̽��ֱ�� of Cambridge - open access

New journal aims to tackle biggest problems in scholarly communication

cjb250 — Wed, 18 Sep 2019 10:31:55 +0000

Experimental Results aims to tackle the crisis in the reproducibility of results, provide an outlet for standalone research that currently goes unpublished and to make peer review faster, less onerous and more transparent.

Submissions are now open for the journal, which will give researchers a place to publish valid, standalone experimental results, regardless of whether those results are novel, inconclusive, negative or supplementary to other published work.

It will also publish the outcome of attempts to reproduce previously published experiments, including those that dispute past findings.

̽��ֱ��ambitious publication is the brainchild of Fiona Hutton, the Press’s Head of STM Open Access Publishing and addresses concerns she has had since her days in the lab as a cancer research scientist and throughout her career in research publishing.

She said: “Scholarly communication isn’t really reflective of the research process, because the focus is on publishing a concise narrative. ̽��ֱ��reality is that research results are often confusing, inconclusive, or don’t fit a narrative. Discovery is damaged when the focus becomes the research paper rather than the research output itself.

“I've had countless conversations with scientists about the value of publishing all valid experiments, not just those that fit the narrative of a particular paper or which are deemed to have a high impact. It would save so much time if researchers could see that a particular experiment had already been carried out and what the results were.

“Openly available raw results for these experiments could also be used and interrogated in different ways; ways that the original researcher did not identify, further facilitating discovery and justifying investment in that research."

In addition, Experimental Results will shake up peer review, introducing scorecards to make the process easier, more open and more attractive to potential reviewers, with each reviewer identified by name and with each review published alongside the article in question with its own DOI.

This will allow the journal’s reviewers to have their work recognised. They will also be given discounts on the cost of publishing their own articles in Experimental Results.

Fiona added: “Our goal is to be progressive, to ensure research outputs are correctly reviewed, and to ensure the reviewers we rely on so heavily are rewarded. This makes sense, much like the journal itself makes sense in its reflection of the actual research process.”

While some journals publish full-paper negative or inconclusive results, published stand-alone results are a rarity. Experimental Results will address the issue in a structured way, with open research practices underpinning the entire concept.

̽��ֱ��journal will be fully open access, assessed through open peer review, and link to open data where possible.

Fiona said: “Part of the problem is that the peer review process doesn’t actually involve checking the results or repeating the experiment.

“Lots of results come out that people can’t repeat but what do they do? Even if they know of other labs that can’t repeat that experiment, if it’s published in a high impact journal then it’s very difficult to dispute those results. Experimental Results will be a venue for researchers to quickly publish reproducibility experiments.”

̽��ֱ��Press’s STM Publishing Director, Caroline Black, said: "We are seeing an increasing acknowledgement that all research outputs – not just the positive, exciting results - should be part of the published record for the advancement of knowledge and reduction of wasted time on redoing work unnecessarily.

“In the past it would have been difficult to publish negative, confirmatory or inconclusive results, as journal editors made decisions on the basis of innovation, interest level and potential for citations. That's beginning to change now.

“People are also looking for alternative types of publication; it's not all about the traditional journal article, complete with introduction, discussion and conclusion setting out the importance of the results. It's great that we are at the forefront of providing them with a new platform."

Press release from Cambridge ̽��ֱ�� Press

A new journal from Cambridge ̽��ֱ�� Press will take a radical new approach to both publishing and peer reviewing research.

Scholarly communication isn’t really reflective of the research process, because the focus is on publishing a concise narrative. ̽��ֱ��reality is that research results are often confusing, inconclusive, or don’t fit a narrative

Fiona Hutton

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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6,000 and counting: Cambridge Vice-Chancellor joins Stephen Hawking in making his PhD ‘Open Access’

sjr81 — Wed, 27 Feb 2019 17:00:09 +0000

Cambridge also becomes first UK university to publish position statement on Open Research.

Step inside the mind of the young Stephen Hawking as his PhD thesis goes online for first time

sjr81 — Sun, 22 Oct 2017 23:01:00 +0000

̽��ֱ��1966 doctoral thesis by the world’s most recognisable scientist is the most requested item in Apollo with the catalogue record alone attracting hundreds of views per month. In just the past few months, the ̽��ֱ�� has received hundreds of requests from readers wishing to download Professor Hawking’s thesis in full.

