policy is also a very desirable career choice for many STEM graduates, and with the growing importance of open science, these skills would be an important addition to your CV.</p> <p>You can also support and join open science initiatives. One example I’ll be talking more about is the <a href="http://bulliedintobadscience.org/">BulliedIntoBadScience</a> campaign, an initiative by ECRs for ECRs who aim for a fairer, more open and ethical research and publication environment.</p> <h2 id="what-can-institutions-and-senior-academics-do">What can institutions and senior academics do?</h2> <p>One of the most depressing observations when promoting open research is the lack of support by senior academics, whether they have vested interests, are <em>only</em> mis-informed about open science, or just have no incentive to drive any change. Fortunately, it’s also important to highlight that there are established academics who support open research, but they are a minority.</p> <p>Here are eight actions that researchers and institutions should follow to improve open research and open ECR:</p> <ol> <li>Sign the Declaration on Research Assessment (<a href="http://www.ascb.org/dora/">DORA</a>), make hiring and promotion criteria explicit and highlight that the content and quality of research outputs are more important than the venue they are published in.</li> <li>Positively value the commitment to open research and publishing practices when considering candidates for positions and promotions.</li> <li>Endorse immediate open publishing, favouring publications in journals that are 100% open access.</li> <li>Endorse posting of pre-prints in recognised pre-print servers to avoid publishing delays that are detrimental to career progress for ECRs.</li> <li>Endorse, support and promote the open publication of data and other scientific outputs such as software.</li> <li>Educate researchers about publishing practices via public statements, mandatory courses, and inductions that cover open research/data/access, mandates, the hidden costs of traditional publishing and how to protect ECRs from exploitative publishing practices.</li> <li>Report to the public how much institutions pay for research to be published, to raise awareness about the significant drain on public funding.</li> <li>Make all postdocs and ECRs full voting members of their institutions to increase diversity and stay connected to the changing needs of this underrepresented group.</li> </ol> <p>These points are taken from the <a href="http://bulliedintobadscience.org/">BulliedIntoBadScience</a> campaign, an initiative by ECRs for ECRs who aim for a fairer, more open and ethical research and publication environment.</p> <blockquote> <p>Whether you are an ECR or a senior academic, <a href="http://bulliedintobadscience.org/#ecrs:_sign_the_letter">sign</a> our letter or <a href="http://bulliedintobadscience.org/#non-ecrs:_support_the_campaign">support us</a> and our campaign!</p> </blockquote> <p>Funders have a paramount role to play in the promotion of open research. Many, especially the Wellcome Trust in the UK, have established mandates and requirement to promote some aspects of open research, such as open access publication of all the research they fund (see above). There is however much more they can do to actively promote open researcher in general, and open ECR in particular.</p> <h2 id="inclusivity-open-science-and-open-science">Inclusivity: open science and open science</h2> <p>There is</p> <blockquote> <p>Open Science as in widely disseminated and openly accessible</p> </blockquote> <p>and</p> <blockquote> <p>Open Science as in inclusive and welcoming</p> </blockquote> <p>On being inclusive - <a href="https://twitter.com/CameronNeylon/status/895546085468495873">Twitter thread</a> by <a href="https://twitter.com/CameronNeylon">Cameron Neylon</a>:</p> <blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">The primary value proposition of <a href="https://twitter.com/hashtag/openscience?src=hash">#openscience</a> is that diverse contributions allow better critique, refinement, and application 3/n</p>&mdash; CⓐmeronNeylon (@CameronNeylon) <a href="https://twitter.com/CameronNeylon/status/895546764861853696">August 10, 2017</a></blockquote> <script async="" src="//platform.twitter.com/widgets.js" charset="utf-8"></script> <blockquote class="twitter-tweet" data-conversation="none" data-lang="en"><p lang="en" dir="ltr">It was a damned hard community to break into. Any step I took to be more open, I felt attacked for not doing enough/doing it right.</p>&mdash; Christie Bahlai (@cbahlai) <a href="https://twitter.com/cbahlai/status/871413258107981824">June 4, 2017</a></blockquote> <script async="" src="//platform.twitter.com/widgets.js" charset="utf-8"></script> <p>As far as I was concerned for a long time (until June 2017 to be accurate - this section is based this <a href="https://lgatto.github.io/open-and-open/">Open science and open science</a> post), the former more technical definition was always what I was focusing on, and the second community-level aspect of openness was, somehow, implicit from the former, but that’s not the case.</p> <p>Even if there are efforts to promote diversity, under-represented minorities (URM) don’t necessarily feel <a href="http://science.sciencemag.org/content/357/6356/1101.full">included</a>. When it comes to open science/research URMs can be further discriminated against by greater exposure or, can’t always afford to be vocal.</p> <ul> <li>Not everybody has the privilege to be open.</li> <li>There are different levels in how open one wants, or how open one could afford to be.</li> <li>Every voice and support is welcome.</li> </ul> <h2 id="conclusions">Conclusions</h2> <blockquote> <p>It’s all about research quality and integrity!</p> </blockquote> <p>Make sure you are ready to be open (for yourself now, your future self, open the your group/institute, or open to the research community or to the public)</p> <ul> <li>manage and annotate you data</li> <li>backup everything up</li> <li>open source development</li> <li>online presence</li> <li>…</li> </ul> <p>and be as open and promote openness as much as you can.</p> <blockquote> <p>There’s more than one open.</p> </blockquote> <p>Better research also means more diverse and inclusive research and a inclusive research environment. And, there are many useful ways and levels to be open.</p> <blockquote> <p>You want to do more. Yes please!</p> </blockquote> <p>Inertia is very strong in academia. There are many stakeholders involved, and too few that really want to drive change, due to vested interests and the comfort of their position. There are too many battles to fight, so pick yours wisely, otherwise you seriously risk to be exhausted and completely demoralised.</p> <blockquote> <p>If you want to go fast, go alone. If you want to go far, go together. - African Proverb</p> </blockquote> <p>There’s room for innovation and exploration, as well as influencing and advising the current establishment (slower, but as important).</p> <p>It is not easy to predict where Open Research/Science will get in the future. Open access has had both positive (widening access) and negative effects (when being re-purposed for commercial benefits, see also a recent interview with Leslie Chan, <a href="https://ocsdnet.org/confessions-of-an-open-access-advocate-leslie-chan/">Confessions of an Open Access Advocat</a>). As ECRs, we are the future of research and the future of research dissemination. We mustn’t be afraid of experimenting, debating, and challenging the establishment.