Blog archive for February, 2008

White paper released to help universities comply with NIH’s Public Access policy

February 29th, 2008 by Kaitlin Thaney

Come April 7, NIH-funded researchers will be mandated to archive their work in PubMed Central no later than 12 months post-publication. To help universities prepare for this, Science Commons, SPARC and ARL have jointly released a white paper that explores the copyright-related issues involved with the new NIH Public Access Policy. The paper, “Complying with the National Institutes of Health Public Access Policy: Copyright Considerations and Options,” arms university provosts, researchers and administrators with the information needed to fully comply with the mandate, announced this past January.

From SPARC’s press release:

[S]aid Heather Joseph, executive director of SPARC: “The sooner we can get effective implementing mechanisms in place, the sooner researchers, institutions, and the public can put PubMed Central to work. With April implementation drawing near, this paper will be a great tool to help administrators jumpstart the local planning process.”

[…] “Congress and the NIH recognize that the Internet makes a difference,” said John Wilbanks, Vice President of Science Commons. “Faculty authors can no longer sign away their copyrights in a business-as-usual manner when doing so means that their work will never be openly accessible over the Internet. This white paper is a step in making sure authors and universities understand how to move forward with a solid legal footing.”

The press release and the white paper can be accessed in their entirety on SPARC’s Web site, as well as in the Science Commons Reading Room. Many thanks to Michael Carroll for authoring this wonderful resource.

Beyond open access

February 27th, 2008 by dwentworth

In the introduction to his interview [PDF] with our own John Wilbanks, UK journalist Richard Poynder succinctly captures the Science Commons perspective on open access — that making research freely accessible online is only the beginning of making it useful for scientists:

John Wilbanks, VP of Science Commons, has an even broader view of the role the Internet has to play in science. Like Murray-Rust, Wilbanks believes it is essential for research papers to be machine-readable. Likewise, he believes we need to develop an appropriate legal infrastructure to facilitate this. He also believes it is essential that science databases are freely available, and that these databases are interoperable — not just with one another, but with research literature.

In addition, Wilbanks believes the Internet should be viewed as a platform for facilitating the free circulation and sharing of the physical tools of science — cell lines, antibodies, plasmids etc. In a sense, he wants to see these tools embedded into research papers — so if a reader of an Open Access paper wants more detailed information on, say, a cell line, they should be able to click on a link and pull up information from a remote database. […]

The end game, explains Wilbanks, is to make the research process as seamless and frictionless as possible. This implies that the scholarly paper is no longer simply an article to be viewed by as many eyeballs as possible, but also the raw material for multiple machines and software agents to data mine, a front-end to hundreds of databases, and the launch pad for an ecommerce system designed to speed up the process of research.

In this light, Open Access is not an end in itself, but the necessary precondition for a complete revolution in the way that science is done…


The interview is part of a series stretching back to 2001, which includes talks with the great Peter Murray-Rust, Peter Suber, BioMed Central founder Vitek Tracz and many others leading the charge for open access. Highly recommended.

Netsquared hosts data mashup challenge

February 25th, 2008 by Kaitlin Thaney

If you’re interested in open data or open notebook science, listen up. Netsquared is putting its money where its mouth is and offering a $100,000 cash prize for the best data mashups for social change.

From their announcement:

NetSquared, a project of TechSoup, has created the Challenge because they believe you have great ideas for how data can create insight, and they want to create a platform to facilitate those kinds of mashups being built. Plus, they¹ve got cash prizes to award to the folks who come up with the most innovative mashups for social change. You can find out more here.

Interested? Just follow these three steps.

First, apply. Applications will be accepted until March 14.

Step two: NetSquared will help connect you to the tech support needed to get your Mashup project off the ground.

Finally, step three: start designing.

Voting will begin the week of March 17th by the NetSquared Community, looking for the most innovative mashups in line with their guidelines. The top 20 projects will be announced on March 24, and the winners will be offered a chance to attend the NetSquared Conference in San Jose, Calif. this May. The top twenty projects will receive a share of a $100 K prize. Shares will be determined by voting at the event.

For ideas, take a look at some of their favorite mashups in this area –,, ActiveTrails, and Tunisian Prison Map projects. To find out how you can apply, visit their Web site.

A commons-sense approach to winning the drug discovery lottery

February 23rd, 2008 by dwentworth

In a new piece [free reg. req.] this week from GenomeWeb Daily News, Aled Edwards — director and CEO of the Structural Genomics Consortium — describes the drug discovery process as a “lottery,” and argues that increasing the chances for discovery will require that people in “academia, industry, and funding bodies collaborate and keep new structural data accessible to all researchers who might be interested in using it.”

The sentiment echoes those of Science Commons’ own John Wilbanks, who earlier this year wrote a post on the Nature Network comparing drug discovery to a game of roulette. It’s a game, says Wilbanks, that people win by “betting on every square, then patenting the one that wins and extracting high rents from it.” The biggest problem in this scenario, he argues, isn’t the existence of patents, but the sheer complexity of the human body, and how much we still have to learn about it:

Human bodies make microprocessors look like children’s toys in terms of complexity. …Complexity is the problem both in terms of our understanding of bodies and drugs and in terms of reworking the models around discovery. This system regularly and utterly defeats the best efforts of many entrepreneurs and policy reformers to change things for the better.

