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October 20, 2003 Editor: Jonathan Weitzman
Biologists are in good Company
UK-based charity The Company of Biologists has decided to join the experiment by several traditional publishers to offer an ‘Open Access option’ to their authors.
From January 2004, any author whose paper is accepted for publication in one of The Company of Biologists (COB) journals will have the option of paying to ensure that their published article will be immediately and freely accessible via the Internet. This is a bold step for the charity that operates as a not-forprofit publisher based in Cambridge, UK, with publications including three prestigious journals - Development, Journal of Cell Science and The Journal of Experimental Biology. A statement from the Company of Biologists explains that they are exploring the author-pays model “in response to the biological community’s drive for freedom of access to scientific research,” adding that “authors choosing to take advantage of the Open Access alternative will be charged a publication fee, which, as an introductory offer, will be heavily subsidised by The Company of Biologists.” Initially at least, the author-pays model for some articles will run in parallel with the existing subscription model for all others. The author-funded approach is emerging as a dominant strategy for traditional publishers who are interested in experimenting with hybrid author-pays and subscription models as part of a slow and cautious transition towards Open Access publishing. Oxford University Press (OUP) recently announced that it would be conducting a similar experiment with its flagship journal, Nucleic Acid Research, in the initial stage of a transition process that will move towards author-funded
Conversation with MacKenzie Smith about DSpace technology and self-archiving
little risk to their subscription incomes; this approach, sometimes referred to as the WalkerProsser model, was developed by several American entomology journals. “I think that nobody doubts that making the scientific literature immediately accessible to everyone should be our ultimate goal,” says Richard Sever, the Executive Editor of Journal of Cell Science. “The challenge for non-profit publishers such as COB is to move from a business model that has served us well for decades to a completely different model without jeopardizing the future of our journals or becoming prey to our commercial competitors. We hope our hybrid experiment will allow us to do this and also to test the level of real enthusiasm amongst authors.” These experiments should be supported by the Open Access movement as they represent a genuine commitment by high-profile publishers to ‘test the waters’ and explore the feasibility of shifting their well-respected (and profitable) journals towards Open Access. Questions remain, however, about exactly how open the access is. A recently agreed definition of full Open Access includes not just immediate free access to electronic versions of each research article, but also the right to copy and distribute the work, as well as a commitment to deposit the article in a public repository (see Open Access Now, July 14, 2003) – and the latter aspects of the definition are crucial for indexing, searching and data mining. The Company of Biologists is replacing copyright transfer with an exclusive licence agreement, which allows authors to retain ownership of their work while providing the journals with the exclusive rights to publish it. Clearly, success with this experiment would encourage The Company of Biologists to accelerate its transition to full Open Access. www.biologists.com
journals over a five-year period (see Open Access Now, September 8, 2003). “Two important issues to address are how the Company might recover its publishing costs if we do move to full Open Access and how much publication fees will have to increase to achieve this,” says Jim Smith, Editor-in-Chief of the journal Development. “In this regard it is good news that several funding bodies are receptive to the idea of providing publication costs as a specified component of the grants they award.” The Company of Biologists and OUP will each charge authors £500 per published article, which may represent less than a third of the real costs of publishing each article. Both publishers are to offer their versions of Open Access for a trial period and both predict that the pace of the transition will be determined by how well authors respond. The hybrid model offers them a way to manage the transition period, with
STOP PRESS • STOP PRESS • STOP PRESS • STOP PRESS
As we went to press, the Wellcome Trust, the UK's leading biomedical research funder, issued a strong statement in support of Open Access, and announced that it would meet any associated publication charges. Look out for in-depth coverage of this development in the next issue of Open Access Now. A1
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Open Access Now
Interview
A journey into DSpace
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nstitutional full-text repositories have recently emerged as a promising way of providing increasing access to scholarly research material. DSpace is an institutional digital ‘super-archive’ system jointly developed by Massachusetts Institute of Technology Libraries and Hewlett-Packard Laboratories. Open Access Now talked to MacKenzie Smith, director of the MIT DSpace team, about the DSpace project.
Much of the high-profile focus of the Open Access movement has been on providing Open Access alternatives to traditional subscription-based research journals. But the Internet also provides another way for researchers and their host institutions to provide free access to their research articles, in the form of institutional or ‘self’ archives. As with so many web-based technologies, however, self-archiving is not quite as straightforward as it might seem. pressing need for systems to collect, preserve, index and distribute them. But the time and technical expertise required to do this properly are beyond the resources of most laboratories or departments. The DSpace system provides a way to manage research materials and publications in a professionally maintained repository, to give them greater visibility and accessibility over time. “We designed a platform that was somewhat neutral about the politics of access,” Smith notes. “We wanted to create a tool that universities could use to support Open Access, if that was their goal, but that would not prohibit them from having restricted-access material as well, if that were necessary. And because the initiative came out of the library and archive community at MIT, we were very concerned about the issues of long-term access and preservation. If researchers move to a model of self-archiving over time and there are fewer and fewer things being published in print, then you have to worry about the scholarly record for the future. So, we tried to design a platform that would also help support institutions that want not only to make the material more accessible to the public but also to preserve it so that it’s still there in a hundred years’ time. The two main functional aspects of DSpace are preservation and access to the material.” DSpace manages and distributes digital items, made up of digital files (or bit streams) and allows for the creation, indexing, and searching of associated metadata to locate and retrieve the items. Each DSpace service is comprised of ‘communities’ – research
DSpace and Open Access
DSpace began three years ago with a US$1.8 million collaboration between Massachusetts Institute of Technology (MIT) Libraries and Hewlett-Packard (HP) to develop a dynamic repository for intellectual output in digital formats. “DSpace was originally conceived as a tool to assist universities, and particularly research universities, with making research material more
Picture courtesy of MIT
“We are trying to get the barriers down so low that people can do self-archiving without even thinking about it,” says MacKenzie Smith
a web-based application, so if the material is made publicly available then access can easily be unlimited. “You can limit access to the university campus community, or even to your department or lab,” says Smith. “Our philosophy is to give people the tool to do what they want to do, but constantly encourage them and remind them of our greater goal – to make more of this information available to the public. We have noticed that a lot of faculty are reluctant or nervous about all this and we realize that it may take some time to convince them that it’s a good idea. Open Access is something that some disciplines have embraced in a big way, while other disciplines have reservations and concerns.” Smith is keen to emphasize that what an institution does with DSpace is entirely a matter of the policy of that institution. “At MIT we made a series of decisions about how we are going to use this platform. For example, we have limited it to faculty research material and teaching material; we don’t accept student work or material from non-affiliated researchers. But another university could decide to do something quite different with it – requiring all campus members to deposit their articles, or whatever.” MIT has a policy of encouraging, rather than forcing, faculty to deposit material in the electronic archive. “We don’t dictate how people use this system; we encourage them and show them by example what you can do with it,” says Smith. Development of the software by MIT and HP took nearly two years and the DSpace system has been in production at MIT for about a year. “At MIT there is a very wide understanding of the system, what it’s for and what
The two main functional aspects of DSpace are preservation and access to the material
easily available, through Open Access wherever that was possible,” explains Smith. Universities and research institutions are developing research materials and scholarly publications in increasingly complex digital formats, and there is a groups that contribute content to DSpace. The communities might be departments, laboratories, research centers, or any other administrative unit within an institution. Communities determine their own content guidelines and decide who has access to the community’s contributions. DSpace is
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it does,” says Smith. But she admits that adoption by the MIT faculty has been fairly slow. “It takes a while, and part of the reason for that is that communities have to make a lot of decisions about policies – who can submit, who has access, what is the workflow involved,” she explains. “Communities have to sit down and think hard about how people will submit files and how they will be processed before being posted; this can take anywhere from six months to a year depending on the department. It is really making people think about how they want to share their research material.”
Greater sharing
Smith also explains how implementing DSpace at MIT has encouraged faculty to think about what it is that they want to share, and with whom. DSpace is designed with a flexible storage and retrieval architecture adaptable to a multitude of data formats and distinct research disciplines. Each DSpace community has its own customized user portal that can be adapted to the community’s own practices and terminology. DSpace accepts all manner of digital formats: from standard documents, such as such as articles and preprints, to working papers, conference papers, books, or theses, as well as large datasets, visual images and audio files. “We work closely with our faculty about what kind of things they can be putting into the system,” says Smith. She notes that MIT researchers have been particularly receptive to ways to openly distribute supplementary material, genome-scale datasets and images. DSpace provides permanence, which is preferable to storing information on a random departmental webserver. “We have made a policy decision to make the service free for MIT faculty. If they need additional help – like extensive storage space or help creating metadata – then we have cost-recovered services to support them.” “Every university worth its salt has some kind of library or archive and those were set up mainly to store things that were published outside the university that the faculty needed access to. But now more and more things, such as technical reports and working papers, are being published internally and fewer things are getting to some kind of formally published form. So that has become the scholarly record now. But who is taking care of all these datasets and image sets? Some academics are trying to do all of it themselves, but they don’t really have the resources. A few disciplines have a central archive for it but most
of them don’t. So it seems kind of obvious that universities and other research institutions have to start doing this for at least their own material. And platforms like DSpace are designed to help with this problem.” Smith says that the MIT Library team are hoping to attract as many research papers as possible because of the issues of Open Access. “But the system isn’t limited to dealing with papers,” she adds. “It’s meant to start to get research institutions positioned to deal with all the research information they are creating. For example, we are in the process of converting about 10,000 theses to put in to DSpace. Some of the things we are learning are very surprising. For example, a lot of faculty are very worried about their teaching material: they are creating all these great online course materials and there is nowhere to put them, so they have to try to do it themselves or rely on inadequate course-management systems.” There is also a lot of non-textual material, which has made it hard to develop effective search strategies. Currently, the MIT DSpace system preserves files in the format in which they were deposited without automatic conversion to a standardized format. But the developers are continuing to think about strategies for long-term preservation.
Photo courtesy of Donna Coveney, MIT
MIT’s Killian Court and the Great Dome - a landmark at the Institute
The Federation is currently being defined by a core group of eight universities who are evaluating DSpace in different institutional contexts, and a further 120 institutions worldwide who are looking into the system. “The system has also been downloaded about 5,000 times,” says Smith. “We provide a fair amount of technical documentation and other kinds of help to get people started and as much additional support as we can manage with our limited financial resources.” In the spirit of open-source software, many people have developed tools to help other users take advantage of Dspace. Smith says that a reasonable IT team can set up DSpace within a week. “But if you want to turn it into a production system then it takes longer to develop the necessary policies and administrative processes.” One important aspect of institutional repositories is that they can encourage “If faculty get addicted to using systems like DSpace and start to put in all their research articles, and if every research institution in the world has something like this, then over time it could become a serious alternative to commercial publishing as a means of communication between scholars,” Smith speculates. “Whether that is what happens, we will have to wait and see. But we certainly set the system up so that could happen. We are promoting it and trying to get every research institution in the world to do this, or something like it, and they should all be interoperable. We all support the same standards, and the systems can all talk to each other, so you can imagine a sort of virtual library of every research publication in the world.” “Some disciplines are very eager to move ahead and some just don’t get it. But you have to start somewhere,”
The DSpace Federation
The original goal of the DSpace developers was to create a system that could be widely used by universities and research institutions. The DSpace system is freely available as opensource software: it is available for anyone to download and run at any type of institution, organization, or company (or even just as an individual). Users are also allowed to modify DSpace to meet an organization’s specific needs. To encourage wide-scale use of Dspace, MIT Libraries and HP established the DSpace Federation, with the goal of bringing together sets of universities or research organizations that share similar concerns and problems. Currently the DSpace Federation Project is supported by a grant from the Andrew W. Mellon Foundation and aims to test the application of DSpace in a variety of university settings, to discuss what sort of multi-institutional federated services might usefully be built on the DSpace platform, and to explore how interoperability among these organizations’ systems may create a far more valuable resource than is possible through individual systems.
You can imagine a sort of virtual library of every research publication in the world
an institution-wide commitment to Open Access. Smith admits that ‘super-archives’ are not yet accelerating Open Access. “But the first step is to provide the platform that allows it to happen at all. Then the second step is to go out and promote it and explain to faculty why there are problems and encourage them to think about how they would want to use a tool like this.” concludes Smith. “Researchers in the life sciences are pretty good in general about the idea of sharing. The first step is to provide the tools to enable it and the next is to get out there and let people know about it. We are trying to get the barriers down so low that people can do self-archiving without even thinking about it.” www.dspace.org
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Open Access Now
Letters
24 September 2003 Dear Sir, I enjoyed your ‘Who, What & Why?’ about The Directory of Open Access Journals [www.doaj.org]. It is great! May I suggest two additional links: 1) We are now planning The Second Nordic Conference on Scholarly Communication, “Towards a New Publishing Environment”. The conference is arranged by Lund University Libraries [www.lub.lu.se] in Lund, Sweden, 26-28 April 2004, and we have invited a number of well-known international speakers [www.lub.lu.se/ncsc2004]. 2) The Swedish Resource Centre for Scientific Communication (ScieCom) [www.sciecom.org] is a collaborative project between Swedish university and college libraries, and is sponsored by BIBSAM (the Royal Library's Department for National Co-ordination and Development). ScieCom has its administrative and co-ordinating base at the Lund University Libraries Head Office, Lund University. ScieCom was created in response to the current crisis in the field of scientific communication. The aim is to provide information about what is happening, to stimulate discussion and debate, and to describe initiatives. The project collates, evaluates and describes articles, web resources and other relevant material. Best regards, Berit Nilsson Lund University Libraries, Head Office, Lund, Sweden. Send your letters to: openaccess@biomedcentral.com
Research news from BioMed Central journals
Exploring cell shape the high-throughput way
Researchers at the Howard Hughes Medical Institute in Boston have used a high-throughput screening method for finding out what Drosophila cytoskeletal proteins do. The technique, which makes use of RNA-interference with cells in culture, will allow scientists to “look at any cell biological process and systematically test the set of genes that could be involved.” The procedure, described in the next issue of Journal of Biology, involves adding specific double-stranded RNA to arrays of cells in culture. After three days, when the targeted gene should be inhibited, the cells are photographed using an automated
microscope. Clustering genes by their effects has allowed the researchers to assign functions to previously uncharacterised genes. Journal of Biology 2003, 2:27 jbiol.com/content/2/4/27.
be effective against some cancers. Journal of Biology 2003, 2:28 jbiol.com/content/2/4/28
Resistance exercise resets the body clock
Resistance exercise may directly reset the body clocks in skeletal muscle, according to research published in Genome Biology. Dr Alex Zambon, the lead author on the study said, “Our findings support the idea that peripheral clocks can regulate themselves independently of the central clock in the hypothalamus.” The research team used microarrays to analyze the expression of a wide range of genes in biopsies from exercised and non-exercised human skeletal muscle. They found that exercise caused a phase shift in the expression of genes that normally varied in a 24hour cycle. This had the effect of ‘winding on’ the muscle clock. Genome Biology 2003, 4:R61 www.genomebiology.com/2003/4/10/ R61
Links between diabetes and cancer?
An unexpected link between diabetes and Peutz-Jeghers syndrome, a hereditary disease that increases the risk of suffering from cancer, has been uncovered by researchers at the University of Dundee. The team was looking for a protein that activates AMP-activated protein kinase, an enzyme that reduces blood glucose levels and is activated by commonly used diabetes drugs such as metformin. They hoped that this protein would be a target for new anti-diabetes drugs. Their search ended with an enzyme called LKB1. Surprisingly, lack of LKB1 is a known cause of Peutz-Jeghers syndrome. This unexpected link might mean that some drugs that treat diabetes might the Steering Committee that guides CNI’s activities. CNI’s Executive Director is Clifford Lynch, who is based at the organization’s offices in Washington, DC. The Coalition is comprised of around 200 members, including higher education and library institutions, professional and scholarly organizations, and publishing and information technology companies.
Who, What & Why?
As a short guide to the players and technical terms relevant to Open Access publishing, ‘Who, What & Why?’ keeps readers informed about the world of Open Access. This week we focus on the Coalition for Networked Information (CNI).
Open Access journals: use them, read them, cite them and... submit to them
To submit a manuscript or for more information, visit the BioMed Central website: www.biomedcentral.com
Why does CNI exist?
CNI was established to broaden thinking beyond issues of network connectivity and bandwidth to encompass networked information content and applications. It was felt that new partnerships and new technologies were required to reap the benefits of the Internet for scholarship, research, and education. The Coalition seeks to further these collaborations, to explore new institutional roles, and to catalyze the development and deployment of the necessary technology base. The CNI program is structured around three central themes: developing and managing networked information content; transforming organizations, professions and individuals; and building technology, standards and infrastructure.
What is CNI?
The Coalition for Networked Information (CNI) describes itself as “an organization designed to advance the transformative promise of networked information technology for the improvement of scholarly communication and the enrichment of intellectual productivity.” It was founded in 1990 and has addressed many issues related to the development and use of networked information in the research and education communities.
Open Access Now
Open Access Now is a newsletter informing researchers in the life sciences about the issues involved in Open Access publishing. We welcome any feedback, comments and suggestions for articles: openaccess@biomedcentral.com Visit our website: www.biomedcentral.com/openaccess Editor: Jonathan Weitzman, PhD Production: Jonathan Draper Publisher: BioMed Central
Who is behind CNI?
The Coalition is sponsored by the Association of [North American] Research Libraries (ARL) and the non-profit coalition EDUCAUSE, which provide oversight and appoint
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www.cni.org
The Open Access Publisher
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