</p> <p><strong>Acknowledgements:</strong> I have been influenced by many throughout my ongoing journey towards better (open) research. I would like to thank some of those that have inspired me, either directly or indirectly, along the way. In no particular order, I would like to thank <a href="http://corinalogan.com/">Corina Logan</a>, <a href="https://twitter.com/StephenEglen">Stephen Eglen</a>, <a href="https://twitter.com/martateperek">Marta Teperek</a>, <a href="https://twitter.com/dannykay68">Danny Kingsley</a>, members of the <a href="http://www.openconcam.org/">OpenConCam group</a>, <a href="https://twitter.com/sr120">Steve Russel</a>, <a href="https://twitter.com/yvonnenobis">Yvonne Nobis</a>, <a href="http://bjoern.brembs.net/">Bjoern Brembs</a>, <a href="http://www.michaeleisen.org/blog/">Micheal Eisen</a>, <a href="https://twitter.com/petermurrayrust">Peter Murray-Rust</a>, <a href="https://twitter.com/rupertgatti">Rupert Gatti</a>, <a href="https://gowers.wordpress.com/">Tim Gowers</a>, the <a href="https://bioconductor.org/">Bioconductor project</a>, the <a href="https://www.software.ac.uk/">Software Sustainability Institute</a>, <a href="https://twitter.com/gvwilson">Greg Wilson</a> and the <a href="https://software-carpentry.org/">Software/Data Carpentry</a>. And probably many more.</p> <div class="footnotes"> <ol> <li id="fn:1"> <p>ECR can broadly be define as a post-graduate student, a researcher in academia or industry or at a non-governmental organisation who is unemployed or on a temporary contract, or within 10 years of obtaining a permanent post. It doesn’t primarily relate to the age of the person. <a href="#fnref:1" class="reversefootnote">&#8617;</a></p> </li> <li id="fn:2"> <p>Predators aren’t the poor quality journals that disseminate spam, these are <em>opportunistic</em> publishers. The real predators are the big traditional and commercial that have taken control of scholarly dissemination and do everything they can to maintain it and maximise their gains. See for example <a href="https://lgatto.github.io/software-data-papers/">Why Software and data papers are a bad solution to a real problem</a>. <a href="#fnref:2" class="reversefootnote">&#8617;</a></p> </li> <li id="fn:3"> <p>Github is an online interface to the <code class="highlighter-rouge">git</code> version control software, which allows to track changes in any text file, revert back to any version. On top of a web interface to the version controlling, Github allows to file at track issues, and tremendously facilitate collaborative online development. I use it for pretty all my research and coding projects, papers, collaboration, analysis reports, … <a href="#fnref:3" class="reversefootnote">&#8617;</a></p> </li> <li id="fn:4"> <p>There is often no perfect solution, and a combination of the above might be desirable. <a href="#fnref:4" class="reversefootnote">&#8617;</a></p> </li> </ol> </div>Laurent GattoThis post constitutes my talk at the OPEN SCIENCE IN PRACTICE 2017 summer school in Lausanne, on the 25 September 2017. The slides used during the presentation are available here.September data champions meeting2017-09-14T00:00:00+00:002017-09-14T00:00:00+00:00https://lgatto.github.io/DataChampions-Sept-2017<p>The <a href="http://www.data.cam.ac.uk/datachampions">Data Champions Initiative</a> was set up as a way to promote best practice in terms of data management within the University departments and institutes, and to give those that promote them, explicit visibility for their efforts. This is a reflection on my role and contributions as data champion and a summary of related activities that I will present at the meeting.</p> <aside class="sidebar__right"> <nav class="toc"> <header><h4 class="nav__title"><i class="fa fa-file-text"></i> On This Page</h4></header> <ul class="toc__menu" id="markdown-toc"> <li><a href="#introduction" id="markdown-toc-introduction">Introduction</a></li> <li><a href="#the-open-research-pilot-project-orpp" id="markdown-toc-the-open-research-pilot-project-orpp">The Open Research Pilot Project (ORPP)</a></li> <li><a href="#the-role-of-peer-review-in-promoting-open-science" id="markdown-toc-the-role-of-peer-review-in-promoting-open-science">The role of peer review in promoting open science</a> <ul> <li><a href="#tips" id="markdown-toc-tips">Tips</a></li> <li><a href="#quick-survey" id="markdown-toc-quick-survey">Quick survey</a></li> <li><a href="#my-ideal-review-system" id="markdown-toc-my-ideal-review-system">My <em>“ideal”</em> review system</a></li> </ul> </li> <li><a href="#an-early-careers-view-on-modern-and-open-scholarship" id="markdown-toc-an-early-careers-view-on-modern-and-open-scholarship">An early careers view on modern and open scholarship</a></li> <li><a href="#conclusions" id="markdown-toc-conclusions">Conclusions</a></li> </ul> </nav> </aside> <!--more--> <h2 id="introduction">Introduction</h2> <p>So I’ll start with a apology</p> <blockquote> <p>I’m sorry for being a bad data champion.</p> </blockquote> <p>Why I am a bad data champion?</p> <p>My personal and limited experience indicates that my department isn’t a place worth spending my time and energy in terms of good (and open) data management. Why? Because I don’t see it as a place that values that kind of skill set, open data, data management, reproducible science… Time and effort invested in my department will mostly remain unnoticed, and won’t benefit me.</p> <p>Now that I have that out of the way, I can however share other efforts I’m involved in, that are related to the data champions effort and ethos. Here are some projects that I have been asked to share with you. They might not necessarily strike as being in line with the data champions efforts as outlined at the beginning of the initiative. But there is a lot of work to be done in terms of good data management in the light of more open, transparent and trustworthy science. I have spend a lot of time and efforts over the last years thinking about open research. I don’t have perfect solutions, only opinions (that I think would make, IMHO, a positive change). And I have settled to argue about issues and venues that I see as the most appropriate.</p> <h2 id="the-open-research-pilot-project-orpp">The Open Research Pilot Project (ORPP)</h2> <p>The ORPP is a joint project by the <a href="http://osc.cam.ac.uk/">Office of Scholarly Communication</a> at the University of Cambridge and the <a href="https://wellcome.ac.uk/what-we-do/our-work/open-research">Wellcome Trust Open research team</a>. From <a href="http://osc.cam.ac.uk/open-research/open-research-pilot-project">the official page</a>, the pilot project looks at:</p> <ul> <li>the support research groups need in order to make all aspects of their research open,</li> <li>why they want to do this,</li> <li>how it benefits them,</li> <li>how it improves the research process</li> <li>what barriers there might be that prevent the sharing of their research.</li> </ul> <p>Four research groups have been selected to participate. So far, the project proceeds through meetings with all participants (every 6 months), discussions between the research groups and their recognised OSC collaborator, blog posts and occasional emails on a dedicate (private) mailing list.</p> <p>I have written more about the ORPP <a href="https://lgatto.github.io/open-research-project/">here</a>, where I share my first post-kick off meeting thoughts about the project, and <a href="https://lgatto.github.io/spatialmap-proposal/">here</a>, where I wrote an public grant application describing the <em>SpatialMap</em> project.</p> <p>My opinion at the moment is that, ironically, the project itself isn’t open enough to really bring anything new to the debate (but maybe, that is by design?). So far, all problems and needs that have been highlighted (bad incentives, lack of rewards for being an open researcher, need for better funding for open science, funding for maintenance, sustainability, …) have been known and discussed online extensively; the project would possibly benefit from the communities wisdom and input. Also, so far, the project replicates the main issue that we have with involving time to promote open research: it is an activity that is mainly driven by individual researchers’ desire to improve a research environment that doesn’t promote the best possible research, without clear benefits for the researchers themselves.</p> <p>My hope is that the participants will be in a position to provide direct input to the Wellcome Trust and positively influence their impact on the promotion of <em>open science</em> and <em>open scientists</em>.</p> <h2 id="the-role-of-peer-review-in-promoting-open-science">The role of peer review in promoting open science</h2> <p>This is based on a talk I gave at a <a href="https://lgatto.github.io/osc-peer-review/">peer review meeting</a> organised by the OSC in March 2017. The slides are <a href="https://rawgit.com/lgatto/2017-03-30-OSC-peerreview/master/slides.html">available here</a>. There is more about <a href="https://lgatto.github.io/peer-review-cup-discussion-panel/">peer review here</a>, featuring a round discussion at Cambridge University Press as part of <a href="https://twitter.com/search?f=tweets&amp;vertical=default&amp;q=%23PeerRevWk17">#PeerRevWk17</a>.</p> <p>Main main argument, that is most relevant to the data champions initiative is encapsulated in this question:</p> <blockquote> <p>Reviewing data/software/methods: is this asking too much from reviewers?</p> </blockquote> <p>The above implies that the review can be very quick</p> <blockquote> <p>If no data/software are available, there can’t be any review.</p> </blockquote> <h3 id="tips">Tips</h3> <p>(See <a href="https://rawgit.com/lgatto/2017-03-30-OSC-peerreview/master/slides.html">slides</a> for details)</p> <ul> <li><strong>availability</strong>: data/software availability and a <em>reasonable</em> description thereof</li> <li><strong>meta-data</strong></li> <li><strong>do numbers match?</strong>: Experimental design: 2 groups, 3 replicates, but data files or columns: not a multiple of 6! Also look at the file names; is there are consistent naming convention?</li> <li><strong>what data, what format</strong>: Is it readable with standard and open/free software? Raw, processed, how to get from one to the other? Summary table?</li> <li><strong>license</strong>: If you share anything, make sure users are allowed to re-use it, and are aware of the terms under which they can re-use it. Examples: CC-BY, CC0, GPL, BSD, …</li> </ul> <h3 id="quick-survey">Quick survey</h3> <ul> <li>Is this asking too much?</li> <li>Who would like to see this done systematically?</li> <li>Who does this in their peer review activities?</li> </ul> <p><strong>The real question</strong> however is</p> <blockquote> <p>who applies these principles when they prepare data?</p> </blockquote> <h3 id="my-ideal-review-system">My <em>“ideal”</em> review system</h3> <ol> <li>Submit your data to a repository, where it get’s checked (by specialists, data scientists, data curators) for quality, annotation, meta-data.</li> <li>Submit your research with a link to the peer reviewed data. First review the intro and methods, then only the results (to avoid positive results bibs).</li> </ol> <p>As data champions, I think it is important to promote the importance of data and data management on a day-to-day basis, but also to express this ethic in our academic capacity, such as peer review.</p> <h2 id="an-early-careers-view-on-modern-and-open-scholarship">An early careers view on modern and open scholarship</h2> <p>This is a slide from a <a href="https://htmlpreview.github.io/?https://github.com/lgatto/2017_06_09_RDMF_London/blob/master/slides.html#section">talk I gave at the Research Data Management forum</a> (RDMF) in July 2017, revering to the ORPP above.</p> <p>In my opinion, barriers to Open Research (and the issues Data Champions are addressing) are not technological, but rather at political, institutional, community level.</p> <blockquote> <p>A critical point that is missing is the academic promotion of open research and open researcher (*), as a way to promote a more rigorous and sound research process and tackle the reproducibility crisis. What should the incentives be? How to make sure that the next generation of academics genuinely value openness and transparency as a foundation of rigorous research? (<a href="https://lgatto.github.io/open-research-project/">link</a>)</p> </blockquote> <p>(*) and here, I extend this to roles such as data champions, data maintainers/curators, research software engineers.</p> <h2 id="conclusions">Conclusions</h2> <p>As data champions, our duty is to promote good data, good data management and good data analysis, and, directly or indirectly, more open and trustworthy research. ‘Open’ here refers to open to your future self, open the your group/institute, or open to the research community and to the public.</p> <p>But I think we also need to reflect on the incentives in place to do what we do, and the costs that these efforts have. Not because I believe we shouldn’t make these efforts, but because we deserve to be recognised and valued for our efforts.</p>Laurent GattoThe Data Champions Initiative was set up as a way to promote best practice in terms of data management within the University departments and institutes, and to give those that promote them, explicit visibility for their efforts. This is a reflection on my role and contributions as data champion and a summary of related activities that I will present at the meeting.Peer review week: Panel discussion at Cambidge University Press2017-09-13T00:00:00+00:002017-09-13T00:00:00+00:00https://lgatto.github.io/peer-review-cup-discussion-panel<p>On the 17 August 2017, I participated in a panel discussion about peer review organised by Cambridge University Press (CUP). This post summarises some of the questions and discussion that I wrote in preparation for the discussion. The panel discussion was filmed and a 30 minutes video will be produced as part of the <a href="https://peerreviewweek.wordpress.com/">Peer Review Week</a>.</p> <!--more--> <p>The panel <a href="https://www.youtube.com/watch?v=m5hnXW9oBjY">discussion video</a> has now been published</p> <iframe width="560" height="315" src="https://www.youtube.com/embed/m5hnXW9oBjY?rel=0" frameborder="0" allowfullscreen=""></iframe> <p>The official CPU Peer Review Week page is <a href="https://www.cambridge.org/core/services/peer-review-week-2017">here</a>.