So what’s the solution? According to Wilbanks, it’s a “commons approach,” which entails precisely the kind of collaboration that Edwards advocates:

It requires open access to content, journals and databases both. It requires that database creators think about their products as existing in a network, and provide hooks for the network, not just query access. It requires that funders pay for biobanks to store research tools. It requires that pharmaceutical companies take a hard look at their private assets and build some trust in entities that make sharing possible. It requires that scientists share their stuff (this is the elephant in the lab, frankly). It requires that universities track sharing as a metric of scientific and societal impact.

It is not easy. But it is, in a way, a very simple change. It just requires the flipping of a switch, from a default rule of “sharing doesn’t matter” to one of “sharing matters enormously.” It is as easy, and as hard, as the NIH mandate on open access. It’s a matter of willpower.

Edwards points out that governments and academic institutions spend “hundreds of billions of dollars” each year on activities related to drug development, and biotech and pharmaceutical companies “spend another $50 billion.” Yet the pace of discovery remains static — and according to Edwards, may even be slowing down.

Clearly, the current approach isn’t working. We at Science Commons are encouraged that more people are coming to understand that it’s time for a new approach to tilt the odds in our favor — so that we can save not only time and money, but also human lives.

As Harvard goes…

February 15th, 2008 by dwentworth

so goes the University of Oregon — and, we hope, many other institutions of higher learning in the US and internationally.

As the wonderful Peter Suber and Gavin Baker have been reporting extensively at Open Access News, Harvard’s decision to adopt an open access policy is causing a tremendous stir of excitement in the media and blogosphere. We at Science Commons are especially excited to learn that one day after the Harvard vote, the University of Oregon adopted a resolution in support of open access — including recommending that when faculty members sign a copyright transfer agreement for their work, they include an addendum to retain their rights, such as our Science Commons addenda.

We agree with BioMed Central president Matt Cockerill: the failure of traditional scientific publishing to make full use of the Internet’s potential is an issue that’s no longer of interest only to “librarians or activists.” If you work at a university and would like to help speed the pace of discovery by promoting open access to scientific research, we encourage you to take a look at our Scholar’s Copyright Addendum Engine (SCAE) and talk to your administrators about making it available to researchers on your university site.

Joshua Lederberg (1925-2008)

February 14th, 2008 by John Wilbanks

Joshua Lederberg, a legendary scientist and one of the members of our Advisory Board here at Science Commons, passed away on February 2. He was 82. (See Rockefeller University’s write-up.)

Dr. Lederberg was a legend for lots of reasons. He won his Nobel at the tender age of 33 – two years younger than I am now – for his work on the organization of genetic material in bacteria.

Though it’s easy to forget these days, back in the late 1950s it was not yet understood that bacteria possess recombinant mechanisms like humans do. His work laid the foundation for a generation of discovery. He also was deeply involved in early artificial intelligence for science (the Dendral project) and the space exploration program, in addition to serving as president of Rockefeller University.

Dr. Lederberg was in many ways a paradigmatic great scientist. He was restless and curious about his work, and his interdisciplinary bent was a bracing reflection of the world of biology before the revolutions wrought in the 1970s and later in biotechnology, which led us to the contemporary world of hyperspecialization. His papers are online at the National Library of Medicine, in an early take on open access.

We didn’t get a lot of his time here at Science Commons. He was a very busy man, even in his last years. But the time that he did graciously share with us formed a huge part of our early thinking, helping us to focus on the things that let scientists be scientists – the infrastructure that invisibly lifts a researcher out of the muck of finding content and into the air, where a researcher can make discoveries, and the systems that facilitate the kind of cross-disciplinary friendships he built throughout his career.

Thank you, Dr. Lederberg, and farewell.

Finding the “sweet spot” for openness in healthcare

February 14th, 2008 by dwentworth

The Committee for Economic Development has released a report [PDF] that looks at ways to harness “openness” to transform healthcare in the US. It gives a broad overview and analysis of the healthcare production chain, identifying areas where increased knowledge-sharing could yield enormous benefits — not least of which is the development of evidence-based medicine.

As Daniel Griffin at the Information World Review blog points out, the report appropriately defines openness in this context as a spectrum rather than a binary, and helpfully distinguishes between information that’s accessible and information that’s “responsive” and “malleable” (remixable). Writes Griffin:

Ultimately [the authors] say [openness] boils down to two things; the first is that information must be accessible, this means that data should be both available and free from restrictions while secondly responsiveness of that information refers to how malleable or redistributable the information is and therefore the more it can be considered ‘open’.

These are important distinctions to make, and the report serves as an excellent introduction to the opportunities and challenges of opening access to biomedical research. Our thanks to Eliott Maxwell for passing it along.

Science Commons gets its 15 minutes

February 7th, 2008 by dwentworth

…or 14 minutes and 35 seconds, to be exact.

Over at the MIT Libraries News site, Ellen Duranceau has posted a new podcast interview [MP3] with our own John Wilbanks. The topic: how to overcome barriers to knowledge-sharing in science — legal, technical and cultural.

The podcast is part of a terrific series of talks with thinkers on open access publishing and innovation. You can check out the Web site or subscribe to the podcasts by pasting the following link into your iTunes or another podcast reader: