Technology Blog

source: Nokia World - CTO keynote

Heather Morrison, Open Access in Physics and Chemistry, or, A Tale of Two Disciplines, a presentation at the McGill Library School, November 27, 2006. Excerpt: There are disciplinary differences in awareness of, and approaches to, open access and other types of “openness”. It is likely that there are no great differences than the differences between physics and chemistry. Physics, as a

source: OA in physics and chemistry

Salvatore Mele, David Dallman, Jens Vigen, and Joanne Yeomans, Quantitative Analysis of the Publishing Landscape in High-Energy Physics, a preprint, self-archived November 26, 2006. Abstract: World-wide collaboration in high-energy physics (HEP) is a tradition which dates back several decades, with scientific publications mostly coauthored by scientists from different countries. This

source: Cross-national co-authorship data could help the transition to OA

Barbara Kirsop, Creating a National Open Access Policy for Developing Countries, Open and Shut, November 29, 2006.  Excerpt:

Meeting in the idyllic surroundings of the Indian Institute of Science campus, in Bangalore, the 44 participants of the [Workshop on electronic publishing and open access, November 2-3, 2006] included scientists and OA experts from India, China, Brazil and South Africa, along with colleagues and OA advocates from a number of other countries….

[W]hy was it felt necessary to hold a workshop on OA so soon after the Salvador Declaration on Open Access for Developing Countries, held in September 2005?  The Bangalore workshop was not intended to be a venue simply for confirming acceptance of the principles of OA, but was convened to bring some of the most scientifically advanced developing countries together to report on progress, and consider a model National Open Access Policy that could be offered to governments, and their funding organisations, as a practical tool for driving OA forward.

The aim, therefore, was to take the next step towards ensuring the implementation of earlier OA declarations, not just to talk about OA….

[S]ince the cost of academic journals is prohibitive for many developing countries, scholarly communication is for them severely restricted.  This is a huge problem: A survey conducted by the WHO in 2003, for instance, found that in 75 of the poorest countries, 56% of the medical institutions had been unable to access any journals over the previous five years….

Furthermore, the cost of printing and distributing local journals means that much developing world research is ‘invisible’ to the rest of the world….As a consequence, the incorporation of regional knowledge into international programmes remains minimal. Yet with the growth of global problems — think only of HIV/AIDS, avian ‘flu, environmental disasters, climate change or crop failure — it is essential that the countries in which these problems are most commonly experienced have access to research findings, and can contribute their crucial experience to finding global solutions.

Without both improved access and regional visibility, the science base of poorer countries will not be strengthened, and it is well documented that without a strong science base economies remain weak and dependent on others….

It is clear…that wherever researchers have embraced OA, the visibility, quality and the impact of local research has flourished, and subscriptions to OA journals have even increased — a clear indication that researchers were previously information-starved….

One Indian institute…is ‘gently persuading’ its scholars to deposit their articles by refusing travel support to those that do not archive their publications!…

It was agreed…that progress could be significantly speeded up if a model National OA Policy could be drawn up, and developing countries encouraged to adopt it.  It was also felt that this would be particularly effective if it was formally accepted by a group of local experts — of which there was no shortage at the workshop — who know and understand the problems faced by developing countries on the ground.  While there was vigorous debate on how to encourage adoption of such a policy, there was no dissent over the need for it, or of its basic form.

Specifically, the draft Policy document urges governments to require copies of all publicly funded research published in peer-reviewed journals to be deposited in an institutional repository as soon as publication is accepted and encourages government grant holders to provide open access to their deposited papers immediately upon deposit. Grant holders are also encouraged to publish in a suitable open access journal where one exists. This should be a condition for research funding for any papers partly or fully funded by the government….

All presentations, lists of participants and the draft model National OA Policy document are available on the workshop web site.

source: Background on the Bangalore model national OA policy

source: Nokia World - Yahoo keynote

Yes, it’s a bit cheesy, and yes the demographics form is needless and naively too personal, but nonetheless, NLP proponents have long boasted no need to know their clients to reframe results, and Mentor Hall’s MindMentor is pretty compelling evidence that maybe they are right: you are guided through a ‘Contrast Frame’ and then confronted with your own perception of your life-skills issue, and presented your own proposal for an action plan to address it.