</p> <p>Note that in the text below, I will systematically refer to the <em>dissemination of research outputs</em> and explicitly avoid talking about <em>publishing research papers</em>. This is for two reasons: (i) we mustn’t limit ourselves to papers (or books) but promote or more diverse set of outputs that better represent the actual work more and (ii) publishing is most often done by publishers that have conflicting interest due to their commercial nature.</p> <h2 id="about-me">About me</h2> <p>My name is <a href="https://lgatto.github.io/about/">Laurent Gatto</a> (I’m <a href="https://twitter.com/lgatt0">lgatt0</a> on twitter). I am a principal investigator in the Cambridge Systems Biology Centre, where I lead the <a href="https://lgatto.github.io/cpu-lab/">Computational Proteomics Unit</a>. I am a computational biologist, and my research focuses on high-throughput biological data and the development and application of computational methods and software to shed new light on biological data and biological processes.</p> <p>I also consider myself an open and digital scholar. I value every aspects of open science, from open and <a href="http://www.nature.com/articles/sdata201618">FAIR</a> (Findable and Accessible and Interoperable and Reusable) data, open and collaborative software development, open access, open peer review (when appropriate), fast dissemination of research through pre-prints, …</p> <p>My views on peer review will reflect my interests and area of research: open and collaborative research, and open dissemination of a variety of research outputs, including papers (not as much books) as well as data and software.</p> <h2 id="what-does-good-peer-review-look-like-to-each-panellist">What does good peer review look like to each panellist?</h2> <p>In my opinion, good peer review should</p> <ul> <li>Support the <strong>dissemination of sound and valid research</strong></li> <li>Highlight <strong>areas that need or could be improved</strong></li> <li>Provide <strong>constructive comments</strong></li> </ul> <p>The focus being on <strong>validity</strong> (as opposed to novelty, relevance, …) and I think that some emphasis should be put on the <strong>data</strong>, <strong>software</strong> and <strong>methods</strong> underlying the claims to promote and support better <strong>reproducibility</strong> of, and thus greater trust in the research.</p> <p>Good peer review should be also <strong>multidisciplinary</strong>. Given the increasing multidisciplinary nature of a lot research, peer review has to follow the trend. I don’t think peer review can still claim it’s gold standard status if peer review relies on a limited number of reviewer that often won’t possess all necessary skills to cover the multidisciplinary nature (and that includes technical expertise in terms of data, data processing, software, …) of the research.</p> <p><strong>Transparency</strong> would also be a feature of good peer review, as transparency leads to greater trust. I don’t necessarily think that transparency implies open/public peer review.</p> <p><strong>Timely</strong> peer review is important, with the reservation however that speed shouldn’t reduce quality and depth of the review. That’s where pre-prints play an important role, so that one can disseminate research independently of a possibly lengthy peer review process.</p> <h2 id="what-do-publishers-do-to-support-good-peer-review-and-what-could-they-do-better">What do publishers do to support good Peer Review and what could they do better?</h2> <p>I personally haven’t seen many publishers do much for peer review. Three spring to mind:</p> <ul> <li><a href="https://peerj.com/">PeerJ</a> has a nice interface to enter your peer review and they explicitly offer the possibility to post reviews (speaker as a peer reviewer here);</li> <li><a href="https://f1000research.com/about">F1000Research</a> and they open review/commenting system (reviewer and author);</li> <li>the consultative peer review of <a href="https://elifesciences.org/about/peer-review">eLife</a>, although I haven’t personally experienced it yet.</li> </ul> <p>But I am not sure that publishers should be those to drive peer review. I would very much prefer active researchers to play the key role here. Read more about my views on publishers role in peer review below.</p> <h2 id="are-current-practices-of-peer-review-appropriate-and-sustainable-in-the-future">Are current practices of peer-review appropriate and sustainable in the future?</h2> <p>I think that serious improvements is needed. Research processes and outputs (in terms of quantity and complexity) have increased, and continue to do so, and pressure to publish is hitting researchers, in particularly early career researchers (ECR) hard. Traditional peer needs to adapt.</p> <p>One aspect that I think is generally accepted is that peer review doesn’t scale. There are too many research papers and in some fields, individual papers draw from many disciplines and skills that can’t be covered by 2 reviewers. We know peer review isn’t perfect, and these conditions will limit its scope. So I think that it is important to accept that peer review, even if it has been considered the gold standard for many years, doesn’t deliver to the same extent anymore, and that it is important to consider other models, such as systematic submission of pre-prints and their acceptance as first-class research outputs (many funding bodies do so) and post-publication peer review.</p> <p>I am of the opinion that there isn’t necessarily a single model that would fit all disciplines and types of publications (journals, books, data, software, …), that a combination of peer review models might be necessary (for instance open, single and double blind), and that it is important for us to experiment and gather data on how best disseminate and review our work.</p> <h2 id="does-peer-reviewing-benefit-the-reviewers-or-is-it-just-for-the-benefit-of-the-authors-and-end-readers">Does peer-reviewing benefit the reviewers, or is it just for the benefit of the authors and end-readers?</h2> <p>Peer review should benefits the author in helping them producing better research outputs, but that’s certainly not universal.</p> <p>The benefits for the peer reviewer are that they learn about some research before it’s published (although that’s not necessarily true with pre-prints). Another important benefit is that by peer reviewing, one becomes known by the more senior peers/editors; it’s a way to become part of an exclusive clubs.</p> <p>There are also big benefits for the publishers - peer review is very low cost for them but is used to promote the perceived quality of their publications (irrespective of the actual average quality of the review), which in turn is expected to sustain their business.</p> <p>Readers will benefit from peer review as long as it improves the quality of the output without delaying it too much.</p> <h2 id="what-are-the-roles-of-open-vs-blind-review">What are the roles of open vs blind review?</h2> <p>Open to debate. I prefer my reviews to be open, but there are also situations where blind review has advantages (in particular for ECR and under-represented minorities).</p> <p>I have never participated in a double blind peer review, but I am pretty sure it wouldn’t be too difficult to the reviewer to identify the group the work originates from.</p> <h2 id="why-hasnt-post-publication-peer-review-taken-off-with-the-pressure-for-rapid-online-publication-should-post-publication-peer-review-be-taken-more-seriously">Why hasn’t post-publication peer-review taken off? With the pressure for rapid online publication, should post-publication peer-review be taken more seriously?</h2> <p>I think that the main reason it hasn’t taken off is lack of incentives. It is still seen as a free, altruistic service outside of the traditional and rigid academic system.</p> <h2 id="could-traditional-pre-publication-peer-review-survive-without-publishers-mediating-it">Could traditional pre-publication peer-review survive without publishers mediating it?</h2> <p>Why not?</p> <p>I don’t see publishers as particularly important players in the dissemination of research papers (things might be somehow different for books, although the lack of open access policies for books is a problem). The problems I see are that publishers deal only with a limited number of research outputs (research manuscripts and books), have failed to support and promote data sharing and reproducible research for many years (there is a slow start among a few now), have promoted ill-informed metrics to promote their business, and are driven, at least partly, by market shares and profit.</p> <p>There’s a spectrum of offenders, of course, and some publishers that genuinely try to innovate in favour of the dissemination of research. From my perspective, the commercial aspects of publishers haven’t had the best impact of dissemination of research outputs, and there is an argument to be made that <a href="http://blogs.lse.ac.uk/impactofsocialsciences/2017/08/15/scholarly-communications-shouldnt-just-be-open-but-non-profit-too/">scholarly communications shouldn’t just be open, but non-profit too</a>.</p> <p>One experiment I would like to see is for publishers to invite authors to submit their pre-prints. I have heard of such cases but I don’t know if this is something that is done more systematically by some journals or publishers.</p> <h2 id="gender-bias-in-peer-review">Gender bias in Peer review</h2> <p>There is a bias, and I believe it doesn’t only affect women, but more generally any under-represented minorities. I am no expert on the matter but feel it is important to acknowledge the issue and make all possible efforts to reduce any biais, both as part of the peer review process as well as part of our efforts to promote <a href="https://lgatto.github.io/open-and-open/">open science</a>.</p> <h2 id="future-of-peer-review">Future of Peer Review</h2> <p>I hope the future of peer review will be linked to the future of research dissemination: open and transparent, focused on faster and broader dissemination of our work.</p> <h2 id="some-additional-post-panel-notes">Some additional post-panel notes</h2> <p>During the panel discussion, Monica Moniz from CUP mention an approach that I find very interesting, which is journals scanning pre-print servers and invite authors to submit their work. I have only heard few such cases on twitter but I think this would be a very nice thing that I would be happy to see. I publishers do that, it would be great for them to publicise it.</p> <p>Publishers get involved at the very end of the process, once the advertisement for the research is ready. Often, when it comes to dissemination of the outputs of that research (data, software), and the review and improvement of the work, it is too late. More openness and transparency are features that we should thrive to initiate as early as possible. Monica mentioned that there were efforts for publishers to get involved early on. While I am sure there is room for collaboration on such initiatives, I think it is important for the research community to remain independent from publishers. History has demonstrated that commercially driven interests of most commercial publishers have harmed the dissemination of research outputs. Publishers shouldn’t be given even more power and control by getting pretending to support researchers throughout the whole research process (see for example <a href="https://epriego.wordpress.com/2017/08/02/scholarly-communications-on-fire/">here</a> and <a href="https://epriego.wordpress.com/2017/08/03/scholarly-communications-on-fire-what-can-we-do/">here</a>). Publishers could however get involved in supporting (financially) and promoting (using) community-led initiatives and platforms.</p> <p>When it comes to submission for peer review, there are also some very simple things publishers could do right away: spare us that silly and stupid formatting, and make sure that the manuscripts we review are in a format that suites reading and reviewing by putting the figures in the text - as far as I understand, submission of figures separately is only for the benefit of the publishers way down the line, if the paper gets accepted.</p> <h2 id="references-and-further-reading">References and further reading</h2> <ul> <li><a href="https://f1000research.com/articles/6-1151/v1">A multi-disciplinary perspective on emergent and future innovations in peer review</a></li> <li><a href="http://www.triple-c.at/index.php/tripleC/article/view/867/1042">Who is Actually Harmed by Predatory Publishers?</a></li> <li><a href="https://lgatto.github.io/osc-peer-review/">How to get the most out of modern peer-review</a></li> <li><a href="http://blogs.lse.ac.uk/impactofsocialsciences/2017/08/15/scholarly-communications-shouldnt-just-be-open-but-non-profit-too/">Scholarly communications shouldn’t just be open, but non-profit too</a>.</li> <li><a href="https://epriego.wordpress.com/2017/08/02/scholarly-communications-on-fire/">Scholarly Communications On Fire</a> and <a href="https://epriego.wordpress.com/2017/08/03/scholarly-communications-on-fire-what-can-we-do/">What can we do?</a></li> </ul>Laurent GattoOn the 17 August 2017, I participated in a panel discussion about peer review organised by Cambridge University Press (CUP). This post summarises some of the questions and discussion that I wrote in preparation for the discussion. The panel discussion was filmed and a 30 minutes video will be produced as part of the Peer Review Week.Bad publishing and bullied into bad science.2017-06-28T00:00:00+00:002017-06-28T00:00:00+00:00https://lgatto.github.io/beyond-bad-publishing<p>The recent long read about scientific publishing in the Guardian is fantastic. It depicts a very telling story of the <a href="https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science">research publishing landscape</a>.</p> <!--more--> <p>There is actually more to it, than <em>only</em> the predatory model of publishing research and big deals. Big commercial publishers have understood that this lucrative business model holds on them <em>controlling</em> not only the research outputs, but the whole process. Their current moves are to provide integrated platforms to control and quantify researchers and research. The truly depressing situation is that senior academics and university managers buy into these initiatives, despite the catastrophic example of giving control of (only) the papers.</p> <p>The Guardian article begs for more questions - <strong>What can we do? Who can do anything, anyway?</strong></p> <p>There are two stakeholders that, in my opinion, can improve on the current situation: researchers themselves, and funders and <strong>NOT</strong> publishers, who are part of the problem, not the solution (here are some <a href="http://bit.ly/20170609rdmf">slides</a> I presented at the 2017 Research Data Management Forum, where I talked about this topic) Funders slowly push for greater openness in research, including open access and preprints, but they don’t push enough, in my opinion.