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Blog archive for June, 2008

SCOAP3’s Jens Vigen: opening access on a global scale

June 30th, 2008 by dwentworth

Among the biggest challenges for opening access to scientific research is developing sustainable ways to fund it. CERN‘s SCOAP3 has been a global trailblazer, setting up a system where funding bodies and libraries contribute to the consortium, which pays centrally for peer review. The INIST-CNRS in France has a new interview with Jens Vigen, scientific information officer and director of the CERN library. Vigen explains how SCOAP3 came to be, discusses the principles behind the funding system and where the initiative is headed next.

Excerpt (from the Google English translation):

Three elements were important in [CERN launching SCOAP3]: our long tradition of [pre-print publishing], the fact that the Open Access movement among librarians [had] gained momentum since 2003 and the fact that some journals in particle physics models already offered free access long before the concept [was widely] accepted. CERN, which supported and supports these journals, decided to respond to this moment. A briefing was held in September 2005, with researchers to explain the movement and [raise] awareness, then a two-day seminar in late 2005, with those involved in science communication: publishers, funding agencies and researchers. Following this meeting, a task force was set up bringing together publishers, representatives of agencies and researchers. Their discussions led to the model of sponsorship.

In a few weeks, Science Commons will hold a free, open workshop featuring Vigen and others who are leading the charge for open access to scientific research. The workshop, held July 16-17 in conjunction with ESOF 2008 in Barcelona, Spain, is aimed at defining the foundational principles to foster the growth of open science worldwide. Vigen will talk about the state of open access in nations across the globe, as well as offering his perspective on strategies to take the OA movement to the next level.

If you plan to join us, we encourage you to register here. If you have questions, please let us know. We hope to see you there.

A new open access mandate at Stanford

June 28th, 2008 by dwentworth

I’m late to the game on this, but can’t resist passing along the good news: the faculty at the Stanford University School of Education has reportedly voted to adopt an open access (OA) mandate.

Les Carr, who attended the conference where OA luminary John Willinsky shared the news, writes:  “[Willinsky] banged the drum for Open Access and announced an OA mandate for the Stanford School of Education. According to the story, he was describing the Harvard mandate to his colleagues in a meeting and they instantly voted to adopt a similar mandate themselves. Way to go!”

At Science Commons, we work to help scholars retain the rights to share their work, and to bring open access to more institutions [PDF], so it’s extremely encouraging to see faculty authors at Stanford not only embracing OA personally, but also working to implement it at the institutional level — changing the “default setting” for published research from closed to open.

Just in time for the Stanford announcement, C&RL News has published an article that puts the decision in a larger context. The piece, Two new policies widen the path to balanced copyright management: Developments on author rights. explores the implications of the NIH and Harvard mandates, and contains the following apropos observation:

Norms are always more difficult to change than technologies. We are now witnessing a key shift in norms for sharing scholarly work that promises a giant step forward in leveraging the potential of network technologies and digital scholarship to advance research, teaching, policy development, professional practice, and technology transfer.

Hear, hear. Kudos to the faculty at the Stanford School of Education for helping to make it happen.

Update (6/30): Open Access News has additional details.

GSK, caBIG give away cancer data to speed research

June 25th, 2008 by dwentworth

It’s no secret that we’re fans of the National Cancer Institute’s caBIG, the Cancer Biomedical Informatics Grid. So we were thrilled to learn that the organization, which connects more than 60 NCI centers with a common infrastructure, played a central role this past week in what Wired is calling a “Massive Cancer Information Giveaway.” The big prize, provided by GlaxoSmithKline (GSK) and shared freely with cancer researchers via caBIG’s platform:  genomic profiling data for over 300 cancer cell lines. The lines were derived from a wide variety of tumors, including breast, prostate, lung and ovarian cancers.

Why would a major pharmaceutical company give away information that its researchers painstakingly uncovered? Put simply, if the goal is to speed the translation of data into drugs, it helps significantly to have more researchers looking at the data and identifying leads.

“Cataloging this type of information in a network like caBIG leads to a ready-made body of biologic information that can be mined by all cancer researchers to further everyone’s understanding of cancer,” explains Dr. Richard Wooster, Director of Translational Medicine Oncology, Research & Development at GlaxoSmithKline, in the company’s media release.  “In turn, we hope this data will further drive the identification of predictive biomarkers and lead to shorter, more directed clinical trials allowing us to bring drugs more quickly to patients who need them.”