To celebrate Open Access Week 2017, Cambridge ̽��ֱ�� Library’s Office of Scholarly Communication has today announced Professor Hawking’s permission to make his thesis freely available and Open Access in Apollo. By making his PhD thesis Open Access, anyone can now freely download and read this historic and compelling research by the then little-known 24-year-old Cambridge postgraduate.

Professor Hawking said: “By making my PhD thesis Open Access, I hope to inspire people around the world to look up at the stars and not down at their feet; to wonder about our place in the universe and to try and make sense of the cosmos. Anyone, anywhere in the world should have free, unhindered access to not just my research, but to the research of every great and enquiring mind across the spectrum of human understanding.

“Each generation stands on the shoulders of those who have gone before them, just as I did as a young PhD student in Cambridge, inspired by the work of Isaac Newton, James Clerk Maxwell and Albert Einstein. It’s wonderful to hear how many people have already shown an interest in downloading my thesis – hopefully they won’t be disappointed now that they finally have access to it!”

Dr Arthur Smith, Deputy Head of Scholarly Communication, said: “Open Access enables research. By eliminating the barriers between people and knowledge we can realise new breakthroughs in all areas of science, medicine and technology. It is especially important for disseminating the knowledge acquired during doctoral research studies. PhD theses contain a vast trove of untapped and unique information just waiting to be used, but which is often locked away from view and scrutiny.

“From October 2017 onwards, all PhD students graduating from the ̽��ֱ�� of Cambridge will be required to deposit an electronic copy of their doctoral work for future preservation. And like Professor Hawking, we hope that many students will also take the opportunity to freely distribute their work online by making their thesis Open Access. We would also invite former ̽��ֱ�� alumni to consider making their theses Open Access, too.”

While the ̽��ֱ�� is committed to archiving all theses it is often a struggle gaining permission to open up historic theses. With the online publication of Professor Hawking’s thesis, Cambridge now hopes to encourage its former academics – which includes 98 Nobel Affiliates – to make their work freely available to all.

To make more of the ̽��ֱ��’s theses Open Access in Apollo, the Office of Scholarly Communication and Cambridge ̽��ֱ�� Library will digitise the theses of any alumni who wish to make their dissertation Open Access. Interested alumni should contact thesis@repository.cam.ac.uk

At a recent event to celebrate the 1,000th research dataset in Apollo, Dr Jessica Gardner, Director of Library Services, said: “Cambridge ̽��ֱ�� Library has a 600-year-old history we are very proud of. It is home to the physical papers of such greats as Isaac Newton and Charles Darwin. Their research data was on paper and we have preserved that with great care and share it openly on line through our digital library.

“But our responsibility now is today’s researcher and today’s scientists and people working across all disciplines across our great university. Our preservation stewardship of that research data from the digital humanities across the biomedical and that is a core part of what we now do.”

Apollo is home to over 200,000 digital objects including 15,000 research articles, 10,000 images, 2,400 theses and 1,000 datasets. ̽��ֱ��items made available in Apollo have been accessed from nearly every country in the world and in 2017 have collectively received over one million downloads.

Professor Hawking’s 1966 doctoral thesis ‘Properties of expanding universes’ is available in Apollo at https://doi.org/10.17863/CAM.11283 or in high resolution on Cambridge Digital Library at https://cudl.lib.cam.ac.uk/view/MS-PHD-05437/1

For further information about Open Access Week, visit: www.openaccessweek.org

Stephen Hawking’s PhD thesis, ‘Properties of expanding universes’, has been made freely available to anyone, anywhere in the world, after being made accessible via the ̽��ֱ�� of Cambridge’s Open Access repository, Apollo.

Anyone, anywhere in the world should have free, unhindered access to not just my research, but to the research of every great and enquiring mind across the spectrum of human understanding.

Stephen Hawking

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Pilot programme encourages researchers to share the code behind their work

sc604 — Fri, 02 Jun 2017 07:30:00 +0000

A new pilot project, designed by a Cambridge researcher and supported by the Nature family of journals, will evaluate the value of sharing the code behind published research.