</p> <p>Unfortunately, researchers, in particular early career researcher, are under a lot of pressure to <em>publish</em>, or (and) <em>perish</em>. Quoting Ross Mounce</p> <blockquote> <p>Doing valuable transparent reproducible science, and doing the best to establish one’s career in science appear to be almost mutually exclusive things.</p> </blockquote> <p>(I hope he’s wrong!)</p> <p>Here’s another very relevant article on the topic</p> <blockquote> <p><a href="https://f1000research.com/articles/6-518/v2">We can shift academic culture through publishing choices</a></p> </blockquote> <p>that highlights choices researchers can make to stop exploiting themselves and discriminating against others.</p> <p>If you, as a early career researcher (ECRs), want to make a change, help by participating in the <em>Bullied into bad science?</em> campaign, and sign the <a href="https://cambridge.eu.qualtrics.com/jfe/form/SV_6S9OXAydlFZz8cR">letter</a>, that urges institutions and individuals to better support ECRs by taking a set of actions:</p> <ol> <li>Sign the <a href="http://www.ascb.org/dora/">Declaration on Research Assessment</a> (DORA) as an independent university/institution/individual</li> <li>Positively value a commitment to open research and publishing practices that keep profits inside academia when considering candidates for positions and promotions (in alignment with DORA).</li> <li>Endorse immediate open publishing, favouring publications in journals that are 100% open access.</li> <li>Endorse posting of preprints in recognised preprint servers to avoid publishing delays that are detrimental to ECR career progress.</li> <li>Endorse, support and promote the open publication of data and other scientific outputs such as software.</li> <li>Educate researchers about publishing practices via public statements, mandatory courses, and inductions that cover: open research/data/access, mandates, hidden costs of traditional publishing, and how to protect ECRs against exploitative publishing practices.</li> <li>Increase transparency by reporting to the public how much institutions pay for research to be published to raise awareness about the significant drain on public funding.</li> <li>Make all postdocs voting members of their institutions. ECRs are the future of research - give them a voice to promote their own future in the best possible way.</li> </ol> <p>Support a better publishing landscape and a better, more open and trustworthy research by <a href="https://cambridge.eu.qualtrics.com/jfe/form/SV_6S9OXAydlFZz8cR">signing the letter</a> and supporting this initiative.</p> <p><strong>Update</strong>: Here’s an article, <a href="https://www.thetimes.co.uk/article/academics-strike-back-against-bad-science-t5mzcdxv8">Academics strike back against bad science</a>, published in <em>The Times</em> about our campaign.</p>Laurent GattoThe recent long read about scientific publishing in the Guardian is fantastic. It depicts a very telling story of the research publishing landscape.Supporting those that support Open Research2017-06-16T00:00:00+00:002017-06-16T00:00:00+00:00https://lgatto.github.io/support-osc<p>The <a href="http://osc.cam.ac.uk">Office of Scholarly Communication</a> (OSC) is the main structure that focuses on all matters related to open research at the University of Cambridge. It <em>stays abreast of new scholarly communication tools, techniques, policies and practices for the University.</em> The OSC and its team do an outstanding job to support and train all researchers Open Access and Research Data policies.</p> <p>The OSC, despite its critical contributions, is currently <a href="https://www.admin.cam.ac.uk/reporter/2016-17/weekly/6466/section1.shtml#heading2-6">under review</a>. A review is not a very nice position to be in, but it could also be an opportunity to highlight to the top managers of the University what an important role the OSC plays, and hopefully resulting in more open research support at the University.</p> <p>The members of the University were invited to contribute to the review. I sent my comments out; here they are.</p> <p>Dear Office of Scholarly Communication Review Panel,</p> <p>I am writing to provide feedback for the review of the Office of Scholarly Communication (OSC), following the invitation for comments in the University Reporter No 6466, Vol CXLVII No 32. In this letter, I will describe the reasons why open research is an essential mechanism of modern scholarship, document my personal experience with the OSC and how it currently addresses these needs, and how the University could continue to further improve their support the open research.</p> <p>There is a clear and unstoppable trend towards greater openness in research, ranging from wider and more open dissemination of all research outputs (data, software, material and methods, and research manuscripts), to a desire for more transparency in the research processes themselves (open peer review, pre-registration, early publication of pre-prints and consideration of these in grant proposals). The reasons underlying this drive for open research range from wider dissemination within and beyond the scientific community, to supporting better reproducibility and thus greater trust in research outputs. These changes are promoted and supported by many researchers, especially early career researchers (ECRs), by new publishers and data sharing platforms, as well as major UK funders (for example BBSRC, MRC and Wellcome Trust in particular). This changing research landscape is an opportunity for those that can adapt and appreciate the necessity of open research, and a threat to those that cannot or do not want to embrace open research.</p> <p>It is essential for an institution such as the University of Cambridge, that benefits from a unique prestige and position in national and international research to be at the forefront of these changes. To do so, it needs to support its researchers in making these transitions by informing them, and by providing adequate training and infrastructure. In addition, an institution of such a calibre ought to go beyond the mere minimal requirements mandated by funders, but should play a leading and pioneering role in understanding and defining the future directions of this changing open research landscape.</p> <p>Who, at the University of Cambridge, is in a better position to successfully address these fundamental needs of an ever more dynamic research horizon than the Office of Scholarly Communication? The OSC has, over the years, been extremely successful in informing, training and supporting researchers toward greater openness in their research, as required by the funding bodies. For example, the OSC has been instrumental in making scholarly outputs available via green and gold open access (OA) models, administering these dedicated funds, and assisting researchers in complying with their funder’s OA requirements. The OSC has facilitated and even at times enabled the communication around open research between researchers and individual researchers their departments (for instance by expressing their support of the Data Champions directly to their respective Heads of Departments). Importantly, the OSC has been able to reach out widely, from graduate students to PIs, departments and libraries at the University, and the wider community of stakeholders who influence open data, open access and open research in general.