Any researcher is free to download the GSK cancer data through caArray. The caArray tool is free and open source.

Science Commons is a strong believer in the utility of a commons-based approach to drug discovery, and this afternoon, John Wilbanks will give a talk at caBIG to discuss how data sharing agreements can help simplify, standardize and automate sharing. We have begun to explore implementing tools such as the CC0 waiver and our machine-readable contracts for transferring materials at caBIG, and we look forward to deepening our involvement as its legal and technical infrastructure continues to take shape.

Update: For another perspective on the giveaway, check out GSK’s big bang on open drug discovery [Business Standard via Rediff News]: “Big pharma claims that it costs as much $1 billion to bring a new molecule to the market and 8-12 years to develop it. That’s something that few companies can afford anymore. For developing countries, too, [open source drug development] may prove to be the route of the future.”

Pubic domain + community norms = freedom to integrate science

June 23rd, 2008 by dwentworth

In the current issue of the Journal of Science Communication, our own John Wilbanks has a note explaining why Science Commons believes that the best — perhaps the only — way to integrate and make use of the exponentially growing number of scientific databases on the global digital network is to mark them explicitly as part of the public domain. This counters the trend toward using “copyleft” licenses for databases, which, despite the good intentions behind it, threatens the usefulness of the data.

“The public domain for science should be the first choice if integration is our goal,” writes Wilbanks, “and there are other strategies that show potential to achieve the social goals embodied in many common-use licensing systems without the negative consequences of a copyright-based approach.”

To help people and organizations mark their data and databases as free to use without restriction, Creative Commons has developed the CC0 waiver, while the Open Data Commons offers the ODC-PDDL. Using either public domain waiver puts you in compliance with the Science Commons Protocol for Implementing Open Access Data.

You can read the full note at the JCOM site, along with two other relevant pieces by our colleagues in the community:

Poynder interviews Leslie Chan: minding the 10/90 gap

June 20th, 2008 by dwentworth

Richard Poynder today published yet another remarkable — nay, superbinterview. This time, his subject is Leslie Chan, whom Poynder describes as the “unsung hero” of the open access (OA) movement. Chan works tirelessly to increase the visibility and impact of scientific research from developing countries — one way to bridge the “10/90″ gap. What’s that, you ask?

Explains Poynder:

The 10/90 gap is the phenomenon in which 90% of the world’s R&D money is spent on the 10% of diseases that primarily affect people in developed countries, while only 10% is spent on diseases that mainly affect the 90% of people who live in the developing world. [...]

Of course there is more than one reason for this dollar-spend inequity (including the fact that Western-based pharmaceutical companies know they cannot make a large profit from selling drugs to treat diseases primarily affecting poor people), but since much of the research into the neglected diseases is undertaken in developing countries themselves, and the findings published in local journals with limited circulations, the relative invisibility of that research makes it far harder to get funding.

And since research tends to be a cumulative process — in which researchers build on the work of previous research in order to arrive at new understandings, and eventual breakthroughs — the invisibility (and consequent shortfall in funding) of [developing countries] research inevitably lengthens the time before cures are developed for the neglected diseases.

Science Commons is working to make it faster, easier and more cost-efficient to find cures for neglected and orphan diseases. On July 16-17, we’re holding a workshop in Barcelona, Spain, in conjunction with the ESOF 2008 conference. The aim:  to define the basic principles that would enable the emergence of global, collaborative infrastructure for accelerating research. We’re honored to have Leslie Chan join us to talk about OASIS, a resource to provide practical steps for implementing OA.

If you’re interested in coming to the workshop, we invite you to register here (the meeting is free and open to the public, but seating is limited). We hope to see you there.

Berlin 6 conference: what’s next for open access

June 17th, 2008 by dwentworth

Five years ago, the open access (OA) movement added the third “B” — Berlin — to the trio of international declarations supporting OA that now function collectively to define it. This fall, organizers will hold the fifth follow-up conference, Berlin 6, to explore how the movement is progressing and where it’s headed, with sessions on topics close to our hearts here at Science Commons: the convergence of publishing and research, the relationship between open access and open standards, the “next-generation” implications of the OA movement and more. Among the speakers are arXiv.org founder Paul Ginsparg, open access luminary John Willinsky and Tony Hey, who leads Microsoft’s efforts to build long-term public-private partnerships with global scientific and engineering communities. You can find additional details, including the conference program and registration information, on the conference site.

The Berlin 6 conference is one of many events in the coming year that focus on what’s next for the OA movement, including our own free workshop on open science, which takes place next month in conjunction with ESOF 2008. Check out the ever-expanding list at the Open Access Directory (OAD) wiki, and if you have an event coming up that investigates open access, please add yours.

Announcing the Health Commons

June 12th, 2008 by dwentworth

People make chairs more productively, hamburgers more productively, cars more productively, everything else in the world except medicines. — Aled Edwards, Director and CEO of the Structural Genomics Consortium (via CBC News Canada)

The drug discovery process is badly broken. Despite the scientific and technological advances that make genetic decoding commonplace, the time it takes to go from gene target to cure still stands at 17 years.

Science Commons’ mission is to speed the translation of basic research to useful discoveries, and we believe that a new approach is necessary to find more cures, faster. Today, we’re opening up the Health Commons, a project aimed at bringing the same efficiencies to human health that the network brought to commerce and culture.

The project, founded by Science Commons in collaboration with CommerceNet, CollabRx and the Public Library of Science (PLoS), is introduced in a 6-minute video presentation and white paper posted on the Science Commons website. The paper, Health Commons: Therapy Development in a Networked World [PDF], is co-authored by John Wilbanks, Vice President of Science at Creative Commons, and Marty Tenenbaum, an Internet commerce pioneer and founder of CommerceNet and CollabRx.

[Click below to watch the video presentation.]

“Biomedical knowledge is exploding, and yet the system to capture that knowledge and translate it into saving human lives still relies on an antiquated and risky strategy of focusing the vast resources of a few pharmaceutical companies on just a handful of disease targets,” explains Wilbanks in the project introduction.

The Health Commons proposes a different approach: enabling more companies, foundations, laboratories or even individuals to conduct research on disease targets efficiently, by providing better access to the resources that large pharmaceutical companies assemble and integrate “in house.” To do this, Health Commons will facilitate the emergence of a “virtual marketplace,” or ecosystem, through which participants can more easily access the data, knowledge, materials and services for accelerating research.

The components might include databases of the results of chemical assays, toxicity screens and clinical trials; libraries of drugs and chemical compounds; repositories of biological materials (tissue samples, cell lines, molecules); computational models predicting drug efficacies or side effects; and contract services for high-throughput genomics and proteomics, combinatorial drug screening, animal testing and biostatistics.

“The resources offered through the [Health] Commons might not necessarily be free, though many could be,” explains Wilbanks. “However, all would be available under standard pre-negotiated terms and conditions and with standardized data formats that eliminate the debilitating delays, legal wrangling and technical incompatibilities that frustrate scientific collaboration today.”

Science Commons welcomes your interest in the Health Commons. If you’d like to collaborate with us to accelerate drug discovery, we encourage you to contact us.

ESOF 2008 satellite event: Collaborating for the future of open science

June 4th, 2008 by dwentworth

Momentum is building behind “open” approaches to scientific endeavor, which have tremendous potential for accelerating discovery by making research faster, easier and more efficient. These approaches are often collectively referred to as “open science,” but both the term and its underlying principles have yet to be defined by the global scientific community.

Science Commons works to connect and empower people and organizations developing open science in nations across the globe. This July, we are convening a free, open workshop in Barcelona, Spain, to discuss and define the basic principles for open science, including identifying the key tenets for a system to be recognized as an “open science” system. The goal is to conclude the workshop with a set of shared principles that can effectively guide the development of a collaborative infrastructure for knowledge sharing — one that increases the value of each independent contribution to the global knowledge commons.

The workshop, one of three satellite events preceding the Euroscience Open Forum (ESOF), takes place July 16 -17, 2008, and will be held at the Institut d’Estudis Catalans. It will feature keynote presentations by James Boyle, Chairman of the Board at Creative Commons and a founder of Science Commons, and Mario Campolargo of the European Commission. Our co-sponsors are the Scholarly Publishing and Academic Resources Coalition (SPARC), the Center for the Study of the Public Domain at Duke University (CSPD) and the Institut d’Estudis Catalans (IEC).