For years, scientists have discussed whether and how to share data from painstaking research and costly experiments. Some are further along in their efforts toward ‘open science’ than others: fields such as astronomy and oceanography, for example, involve such expensive and large-scale equipment and logistical challenges to data collection that collaboration among institutions has become the norm.

Recently, academic journals, including several Nature journals, are turning their attention to another aspect of the research process: computer programming code. Code is becoming increasingly important in research because scientists are often writing their own computer programs to interpret their data, rather than using commercial software packages. Some journals now include scientific data and code as part of the peer-review process.

Now, in a commentary published in the journal Nature Neuroscience, a group of researchers from the UK, Europe and the United States have argued that the sharing of code should be part of the peer-review process. In a separate editorial, the journal has announced a pilot project to ask future authors to make their code available for review.

Code is an important part of the research process, and often the only definitive account of how data were processed. “Methods are now so complex that they are difficult to describe concisely in the limited ‘methods’ section of a paper,” said Dr Stephen Eglen from Cambridge’s Department of Applied Mathematics and Theoretical Physics, and the paper’s lead author. “And having the code means that others have a better chance of replicating your work, and so should add confidence.”

Making the programs behind the research accessible allows other scientists to test the code and reproduce the computations in an experiment — in other words, to reproduce results and solidify findings. It’s the “how the sausage is made” part of research, said co-author Ben Marwick, from the ̽��ֱ�� of Washington. It also allows the code to be used by other researchers in new studies, making it easier for scientists to build on the work of their colleagues.

“What we’re missing is the convention of sharing code or the tools for turning data into useful discoveries or information,” said Marwick. “Researchers say it’s great to have the data available in a paper — increasingly raw data are available in supplementary files or specialised online repositories — but the code for performing the clever analyses in between the raw data and the published figures and tables are still inaccessible.”

Other Nature Research journals, such as Nature Methods and Nature Biotechnology, provide for code review as part of the article evaluation process. Since 2014, the company has encouraged writers to make their code available upon request.

̽��ֱ��Nature Neuroscience pilot focuses on three elements: whether the code supporting an author’s main claims is publicly accessible; whether the code functions without mistakes; and whether it produces the results cited. At the moment this is a pilot project to which authors can opt in. It may be that in future it becomes mandatory and only when the code has been reviewed will a paper then be accepted.

“This extra step in the peer review process is to encourage ‘replication’ of results, and therefore help reduce the ‘replication crisis’,” said Eglen. “It also means that readers can understand more fully what authors have done.”

An open science approach to sharing code is not without its critics, as well as scientists who raise legal and ethical questions about the repercussions. How do researchers get proper credit for the code they share? How should code be cited in the scholarly literature? How will it count toward tenure and promotion applications? How is sharing code compatible with patents and commercialization of software technology?

“We hope that when people do not share code it might be seen as ‘having something to hide,’ although people may regard the code as ‘theirs’ and their IP, rather than something to be shared,” said Eglen. “Nowadays, we believe the final paper is the ultimate representation of a piece of research, but actually the final paper is just an advert for the scholarship, which here is the computer code to solve a particular task. By sharing the code, we actually get the most useful part of the scholarship, rather than the paper, which is just the author’s ‘gloss’ on the work they have done.”

Adapted from a ̽��ֱ�� of Washington press release.

New project, partly designed by a ̽��ֱ�� of Cambridge researcher, aims to improve transparency in science by sharing ‘how the sausage is made’.

Having the code means that others have a better chance of replicating your work.

Stephen Eglen

Lorenzo Cafaro

Close up code

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Opinion: ̽��ֱ��science ‘reproducibility crisis’ – and what can be done about it

cjb250 — Mon, 20 Mar 2017 09:57:15 +0000

A survey by Nature revealed that 52% of researchers believed there was a “significant reproducibility crisis” and 38% said there was a “slight crisis”.

We asked three experts how they think the situation could be improved.

Open Research is the answer

Danny Kingsley, head of the Office of Scholarly Communication, ̽��ֱ�� of Cambridge

̽��ֱ��solution to the scientific reproducibility crisis is to move towards Open Research – the idea that scientific knowledge of all kinds should be openly shared as early as it is practical in the discovery process. We need to reward the publication of research outputs along the entire process, rather than just each journal article as it is published.

As well as other research outputs – such as data sets – we should reward research productivity itself as well as the thought process and planning behind the study. This is why Registered Reports was launched in 2013, where researchers register the proposal and how the research will be conducted, before any experimental work commences. It allows editorial decisions to be based on the rigour of the experimental design and increases the likelihood that the findings could be replicated.

In the UK there is now a requirement from most funders that the data underpinning a research publication is made available. However, although there are moves towards open research, many argue against the sharing of data among the research community.

Questionable findings are often hidden. Shutterstock

Researchers often write multiple papers from a single data set and many fear that if this data is released with the first publication then the researcher will be “scooped” by another research group, who will publish findings from similar data sets before the original authors get the chance to publish follow up articles – to gain maximum credit for the work. If the publication of data itself could be recorded as a “research output”, then being scooped would no longer be such an issue, as such credit will have been given.

One benefit of sharing data could be an improvement in its quality – as previous research has shown. And there have been small steps towards this goal, such as a standard method of citing data.

We also need to publish “null” results – those that do not support the hypothesis – to prevent other researchers wasting time repeating work. There are a few publication outlets for this, and a recent press release from ResearchGate indicated that it supports the sharing of failed experiments through its “project” offering. It lets users upload and track experiments as they are happening – meaning no one knows how they will turn out.

Psychology is leading the way out of crisis

Jim Grange, senior lecturer in psychology, Keele ̽��ֱ��

To me, it is clear that there is a reproducibility crisis in psychological science, and across all sciences. Murmurings of low reproducibility began in 2011 – the “year of horrors” for psychology – with a high profile fraud case. But since then, ̽��ֱ��Open Science Collaboration has published the findings of a large-scale effort to closely replicate 100 studies in psychology. Only 36% of them could be replicated.

̽��ֱ��incentive structures in universities and the attitude that you “publish or perish” means that researchers prioritise “getting it published” over “getting it right”. It also means that some, implicitly or explicitly, use questionable research practices to achieve publication. These may include failing to report parts of data sets or trying different analytical approaches to make the data fit what you want to say. It could also mean presenting exploratory research as though it was originally confirmatory (designed to test a specific hypothesis).

However, many psychology journals now recommend or require the preregistration of studies which allow researchers to detail their predictions, experimental protocols, and planned analytical strategy before data collection. This provides confidence to readers that no questionable research practices have occurred.

Erasing data: a questionable research practice. Shutterstock

Registered Reports has taken this further. But of course, once results are produced, isolated findings don’t mean much until they have been replicated.

I make efforts to replicate results before trying to publish and you’d be forgiven for thinking that replication attempts are common in science, but this is simply not the case. Journals seek novel theories and findings, and view replications as treading over old ground which offers little incentive for career-minded academics to conduct replications.

This has also led to the introduction of Registered Replication Reports in Perspectives on Psychological Science. This is where teams of researchers each follow identical procedures independently and aim to replicate important findings from the literature. A single paper then collates and analyses them to establish the size and reproducibility of the original study.

Although psychology is leading the way for improvements with these pioneering initiatives, it is certainly not out of the woods. But it has started to move beyond a crisis and make impressive strides – more disciplines need to follow suit.

This is a publication bias crisis

Ottoline Leyser, director of the Sainsbury Laboratory, ̽��ֱ�� of Cambridge

Reproducibility is a fundamental building block of science. If two people do the same experiment, they should get the same result. But there are many good reasons why two “identical” experiments might not give the same result such as unknown differences that have not been considered – and some exciting discoveries have been made this way.

So if a lack of reproducibility is itself not necessarily a problem, why is everybody talking about a crisis? In some cases poor practice and corner cutting have contributed to lack of reproducibility, and there have been some high profile cases of out and out fraud. It’s a major concern, but what is causing it?

In 2014 I chaired a project on the research culture in Britain for the Nuffield Council on bioethics, which was motivated by concerns about research integrity including over-claiming, rushing prematurely to publication and incorrect use of statistics. ̽��ֱ��main conclusions were that poor practice is incentivised by hyper-competition with overly narrow rules for winning.