</p> <p>The OSC has been leading the way with various innovative projects to promote open research practice and open researchers, such as the Data Champions initiative and the Open Research Pilot Project (in collaboration with the Wellcome Trust). The OSC has successfully engaged with many stakeholders, in particular with researchers and funders, positioning themselves as a major player in open research. They are up-to-date with changes in funder requirements, participate in and foster discussions about the evolution of these requirements, and hence are ahead of the curve in terms of support and service to researchers. These successful activities have reached beyond the University of Cambridge, and the OSC is seen by researchers, data managers, managers and librarians around the world, as a prime example of successful engagement and support with their research community.</p> <p>All major funders are going to increasingly regard best practice in open science as an prime requirement when submitting applications. It is essential for the researchers at this University to continue to benefit from the support they currently benefit from to remain competitive. It is hard to imagine this University maintaining its world-class reputation, without being at the forefront all aspects of modern, open research, and the OSC is currently the only entity at the University of Cambridge, capable of successfully accomplishing these tasks.</p> <p>On a personal level, as a modern and open scholar, I have immensely benefited from the support, networking opportunities, and collaborations (I am an active participant in the Data Champions initiative and one of the fours participating research groups in the Open Research Pilot Project) offered by the OSC. This level of support is not available anywhere else in the University, whether at the level of the laboratory, the Department, the University Library or any other official structure withing the University. The OSC helped me realise my potential as modern, successful open scholar.</p> <p>I consider it an absolutely necessary for the University of Cambridge to support open research in general, and the OSC in particular. Firstly, I would urge the University to:</p> <ul> <li>to give the OSC its full support, including financial, so that the OSC can maintain and expand its highly qualified team and continue to support the community.</li> </ul> <p>In addition, the University, in collaboration with the OSC, should</p> <ul> <li> <p>Sign the Declaration of Open Research Assessment (<a href="http://www.ascb.org/dora/">DORA</a> (following the examples of UCL and Imperial College)</p> </li> <li> <p>Positively value a commitment to open research and publishing practices.</p> </li> <li> <p>Endorse immediate open publishing, including pre-prints.</p> </li> <li> <p>Endorse and value the open publication and dissemination of all research outputs, including data, software, material and methods, in accordance with the <a href="http://www.rcuk.ac.uk/documents/documents/concordatonopenresearchdata-pdf/">UK Concordat on Open Research Data</a>.</p> </li> <li> <p>Actively support and train all students and researchers in best open research practice in accordance with the <a href="https://www.vitae.ac.uk/policy/vitae-concordat-vitae-2011.pdf/@@download/file/Vitae-Concordat-Vitae-2011.pdf">UK Concordat to Support the Career Development of Researchers</a> and the <a href="http://www.universitiesuk.ac.uk/policy-and-analysis/reports/Pages/research-concordat.aspx">UK Concordat on Research Integrity</a>.</p> </li> <li> <p>Promote greater transparency by publicly reporting it’s own expenditure in journal substations and article processing charges, and transition it journal subscriptions to distance itself from commercial publishers and support OA publishing.</p> </li> <li> <p>Enable a wider participation of the academic community, in particular ECRs, into the discussions and decision making at the various levels at the University by, for example, registering all post-doctoral researchers in the Regent House.</p> </li> </ul> <p>In my opinion, the University’s support for open research plays a critical role, both to support its own position on the national and international scene, and to support its researchers, in particular the ECRs to remain among the very best in the world. I urge the members of the panel to continue to and increase their support the OSC.</p> <p>Yours sincerely</p> <p>Dr Laurent Gatto</p>Laurent GattoThe Office of Scholarly Communication (OSC) is the main structure that focuses on all matters related to open research at the University of Cambridge. It stays abreast of new scholarly communication tools, techniques, policies and practices for the University. The OSC and its team do an outstanding job to support and train all researchers Open Access and Research Data policies.Research outputs management plans2017-06-09T00:00:00+00:002017-06-09T00:00:00+00:00https://lgatto.github.io/output-management-plans<p>During the <a href="https://htmlpreview.github.io/?https://github.com/lgatto/2017_06_09_RDMF_London/blob/master/slides.html">talk</a> about early career researchers’ view on modern and open scholarship I presented at the <a href="http://www.dcc.ac.uk/events/research-data-management-forum-rdmf/rdmf17">Research Data Management Forum 2017</a> in London, I described a short table comparing different aspects related to data and software management.</p> <!--more--> <p>As mentioned during the presentation, I see many commonalities between data and software, and their management. In my grant applications, as a computational scientist, I use the data management plan to document the management of my software outputs (<a href="http://riojournal.com/articles.php?id=11624">here’s</a> an BBSRC DMP that I published recently). The table reads</p> <table> <thead> <tr> <th>Data</th> <th>Software</th> </tr> </thead> <tbody> <tr> <td>Static</td> <td>Dynamic</td> </tr> <tr> <td>Meta-data</td> <td>Documentation</td> </tr> <tr> <td>Large</td> <td>Small</td> </tr> <tr> <td>QC</td> <td>Testing</td> </tr> <tr> <td>DMP</td> <td>SMP</td> </tr> <tr> <td>DB, public repo</td> <td>Version control in public repo</td> </tr> </tbody> </table> <p>As was clear from some discussions I had over coffee and lunch, most of these points could be further discussed on their own, but I would like to follow up on the bigger picture.</p> <p>I stated that, for clarity, despite the many commonalities, it might be useful to have dedicated data and software management plans, and provide specific guidelines to reviewers and applicants. But, do we really want to have a data management plan, a software management plan, a material management plan, … Probably not, as these outputs are not independent anyway. Grant applicants would feel compelled to fill out as many plans as possible, thus reinforcing the <em>box ticking</em> feeling that is sometimes already associated with data management plans. In an ideal situation, as discussed with <a href="http://www.twitter.com/kevingashley">Kevin Ashley</a> (thank you for bringing this up), we would rather be looking at a unique, unified and integrated output management plan, that documents all research outputs, their management, their preservation and their dissemination in a coordinated way.</p> <p>Unfortunately, I feel that in the current climate, DMPs are not always taken seriously enough, or may be those that write them (senior researchers) do lack the skills and experience needed for effective data and software management. May be there is still a need to make it explicit that research has various different and valuable outputs, beyond the mere advertisement that is eventually published in a research journal, that these outputs are important, and that there is a need for explicit guidance as to how to document their management. I’m sure these alternatives must have been debated already (this was touched upon, albeit briefly, at a recent BBSRC/SSI software workshop I joined). I would be curious to hear what others think about this.</p>Laurent GattoDuring the talk about early career researchers’ view on modern and open scholarship I presented at the Research Data Management Forum 2017 in London, I described a short table comparing different aspects related to data and software management.Open science and open science2017-06-05T00:00:00+00:002017-06-05T00:00:00+00:00https://lgatto.github.io/open-and-open<p>A recent discussion on twitter about <em>Open Sciences</em> made me think about how Open Science can be intimidating, alienating and unwelcoming at times.</p> <!--more--> <p>Here are some tweets that I found particularly revealing:</p> <blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">It was a damned hard community to break into. Any step I took to be more open, I felt attacked for not doing enough/doing it right.</p>&mdash; Christie Bahlai (@cbahlai) <a href="https://twitter.com/cbahlai/status/871413258107981824">June 4, 2017</a></blockquote> <blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">Anyway- I believe in the open sci mission- that&#39;s why I&#39;m still here- but we need to really think about how we move forward.</p>&mdash; Christie Bahlai (@cbahlai) <a href="https://twitter.com/cbahlai/status/871415702376374274">June 4, 2017</a></blockquote> <blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">It&#39;s not just about choosing right licences and putting code on github, it&#39;s about actually improving accessibility and bringing people in</p>&mdash; Christie Bahlai (@cbahlai) <a href="https://twitter.com/cbahlai/status/871416201414574081">June 4, 2017</a></blockquote> <p>This thinking brought me to the conclusion that it is useful to distinguish between</p> <blockquote> <p><strong>Open Science</strong> as in <strong>widely disseminated and openly accessible</strong></p> </blockquote> <p>and</p> <blockquote> <p><strong>Open Science</strong> as in <strong>inclusive and welcoming</strong></p> </blockquote> <p>As far as I am concerned, the former more technical definition was always what I was focusing on, and the second community-level aspect of openness was, somehow, implicit from the former. But that’s not the case, at all. The train of thoughts was that open science leads to reproducible research and to more trustworthy science, favours dissemination of the research process and outputs, provides spaces for more people to express themselves, … thus favouring better recognition based on merit. Unfortunately, academia is not based on merit only (one needs to be “good”, of course, but once a certain level of quality has been attained, there are many other factors that count), and being an open scientists requires all too often a lot of combativeness. And there are cases where open science can have serious drawbacks. For example, when considering open peer review, it is clear that early career researchers have legitimate reasons to feel intimidated by openly criticising the work of a senior, well-respected researcher in their field. Similarly, while I value publishing in open access journals, I would not, as the senior author in a project, impose such a decision to a student or post-doc that works with me, if they felt that another venue was better for their career.</p> <p>So yes, I have always acknowledged that there were different levels in <strong>how open one wanted to be</strong>, or <strong>how open one could afford to be</strong>. I am probably on the very open end of the spectrum. For example all my software is <a href="https://github.com/lgatto">openly available</a>, before publication; I publish <a href="http://biorxiv.org/content/early/2015/07/07/022152">pre-prints</a> before <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004920">submission of the manuscript</a>; I publish data asap - note that I generally don’t generate new data myself; pretty much all my work, at least as corresponding author, is <a href="https://impactstory.org/u/0000-0002-1520-2268">OA</a>; I am a Software and Data Carpentry instructor and publish <a href="https://lgatto.github.io/TeachingMaterial/">all my teaching material</a> under CC-BY; I am involved in various open activities such as <a href="http://www.openconcam.org/">OpenConCam</a>, <a href="http://www.data.cam.ac.uk/datachampions">Data Champions</a>, the <a href="http://osc.cam.ac.uk/open-research/open-research-pilot-project">Open Research Pilot Project</a>, … and I do not have the luxury of tenure. But that’s my personal view, and there is no reason to believe it fits others; more moderate contributions/involvement (also named <a href="https://practicaldatamanagement.wordpress.com/2014/10/23/baby-steps-for-the-open-curious/">baby steps</a>, although I personally don’t like that term very much) are by no means worse, or less laudable. I appreciate I have privileges other don’t have - white male, well funded lab (including funders paying for costly Author Processing Charge), well known institution (I have witnessed how the attention some people give me has changed since I moved to Cambridge), and, when I feel strongly about a topic such as Open Science, I am not afraid of getting into an argument.</p> <p>The reason I believe it is useful to make the above distinction in openness is that the two approaches can sometimes conflict. I have mentioned some reasons above (open peer review and choosing publication venues), but Open Science, or the supposed expectations/requirements of Open Science can be particularly discriminatory for under-represented minorities (URMs), who are already subject to many implicit and/or explicit biases. Here’s a very revealing storyfied twitter tread explaining how well intended openness has risks that, in an already biased system, will affect some people more than others:</p> <blockquote class="twitter-tweet" data-lang="en-gb"><p lang="en" dir="ltr">Re: <a href="https://twitter.com/hashtag/OpenGlobalSouth?src=hash">#OpenGlobalSouth</a> here is Storify of discussion w/ <a href="https://twitter.com/DNLee5">@dnlee5</a> that helped convince me for need for this conference <a href="https://t.co/sy4zyzCfzu">https://t.co/sy4zyzCfzu</a></p>&mdash; Jonathan Eisen (@phylogenomics) <a href="https://twitter.com/phylogenomics/status/868220913472241664">26 May 2017</a></blockquote> <p>In the future, I will pay attention to make this distinction, and clarify that I want to promote both aspects, but that they can, at times, be difficult to harmonise. I will also emphasise that there is a gradient of how open one can be, or can afford to be, depending on circumstances, and that every contribution to Open Science, whether big or more moderate, is welcome and significant.</p>Laurent GattoA recent discussion on twitter about Open Sciences made me think about how Open Science can be intimidating, alienating and unwelcoming at times.
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