Does it work? That’s what Dutch psychologists Jaap Hollander and Jeffrey Wijnberg want to know, so they’ve made it free for the holiday season — and it’s worth a spin; if you’re worried about the lack of privacy policy, you can always fill in false contact info!

In his first month on line, MindMentor did 582 coaching sessions … He achieved a solution percentage of 55%. .. You can imagine we are somewhat euphoric about this result.

MindMentor [is] an intern; a beginning electronic coach/therapist who is showing great promise but who still needs to learn a lot. In order to help him learn, we would like him to do as many coaching sessions as possible. Therefore we have decided to offer his services to the international NLP community, free of charge.
[ MindMentor ]

Your chance for free robo-therapy lasts for the month of December.

source: The MindMender

Jonathan Eisen, Has your scientific research been wasted? The Tree of Life, November 27, 2006.  Excerpt:

…I [am] somewhat depressed over something I did Sunday night. I decided to remove myself from the UC Davis internet proxy to see how many of my past papers that I have published I can obtain without the UC subscriptions. So I went to pubmed, and typed in my name (Eisen JA) and got most of my papers, which are listed at the bottom of this blog….And then I went to see how many of my papers were freely available and how many were not. What I was most interested in was - what is the deal with papers I wrote before becoming an Open Access convert? For many it is easy to figure out if they are freely available - Pubmed has a link saying “Free in PMC” which refers to Pubmed Central. For others, it was a little trickier.

The results were both good and bad and a summary is below. A few things struck me. First, a lot of my life’s work is not readily available without paying other for it. In the day and age of the internet, this means that these papers will simply be read less and less as time goes by. And that makes me very sad. If I had chosen to publish those papers in other journals, anyone in the world could get them at any time. Thankfully I did publish many papers in journals like PNAS, and ASM journals, and NAR - journals that have now decided to release them to Pubmed Central. And also thankfully (but less so) I published some papers in journals that have at least made them freely available on their web sites.

Most surprisingly to me is that a reasonable number of my papers in Nature are freely available on the Nature web site as part of their Genomics Gateway program. Nature deserves serious kudos for doing this and they stand out compared to Elsevier journals (which do not seem to ever do this) and even Science. This is disappointing as Science is published by a scientific society but apparently does not seem to care much about access to publications….

source: Who can read your past publications?

SPARC and CARL have issued a joint press release commending the Canadian Institutes of Health Research (CIHR) for its draft OA policy.  Excerpt:

SPARC (the Scholarly Publishing and Academic Resources Coalition) and CARL (the Canadian Association of Research Libraries) –together representing over 200 academic and research libraries across North America– commend the Canadian Institutes of Health Research (CIHR) for the strength and timeliness of its Draft Policy on Access to Research Outputs.

The Draft Policy will govern peer-reviewed journal publications, research materials, and final research data stemming from CIHR funding, It marks a significant step forward for Canadian science and puts Canada in the forefront of the global open access movement. CIHR is the major federal agency responsible for funding health research in Canada.

In its response to the Draft Policy SPARC presents three recommendations for refinement:  [1] That grantees be required to comply with the policy; [2] That the specifications for qualified archives and repositories should be explicitly detailed; and [3] That articles must be deposited immediately upon publication in an open archive, but to offer the flexibility of allowing the grant or award recipient to perform the deposit or to require the journal (or another agent) to make the deposit on the researcher’s behalf and in compliance with CIHR requirements.

The SPARC letter also highlights the importance of access to data….

In its response CARL asks that CIHR work with stakeholders [1] To develop a Canadian-based solution for housing and making accessible the outputs of CIHR-funded research over the long term; [2] To implement a more structured approach to providing access to research data; and [3] To ensure that compliance to the policy is linked to future funding decisions….

The CARL letter is also supported by the Association of Research Libraries (ARL).

“SPARC commends CIHR’s goals as well as the overall draft policy, which is strong, timely and consistent with emerging practice internationally,” said SPARC Director Heather Joseph. “We encourage CIHR to continue to move forward and implement a policy that effectively ensures the open sharing of CIHR research outputs.” …

The SPARC letter to CIHR is online [here].  The CARL letter is online [here].

source: Two library groups support draft CIHR policy

source: Nokia World - OPK keynote

Frederick Noronha, Scientists push open access for developing nations, SciDev.Net, November 29, 2006.  Excerpt:

Scientists from Brazil, China, Ethiopia, India and South Africa have set guidelines for developing countries to freely access publicly funded research….

The guidelines were agreed at a workshop in Bangalore, India earlier this month (2-3 November) where 44 international participants — including scientists and policymakers — discussed ways to promote open access….

Scientists in the developing world have long complained that their work is invisible to scientists in North America and Europe, said Alma Swan, co-director of Key Perspectives Ltd, a UK consultancy company for scholarly information.  “Now the developing world has the opportunity to create the level playing field it has so long cried out for,” she told SciDev.Net.

While participants agreed on the policy, there was lively debate on how to make governments adopt it, Barbara Kirsop, secretary of the UK-based Electronic Publishing Trust, told SciDev.Net….

Their policy urges governments to require all publicly funded research published in peer-reviewed journals be deposited in an institutional digital database as soon as publication is accepted. This should be a condition for research funding for any papers partly or fully funded by the government.

Eve Gray, a fellow at the Open Society Institute in South Africa said that policymakers in governments and institutions have the power to determine the reach of scientific research.  “They can make [the research] instantly visible, or they can fail their staff,” she told SciDev.Net….

The workshop revealed that Bioline, an online publisher for developing countries, saw a huge increase in requests for scholarly papers when it became open access.  This shows “how much information was unused, unknown, un-accessed before open access”, says Kirsop….

source: More on the Bangalore model national OA policy

Kate Worlock, Exploring the Economic Impacts of Open Access:  An interview with Professor John Houghton, EPS IMI, November 2006 (accessible only to subscribers).  Excerpt:

Professor John Houghton is the Director of the Information Technologies and the Information Economy Program, Centre for Strategic Economic Studies at Victoria University in Melbourne, Australia. He is one of the driving forces behind the EASI-OA research program, which aims to provide a coordinating focus for new research on the economic and social impacts of open access….He spoke to Kate Worlock about his preliminary findings, details of which were presented at the JISC Moving Towards Open Access conference in September 2006.

What were the driving issues behind your research?

Two things: some frustration with the debate on open access, and wanting to engage senior policy makers….

[T]he open access debate…seems to be all about costs. Economists are less interested in the level of cost than in which systems are most cost-effective – the cheapest way of doing things may not necessarily be the most cost-effective. This led to the idea of measuring the impact of, or benefits derived from, the content, as well as the costs of production and publication.

I was a co-author of a report for the OECD on scientific publishing a couple of years ago, with the intention of engaging high-level policy makers who weren’t involved in the debate among publishers, librarians and researchers and raising the issue of open access in their minds. I continue to try to frame the research in such a way as to engage senior policy makers.

In recent work we have looked at the potential impacts of open access on returns to investment in R&D. The Australian report follows on from that by looking at the costs and benefits of scholarly communication – although this is not be easy to do….

What are the key findings to date?

There are three key findings.

• The costs of scholarly communication are substantial.
• The potential impacts of enhanced access to content are also likely to be substantial.
• Policy makers should note that access to content may be an important determinant of returns to R&D spending….

How do you believe that the move towards open access will shape up?

The movement towards open access is likely to be painful, messy and slow, involving many competing business models. Take-up will vary by discipline….

I do not see a long-term future for copyright-based scholarly publishing. The future for publishers probably lies in adding value to open access content through peer review, compilations and toolsets. Publishers will need to face a whole new range of competitors, including technology players such as IBM and software companies, who are focusing on the life sciences as a lead market.

source: An interview with John Houghton on the economic impact of OA

Like a few other anti-spammers, I found myself under a hitherto-unprecedented
level of spam blowback this weekend. Disappointingly, there are still
thousands of SMTP servers configured to send bounce messages in response to
spam.

Even with the anti-bounce ruleset for SpamAssassin, the volume was so great
that our creaky old server had a lot of difficulty keeping up — once
the messages got to SpamAssassin, the load issues had already been created.
Also, Postfix’s anti-spam features really weren’t designed to deal with
blowback.

While attempting to take some shortcuts in the setup on our server to deal with
this, a great idea occurred to me — why not come up with an app that uses Amazon EC2 to flexibly provision enough
server power and bandwidth to pre-filter the SMTP traffic for an MX under
attack?

I’m basically thinking of qpsmtpd, with SpamAssassin and/or other antispam blobs active, running in an Amazon EC2 server image. Multiple images can be brought up, and added to the attacked domain’s MX record at an equal priority, to take load off the main (overloaded) MX.

Now to cogitate a little — details to follow…

Tags:amazon anti spam aws ec2 qpsmtpd s3 smtp

This post was written by Justin, source: Using qpsmtpd and Amazon EC2 to provide SMTP-DDoS protection

Open access helps when disciplines overlap, Research Information, December 2006 /January 2007.  Siân Harris interviews with Mark Cassar, manager for journal development at the American Institute of Physics (AIP).  Excerpt:

What has been AIP’s experience of open access?

Our mission is to diffuse physics knowledge but we also have to be able to stay in business and continue to serve the physics community. Open access is one of the biggest issues now. We have to try out different means of publishing and see what works for our different communities.

We are approaching open access in two ways. The first is the hybrid model. Our ‘Author Select’ option is now offered on all subscription titles. This has not really had a high uptake so far and if we were only looking at the uptake it could be deemed a failure. However, having this author-choice option does not disrupt the traditional model, but it gives those with a funding requirement to make their work open access an opportunity to do so. People who don’t want it don’t have to take it. It has been a good way to gauge the reaction to open access.

The other model is Biomicrofluidics, our new fully open-access, online-only journal. This is the first in a series; our plan is to launch more fully open-access titles. Although this journal is just starting, the response so far has been good. The biomicrofluidics community is smaller than the general physics communities but there is interest and we will probably know more about how it is going in six months or so. Open access is good for interdisciplinary titles such as this one. Being open access enables anyone to look at the full text. If this was a subscription title it might not be high on the list of priorities for subject-specific librarians because only a few researchers from their disciplines might be involved in this area….

What is AIP’s view of author self-archiving?

Our copyright policy allows authors to post the final PDFs of their articles on their own websites or the post-print versions on their employer’s website or institutional repository. Our main requirement with archiving is just that authors can’t charge for people to access their copies of the articles. We also have a policy to help authors to comply with funding-body requirements such as those from the US National Institutes of Health (NIH).

source: AIP on OA

Catherine Jones, Collecting research output, Research Information, December 2006 /January 2007.  Excerpt:

The positive stance that many research councils take on author and institution self-archiving is a familiar topic. But this goes beyond passive support of the concept. Some research councils are also providing tools that help other organisations to build and maintain their repositories. One example of this is Scitate. This institutional-repository software support package has recently been launched by the UK’s Council for the Central Laboratory of the Research Councils (CCLRC) and is the platform used by CCLRC’s own repository.

CCLRC is one of the eight UK research councils and provides large-scale scientific facilities, rather than giving grants to individual researchers….The results of all this research [in CCLRC facilities] go into CCLRC’s repository, ePubs, which has been externally accessible since May 2004. It has over 22,000 metadata records dating back to the mid-1960s, and more than 500 of these have full text attached….

The feasibility study [for the CCLRC repository] included a technology review to look at the well-established DSpace and ePrints tools. However, these software packages had been written with universities in mind, and were not easy to modify to the rather different requirements of a research organisation such as CCLRC. For this reason we decided, in late 2002/early 2003, that it would be more effective to write our own software to meet our needs. The resulting software, which underpins our ePubs repository, is known as Scitate.

The conceptual model for Scitate is based on IFLA’s Functional Requirements for Bibliographic Records. One of the major features of using this model is that it groups related works in the same metadata record. Examples of this are the ability to link the preprint with the final published version or having the conference slides and paper together. This reduces the number of near-duplicates in the collection….

CCLRC’s ePubs implementation of the software uses the CCLRC source of staff information to link a particular author to their unique staff number. This means that if the author is inconsistent about how they name themselves on published works, all the works will be linked together to the approved form used within CCLRC. Authors who have been disambiguated are shown in italics….

ePubs…includes journal articles, preprints, laboratory technical reports, conference presentations and papers, theses and final project reports….

One of the remits of CCLRC is to exploit scientific and technical developments for the benefit of the UK, so we are now exploring the potential market for Scitate beyond our ePubs implementation….

Using the model developed by other suppliers, the Scitate software will be available for free download as an open-source product. However CCLRC is also offering support services to set the system up, to share our expertise in populating the repository, and to provide ongoing support and upgrades to the software….

PS:  Of the eight Research Councils UK, five require open access to the research they sponsor (BBSRC, ESRC, MRC, NERC, and PPARC) and two are still deliberating (AHRC and EPSRC). The CCLRC is the only one that has already decided merely to encourage it.

source: The CCLRC, its OA repository, and its home-grown repository software

Maureen Pennock has written a short review of Fedora, the open-source software for OAI-compliant repositories.

source: Review of Fedora

Lucifer Chu’s Opensource Opencourseware Prototype System (OOPS) has struck again, translating the Johns Hopkins University OpenCourseWare site into Chinese.  For details, see the JHU announcement (undated but apparently released yesterday or today):

In April of this year, the School broke through an educational barrier when it launched its OpenCourseWare (OCW) site….And now, thanks to the Opensource Opencourseware Prototype System (OOPS), a program that translates educational resources into Chinese, the language barrier is being broken as well. OOPS has replicated the School’s OCW site in simplified Chinese (the language of mainland China) and in traditional Chinese (spoken in Hong Kong, Singapore and Taiwan)….

OOPS is the brainchild of Lucifer Chu. In 2003, Chu, known for translating J.R.R. Tolkien’s Lord of the Rings into Chinese, read an article in Wired magazine that described Asian students trying to use MIT’s OCW.

“I was deeply touched,” he says. “After I read the article, I thought, what if?” Chu quit his job at a publishing house and founded the OOPS project to translate MIT’s OCW site for Chinese-speaking people. When the Bloomberg School’s OCW site went live, Chu knew OOPS had to translate it, too.

“Johns Hopkins and MIT are really generous,” Chu says. “The [OCW] materials are all in English, and what I’m trying to do is help give them to developing countries.” Part of the OOPS mission is to reach out to less fortunate people through the donation of knowledge, Chu says. OCW embodies that….

The translation, as well as the design and programming, is done by some 1,700 like-minded volunteers recruited largely by email and word of mouth. The “OOPSers,” as they’re called, include CEOs, professors, engineers, accountants, musicians, designers, lawyers, doctors and students.

After translation, the pages are reviewed by an editor and proofread. The pages must be approved by the OOPS review board composed of content experts in the field before being published on the site.

When Chu founded OOPS, he created a server with two old computers he hid in the dormitory of National Central University in Taiwan, where he is an alumnus. Last year, the university found out. “But I persuaded them that what we’re doing is a good thing,” Chu says. So much so that the university agreed to provide a server. Today, there are six or seven servers at different universities in China, all dedicated to posting translated course content from MIT, the Bloomberg School, Utah State University, and the Japan OCW Alliance. OOPs has completed 55 courses, and 1,020 courses currently being translated

Comment.  I love the OOPS story and found a few more details in an article from the March 2005 Taipei Times.  Chu made $27 million translating The Lord of the Rings into Chinese and now spends 16 unpaid hours per day making making open content available to Chinese readers. 

source: OOPS translates the Johns Hopkins OpenCourseWare into Chinese

CiteXplore is free software from EMBL-EBI to integrate research articles and data files, and to connect both with text-mining tools.  From yesterday’s announcement: 

Today the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) launches CiteXplore, a new freely accessible literature resource service.

Biological researchers require two crucial sources of information: scientific literature published in peer-reviewed journals and databases storing key biological data such as DNA and protein sequences, functions and structures of molecules and microarray data. Tools that integrate these two sources of information are desperately sought.

EMBL-EBI scientists have developed CiteXplore, a tool that links electronic literature resources to bioinformatics databases, to fulfil this need. It integrates abstracts from various resources including the US National Library of Medicine’s MEDLINE database of abstracts from peer-reviewed biomedical journals, biological abstracts from patent applications from the European Patent Office, and Chinese Biological Abstracts from the Shanghai Information Center for Life Sciences, Chinese Academy of Sciences. From these abstracts CiteXplore links to full-text articles at various locations such as PubMedCentral and publisher websites.

CiteXplore also provides a direct link between the scientific literature and the EMBL-EBI’s biological databases. “When you are reading an abstract describing a specific gene or protein, typically you want more information on it, for example its sequence or its function, as well as easy access to the full paper,” says Peter Stoehr, who coordinates CiteXplore. CiteXplore uses powerful text-mining tools developed by EMBL-EBI researchers to link literature and databases automatically, so that at the touch of a button the biological terms are identified in the text and you can call up the record of the molecule that you are looking for.

In future, the range of literature resources hosted in CiteXplore will be extended for better coverage of other domains such as plant science, agricultural and food sciences, and to integrate it with UK PubMedCentral, a recently launched project led by a consortium comprising the British Library, University of Manchester and EMBL-EBI.

Comment.  Note that CiteXplore doesn’t merely integrate text, data, and mining tools.  It also integrates OA abstracts (even for non-OA articles) with full-text OA copies or versions that may exist in repositories around the web.  It doesn’t do this for every non-OA article with an OA version somewhere, but it’s the first tool I’ve seen to make a systematic start.  This is important because there are far more OA abstracts than OA full-text articles. 

source: Free software to integrate text, data, mining tools, and OA abstracts with OA articles

source: Another provost for FRPAA

Heather Morrison, Ray English, or: the Open Access Genie, OA Librarian, November 27, 2006.  Excerpt:

Of the many great pleasures of this year’s Charleston conference - one of the highlights, for me, was the opportunity to meet the opening keynote speaker Ray English.  Ray’s topic, building on the conference theme of Unintended Consequences, was Unintended Consequences of the Profit Motive: Or Why the Open Access Genie is Out of the Bottle.

In a nutshell, Ray is questioning whether the focus on profit - and the subsequent price increases for serials so far above inflation that today’s 8% increases (still, far above inflation) are portrayed as “good news”- is the reason behind the unleashing of the open access genie….

Ray has been one of the leaders of two of the most active associations in open access, since their inception: SPARC, the Scholarly Publishing and [Academic] Research Coalition, and the Association of College and Research Librarians (ACRL) Scholarly Communications Committee….

In the words of Rick Johnson, Founding Executive Director of SPARC and currently SPARC Senior Advisor:

Ray has been a chief contributor almost since the founding of SPARC….He has been a leader within the Open Access Working Group (OAWG), a SPARC-organized framework for collective advocacy of open access as a public policy matter. And now, of course, he is the chair of SPARC….Ray has been especially energetic in his support of expanded public access to taxpayer-funded research. He has been tireless in his efforts to mobilize library support and communicate this to the U.S. Congress….Bottom line: he’s amazing. I benefitted gratefully from his wise counsel throughout my years as SPARC’s director.

SPARC did not begin as an organization for open access advocacy, of course - rather, the original purpose was, and remains transformational change in scholarly communications. In Ray’s words, Open access emerged as a visible movement after SPARC got started and it’s clearly become the most powerful strategy for transformational change….

Ray’s advice for the OA Librarian?
I think the most important thing anyone in the US can do at this point is to support the Federal Research Public Access Act. There are a variety of ways to do that, from individual letters to Congress to developing more organized support. In terms of access to information I think it’s probably the most important bill that’s ever been introduced into Congress. I’d also encourage all librarians to work at the campus level to inform / educate faculty about scholarly communications issues….

For all your contributions to transforming scholarly communications, Ray - past, and hopefully long into the future - thank you.

PS:  Ray deserves all this appreciation and more.  Read the full post for laurels and details I had to omit from this excerpt. 

source: Profile of Ray English

Lorenz, Open Access to Indigenous Research in Norway, Antropologi.info, November 28, 2006.  Excerpt:

More and more theses in Norway are published in digital archives and are freely available in full text. In MUNIN - the digital library of the University in Tromsø (Northern Norway), you can download eight master theses in indigenous studies. They look very interesting….

See the full post for the eight theses with links and abstracts.

source: OA to Norwegian anthropology