There is an excessive focus on the publication of groundbreaking results in prestigious journals. But science cannot only be groundbreaking, as there is a lot of important digging to do after new discoveries – but there is not enough credit in the system for this work and it may remain unpublished because researchers prioritise their time on the eye-catching papers, hurriedly put together.

̽��ֱ��reproducibility crisis is actually a publication bias crisis which is driven by the reward structures in the research system. Various approaches have been suggested to address problems, such as pre-registration of experiments. However, the research landscape is highly diverse and this type of solution is only sensible for some research types. ̽��ֱ��most widely relevant solution is to change the reward structures. In the UK there is a major opportunity to do this by reforming the Research Excellence Framework (REF). Through the REF, public money is allocated to universities based on the “quality” of the four best research outputs, usually papers, produced by each of their principal investigators over approximately six years and it disproportionately rewards groundbreaking research.

We need reward for a portfolio of research outputs, including not only the headline grabbing results, but also confirmatory work and community data sharing, which are the hallmarks of a truly high quality research endeavour. This would go a long way to shifting the current destructive culture.

Ottoline Leyser, Director of the Sainsbury Laboratory, ̽��ֱ�� of Cambridge; Danny Kingsley, Head, Office of Scholarly Communication, ̽��ֱ�� of Cambridge, ̽��ֱ�� of Cambridge, and Jim Grange, Senior Lecturer in psychology, Keele ̽��ֱ��

This article was originally published on ̽��ֱ��Conversation. Read the original article.

Reproducibility is the idea that an experiment can be repeated by another scientist and they will get the same result. It is important to show that the claims of any experiment are true and for them to be useful for any further research. However, science appears to have an issue with reproducibility.

NIAID

Study of Human Immune Response to HIV

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Ten thousand reasons to celebrate Open Access at Cambridge

sjr81 — Mon, 03 Oct 2016 08:58:45 +0000

̽��ֱ��10,000th submission, reporting on the impact of eating a Mediterranean diet on the risk of developing cardiovascular disease in a UK population, was deposited by Signe Wulund at the MRC Epidemiology Unit, on behalf of Dr Nita Forouhi, Programme Leader in Nutritional Epidemiology at the MRC Epidemiology Unit, and several co-authors.

̽��ֱ��Open Access movement has been growing in strength in academia for many years, and it is increasingly being mandated by funding bodies and government.

Dr Forouhi said: “Through open access our research can reach a worldwide audience. It would be a huge pity if interested researchers, practitioners or policy makers could not read about new research, such as our latest findings on the link between the Mediterranean diet and cardiovascular health in a non-Mediterranean setting, because of something as simple as lacking a journal subscription.

“Open access enables wider dissemination of research findings, and in turn, facilitates better research and evidence-based policy and clinical practice.”

̽��ֱ��Cambridge Open Access Service was established within the ̽��ֱ�� Library in 2013 in response to Research Councils UK (RCUK) making Open Access mandatory for anyone accepting their funding. Many other major funders, including the Wellcome Trust, Cancer Research UK and the British Heart Foundation, have similar policies.

In 2014, the Higher Education Funding Council for England announced that Open Access would be compulsory for any article included in the next Research Excellence Framework (REF) exercise. This policy came into force on April 1, 2016, effectively meaning that all research in UK institutions now has to be made freely available.

Since its inception in 2013, the Open Access service has processed 10,000 manuscripts, across all ̽��ֱ�� faculties and departments and worked with 3,000 different members of staff. 6,000 of the papers were covered by the HEFCE open access policy; 4,000 acknowledged RCUK funding and 1,900 COAF (many papers fall into multiple categories, and some into none). More than £5.4 million of Open Access grants from funding bodies have also been distributed.

Meeting these requirements is a major task for the ̽��ֱ��, and one it has tried to make as simple as possible for researchers. Authors are simply required to upload their manuscript to www.openaccess.cam.ac.uk when it’s accepted for publication, and the Open Access team advise them on what they need to do to comply with funder requirements, eligibility for any funding body grants, and handle depositing the article into Apollo, the ̽��ֱ��’s institutional repository.

Ten thousand manuscripts have now been received in this way, and the vast majority of them have been able to be made Open Access, free for anyone who wants to read and benefit from them.

The 10,000th article: ‘Prospective association of the Mediterranean diet with cardiovascular disease incidence and mortality and its population impact in a non-Mediterranean population: the EPIC-Norfolk Study’ in BMC Medicine. [DOI:10.1186/s12916-016-0677-4] can be seen here: http://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-016-0677-4

̽��ֱ��Open Access team at the ̽��ֱ�� of Cambridge is part of the Office of Scholarly Communication (OSC), within the ̽��ֱ�� Library. As well as assisting researchers with Open Access and Open Data compliance, it advises on scholarly communication tools, techniques, policies and practices, and provides training. For more details, visit www.osc.cam.ac.uk.

̽��ֱ�� ̽��ֱ�� of Cambridge has received its 10,000th Open Access submission – highlighting its commitment to making research freely available to anybody who wants to access it, without publisher paywalls or expensive journal subscriptions.

Through open access our research can reach a worldwide audience.

Nita Forouhi

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Your Questions Answered on open access

Anonymous — Fri, 23 Oct 2015 14:18:08 +0000

Open access means making peer reviewed works freely available in digital form, so that anyone with internet access can use them, without financial, legal or technical barriers. It allows users to download, copy, print and distribute works, without the need to ask for permission or to pay.

To the mark the eighth annual Open Access Week, we asked what readers wanted to know about the initiative.

Why do we need open access? How can I use it? Is it better for the sciences or the humanities?

Lucy Montgomery: Open access is a powerful mechanism for widening access to knowledge and for increasing the impact of research beyond universities. Because it makes peer-reviewed scholarship free at the point of use, open access helps ensure people who need knowledge can access it, even if they can’t afford to pay for it.

Patients scouring the internet for the latest information about rare medical conditions, scholars in the developing world, and practitioners who want to apply evidence-based research to challenges they face every day, are just a few examples of groups who benefit from open access.

̽��ֱ��global shift to open access is being driven by a consensus that the public has a right to access publicly funded research outputs. Closed publishing models rely on recovering the costs of publishing research by selling access to it. This made sense in a print-dominated world, when the marginal costs associated with making and distributing physical copies of books and journals was high; it makes much less sense in digital landscapes where the costs of making additional copies of a work once it’s been published are very low.

̽��ֱ��global shift to open access is being driven by a consensus that the public has a right to access publicly funded research outputs. Gideon Burton/Flickr, CC BY-SA

Once a work has been made open access, it’s free for anyone in the world to read or download. This is a boon for anyone who has ever been frustrated by a pay wall, for teachers looking for resources that can be shared easily with students, and for scholars who hope their work will contribute to a wider body of knowledge.

Although open access has been faster to take off in the sciences, it also has important benefits for scholars working in the humanities: helping authors to share their work with the communities that they write both for and about, and making knowledge and ideas available to new audiences.

How can journals meet the costs of editing, typesetting, proofreading, website construction and management if they move from subscriptions to open access?

Keyan Tomaselli: One of the key blind spots in open access discussions is the cost it poses to publishers. Journals that are not funded by foundations or universities are financially vulnerable in an open access environment unless they start charging for publishing articles. This is because their “permissions income stream”, which are paid to journals through national copyright agencies when their articles are reproduced in student course packs, will dry up.

In this model, the burden of payment will shift from reader or library payment for downloads or subscriptions, to author or institution for articles to be published. ̽��ֱ��assumption that open access is free – after data charges are paid – is wrong because though readers can access articles for free, authors and their institutions will end up paying so journals can recoup their costs. Data charges relate to the cost of internet access and downloading.

Too often one forgets that such accessing of the internet has cost implications too. And then there are journal post-production costs, including online platform hosting, marketing, discoverability, and archiving, among other things.

Open scholarship includes open notebook, open data and open review as well as open access. What are more systematic and rigorous treatments of open scholarship?

It’s now possible to put a digital ‘stamp’ on different scholarly outputs. Gideon Burton/Flickr, CC BY-SA

Danny Kingsley: There’s an increasing amount of research and discussion about open scholarship about integrity and researcher support; research management; assumptions and challenges; and about how we capture what’s being produced in repositories.

But although the nature of research is changing profoundly, the current system still only rewards and recognises traditional publication. Opening up scholarship has multiple benefits: research claims can be verified, work doesn’t have to be repeated to recreate the data, and data can be analysed from other perspectives.

It’s now possible to put a digital “stamp” on different scholarly outputs, called digital object identifiers (or DOIs). This means a researcher can be cited when another uses their work, and receive recognition.

By having an “open process” in research, we can put digital stamps on all aspects of research, such as progress in thinking through an online discussion paper, for instance; new techniques; and approaches and experiments. These can themselves be cited and therefore rewarded, rather than only recognising traditional published outputs.

How do we ensure research published under open access continues to have a system of rigorous quality checks, such as peer review, that can cope with the enormous load of research looking for publication?

James Bradley: We can’t ensure rigorous peer review of research will be undertaken under open access. Not only that, we know for sure that the explosion of open access journals has allowed for the publication of not just bogus work, but also work that’s irrelevant or useless for scientific or the whole academic enterprise.

How do we know this? For starters, there was an infamous sting in late 2013 that revealed a nonsensical piece of research was accepted for publication by a large number of open access journals. Then, there’s the research showing the huge numbers of “predatory” journals, which are basically in it for the money. ̽��ֱ��academic or the academic’s institution pays for publication and the piece gets in, regardless of quality. That’s why so many researchers often get emails from start-up journals soliciting our work — for a fee. It’s all about profit.

There’s another form of quality control that transcends peer review and lies in the after-life of a publication. Gideon Burton/Flickr, CC BY-SA

To mitigate this situation, there’s the Directory of Open Access Journals, which is supposed to act as quality control. If you make it on to the list, then you are supposed to be reputable. But some of the journals that have made it to the list are, in fact, “predatory”.

But it’s false to assume that all research that makes it into a front-rank publication is great or that all work in pay-for-publication journals is junk. ̽��ֱ��peer review system has always had flaws. Ultimately, there’s another form of quality control that transcends peer review and lies in the after-life of a publication — the opinion of your peers.

And this can, to some extent, be measured by metrics through citation databases. But it’s also reflected in the status and reputation accorded by your peers. It was ever thus, and most definitely remains the best form of quality control.

To what extent does this issue go beyond the machinations of open access versus the nuances of what’s free and not free, to the problem of the role of the university in a world where capitalism and the internet frame much of what we do?

Tom Cochrane: Open access has three points of origin. These, in no particular order, are the interests of the researcher in greater exposure and readership; the distorted economics of the price of scholarly communication (as distinct from the true cost of academic publishing); and the fact that the internet has made open access possible in the first place.

Openness in access to research outputs, research data and research processes, enhances replication capability, and allows review. Gideon Burton/Flickr, CC BY-SA

As the debate about open access has matured, it has also become clear that greater openness can also provide protection against research fraud or dishonesty. Openness in access to research outputs, research data and research processes, enhances replication capability, and allows review.

Open access has no particular correlation or causal relationship with the broader role of universities, other than to improve the efficiency and integrity of research and to increase the likelihood of greater integration with their various communities. It’s certainly true that we wouldn’t have seen it develop without the internet and, as such, the movement is another case of innovation and disruption of legacy models.

Where are we getting with the movement, year to year? How much concrete progress has there been as opposed to awareness raising?

Virginia Babour: There’s no doubt that the open access has come a long way. There are now mandates for open access in many countries and institutions globally.

These mandates vary in what they require. Some, like the one in the United Kingdom, are primarily supported through publication in open access journals. Others, like Australia’s funding councils' mandates, are via deposition of an author’s research in university repositories.

There’s also been an explosion of different technologies around open access, including new ideas on what can be published - just parts of articles, such as figures, fir instance – and new models for publishing open access books.

Finally, the infrastructure to support open access is developing with licenses for publishing, which lay out clearly how articles can be used. And identifiers for people and documents (even parts of documents), so there can be better linking of scholarly literature.

Open access is an evolving ecosystem. There will be different models to fit different specialities and probably different countries. But that’s fine if it works.

Virginia Barbour, Executive Officer, Australasian Open Access Support Group, Australian National ̽��ֱ��; Danny Kingsley, Executive Officer for the Australian Open Access Support Group, ̽��ֱ�� of Cambridge; James Bradley, Lecturer in History of Medicine/Life Science, ̽��ֱ�� of Melbourne; Keyan Tomaselli, Distinguished Professor, ̽��ֱ�� of Johannesburg; Lucy Montgomery, Director, Centre for Culture and Technology, Curtin ̽��ֱ��, and Tom Cochrane, Adjunct Professor Faculty of Law, Queensland ̽��ֱ�� of Technology

This article was originally published on ̽��ֱ��Conversation. Read the original article.

̽��ֱ��opinions expressed in this article are those of the individual author(s) and do not represent the views of the ̽��ֱ�� of Cambridge.

Meredith Kahn

Open access

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Scientists release Ebola sequencing data to global research community online

cjb250 — Wed, 03 Jun 2015 07:00:47 +0000

̽��ֱ��team of British scientists, funded by the Wellcome Trust, is using semi-conductor next-generation sequencing technology developed by Thermo Fisher Scientific to generate data in a lab facilitated by Public Health England and International Medical Corps. ̽��ֱ��genetic analysis is being made freely available to the scientific community.

Since the first reported case in March 2014, the Ebola outbreak has claimed nearly 11,000 lives in West African countries. Professor Ian Goodfellow, Head of Virology at the ̽��ֱ�� of Cambridge, travelled to Sierra Leone in December last year and then again in March this year to help set up a new diagnostics centre attached to an Ebola Treatment Centre in one of the country’s worst affected parts. He returned a third time, together with his postdoc Dr Armando Arias, to study the virus at a molecular level using the sequencing technology.

“Sequencing the genome of a virus can tell us a lot about how it spreads and changes as it passes from person to person. While this information is invaluable to researchers, the rapid sharing of data does not always occur,” said Professor Paul Kellam at the Wellcome Trust Sanger Institute, who is leading the team to map the genomic data captured by Professof Goodfellow and colleagues. “It used to take months to process samples that had to be brought back to labs in the UK for analysis. Having sequencing capabilities on the ground helps generate data in a matter of days or at the longest weeks, which should have a profound impact on how the Ebola virus is researched and inevitably addressed on a global scale.”

Rapid sequencing enables epidemiologists to decipher the source of individual strains, and helps eliminate the need to rely upon Ebola patients to tell them how and where they contracted the virus, as different strains can be tracked as they are transmitted from person to person.

“Only by understanding the Ebola virus and other pathogens, which cause so much suffering in countries like Sierra Leone, can we take meaningful steps to protect communities from future outbreaks,” said Goodfellow. “My hope is that this technology will be used by the next generation of Sierra Leonean scientists and researchers to help provide a sustainable research and surveillance system in the future.”

̽��ֱ��next-generation sequencing system was installed at the laboratory adjacent to an Ebola Treatment Centre in Makeni, which was funded by the UK’s Department for International Development. In order to ensure a lasting benefit for the project beyond the current crisis, the next-generation sequencing system is expected to be installed at the ̽��ֱ�� of Makeni, where it will be used by local scientists to study Ebola, and other pathogens that affect the region.

“We’ve learned many painful lessons from the Ebola outbreak, not least of which is that as a scientific community we must become less secretive with the data that is generated,” added Dr Jeremy Farrar, Director of the Wellcome Trust. “ ̽��ֱ��collective expertise of the world’s infectious disease experts is more powerful than any single lab, and the best way of tapping into this is to enhance the capacity to generate the data in the countries affected, rather than having to fly samples out to other countries and then to make the data openly and safely available, as soon as possible.”

Adapted from a press release from Thermo Fisher Scientific, USA

A team of scientists, part of the international effort to curb further spread of the Ebola virus in Sierra Leone, has released its first dataset of the virus’ genetic structure online. ̽��ֱ��dataset will allow the global scientific community to monitor the pathogen’s evolution in real-time and conduct research that can lead to more effective strategies against further outbreaks.

Only by understanding the Ebola virus and other pathogens, which cause so much suffering in countries like Sierra Leone, can we take meaningful steps to protect communities from future outbreaks

Ian Goodfellow

CDC Global

Ebola virus

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