Participants are already gearing up for the workshop. Ignasi Labastida i Juan, project lead for Creative Commons Spain and Catalonia, is a co-organizer, and in the current issue of IPR-Helpdesk Bulletin, he calls on universities across Europe to implement the European University Association’s (EUA) recommendations for opening access to the research that faculty produce — an effort that could prove to be a tipping point in transforming the way we share and build scientific knowledge.

For many years, scientists have done research, have written and have reviewed articles, and have paid for accessing journals without expecting any economic compensation because they only wanted attribution and reputation to following their career,” he writes. “This situation of publish or perish has been used by publishers to monopolize that knowledge, mainly created in universities and research centres, and they have used the copyright to lock it even forbidding reproductions on authors’ websites or authors’ institution portals. Fortunately things are changing.”

Hear, hear. If you’d like to join us for a discussion to establish a set of foundational principles that can foster the growth of open science worldwide, we invite you to check out the details and register here. The workshop is free and open to the public, but seating is limited, so if you are able to attend, we encourage you to register now.

Voices from the future of science: Lorrie LeJeune from OpenWetWare

June 3rd, 2008 by dwentworth

In his trio of must-read essays on open science in 2006 (parts 1, 2, 3), cancer researcher Bill Hooker identifies open notebook science as his “personal favorite” expression of a broader movement that includes everything from publishing open access journals to developing common standards for data sharing. The reason? He believes it can help cultivate new cultural norms of openness, transparency and immediacy in the daily life of scientists.

So what exactly is open notebook science? Following in the tradition of preprint servers like arXiv.org but digging even more deeply into the roots of the research process, open notebook science is an effort to document and share science-as-it-happens: exploratory ideas, raw data, lab protocols and more. As the enthusiastic response to author Michael Nielson‘s recent post on sharing more “useful” knowledge shows, the practice is generating an enormous amount of excitement, as well as sparking questions about what’s next. How do we ensure that what we post online is truly “useful”? Can we publish in a way that optimally leverages the network and contributes more signal than noise?

To explore these questions and others for our series of posts on the future of science, I talked with Lorrie LeJeune of the OpenWetWare project. Launched in 2005 by members of the Endy and Knight labs here at MIT (and originally dubbed “Endypedia”), OpenWetWare provides resources to make research easier and encourage researchers to take a more open approach to science. Over the past three years, its wiki-powered site has become a hub for open research, and now serves a community of 4,100 users from research labs all over the world. LeJeune, whose remarkably diverse background includes work both as a molecular biologist and a marketing manager and editor at O’Reilly, joined the project in February as its new Managing Director.

First, can you tell me how you ended up at OpenWetWare? What drew you to the project?

The short answer is because I’m interested in science, open source, disruptive technology and publishing, and OpenWetWare allows me to explore all four areas simultaneously.

The longer answer is that I’ve spent my career following my interests. I have an undergraduate degree in Animal and Veterinary Sciences (specialty in dairy science and microbiology). I worked in biotech in the 1980s doing protein chemistry and yeast genetics. I spent the next fifteen years in publishing, working on digital publishing technologies at the MIT and University of Michigan presses, and as a marketing manager and editor atO’Reilly Media. After a four-year detour through the world of mobile telecommunications at Orange, I learned about OWW. And here I am.

OpenWetWare is generating a lot of interest in open research and especially in replicating the model across many different disciplines in science. Of course, in many cases, there are factors that discourage sharing pre-publication information. Would you say part of what OWW does is help demonstrate what can be shared, as well as the benefits of “baking in” sharing?

Yes, exactly. Many researchers are not opposed to sharing their work, and they do so regularly in the privacy of their labs and their departments. They generally draw the line at sharing with the world until the article is published, and they can get the attribution for the work. Attribution is the key to being successful in academia: getting tenure, getting the grant money, getting the grad students, etc. Most scientists have been taught that to talk about one’s work prematurely opens the door to “scooping,” or having your ideas stolen by another researcher, who will do the work and publish the results before you do and get what should have been your credit.

How does OWW combat that perception?

We make the argument that if you share your information publicly, it is in fact attributed to you, and if someone at some point in the future tries to present your work as theirs, you can point to a trail of content you posted. Granted, there are complexities–especially in the world of wikis where people can edit other people’s stuff. But if you post it, there’s a record that can be traced.

To paraphrase what we state on the OWW wiki, some users of OpenWetWare think that the best thing to happen would be if somebody “stole” your idea and finished the work before you. Then you could go work on another idea. Good researchers usually have more ideas than they have time to explore, and having more people exploring those ideas will in the end benefit your research. OpenWetWare’s mission is to make research better and lower the barriers to sharing. If we can facilitate exploration of more good ideas so that everybody is doing the best work possible, as quickly as possible, everyone wins.

Another reason to be open–especially if you’re working in a nascent field of study–is to bring attention to your work. One fact of life in “open science” discussions is that there are going to be people who think it doesn’t make sense in their (“very competitive”) field to be open about their work. However, there are many, many scientists whose principle problem isn’t being scooped–it’s that no one notices their work. This is especially true among younger scientists still making a name for themselves or folks in smaller fields.

I could argue that there is already significant incentive for young scientists to publicize what they are doing as openly and early as possible. This open group will either be scooped out of existence, or will be more successful thanks to all the unintended benefits of making its work accessible early. We really won’t know which it is, however, until we run the experiment.

All that said, we’ve had a lot of discussions here at OWW about sharing systems that take advantage of the collaborative power of wikis, but also bring in time-stamping, DOIs and other proofing systems that traditional publishing uses. I think the bottom line is if you can be credited with the idea or the experiment or the conclusion, you’d be willing to share it with more people, if not the world. And there are important advantages to sharing early-stage research more widely.

Once a member of your community has decided to publish information, does OWW encourage people to mark it with attribution and usage rights?

We’re still working out the best way to deal with that. The OWW site itself is under Creative Commons and GNU FDL licenses, but we are an early-stage project. Right now, technically speaking, we’re a wiki–with all the power and frailty that wikis have. We are looking at ways to incorporate an official form of time-stamping, using an outside validation body–sort of an online notarization process. And as I said, we are also looking at how to implement DOIs for documents.

Do you plan to explore a “best practices”-type approach–where you offer your community policy guidelines for publishing, as well as dealing with the legal issues surrounding sharing?

Yes, we will have to explore policy guidelines, especially to reassure people that they will be credited with what they publish. The legal issues also have the potential to loom large. Some industry folks may not use OWW because they’re concerned about patenting. On the other hand, many people don’t think about licensing or copyright at all before they publish. If we want to allow sharing of data, we need to make sure we’re using and communicating the right intellectual property and licensing information. Fortunately, our friends at Science Commons are willing to help us in that department!

In terms of developing guidelines for the community, I think we’ve gotten to the point of opening the door, but most researchers are still milling around at the threshold taking an occasional glance out. Not many people have actually stepped through. We (meaning the open research community) need to figure out the rules of engagement. Once we have even a few guidelines for sharing, I think the rate of openness in science will accelerate.

What can we do to spur more revolutions in the way we practice science? Or to put it another way, what can we learn from OWW? Did the project come about in part because the people behind it are relatively young and acclimated to sharing? Or is it that they practice in an area of science well-suited to sharing–a younger science?

Why is OWW happening? Two factors come to mind:

1.) Because it can. Tools for information sharing and social networking have evolved sufficiently to allow it to happen.

2.) The generation of graduate student researchers launching their professional lives now may be the first to have been raised “on the Web,” using Web-based tools. They’re very comfortable sharing their ideas and information in a public, online environment.

I think this is essentially true because it seems to be the more established researchers who worry more about sharing information on the Web. Science has always had a secretive side, and probably will continue to until the funding and tenure systems change. So some of the hesitancy could stem from having cut their scientific teeth in an era where having conversations with colleagues, giving presentations at conferences and publishing in print journals were the only “safe” ways to share ideas. In addition, many senior researchers simply don’t have the time to fool around with learning to edit wiki content. Graduate students have the time, the early training and the motivation to use whatever resources they can find to get their work done.

I agree that sharing is likely easier in some branches of science than others. In the newest branches, like synthetic biology, everyone is on the fringe. More people are struggling just to get their work noticed. And newer fields are smaller. People are more likely to know one another, which in turn makes sharing easier. If you know someone, even slightly, you’re much more inclined to enter into a collaboration with them, so you can move both your own and their work ahead faster.

Of course, even wiki- and Facebook-savvy scientists don’t share everything. They seem more willing to put protocols and other “safe” materials out in front of the public eye than they are unpublished research data.

So I think the upshot is that people are very interested in sharing, but exactly what and how much is shared is still very variable.

What are the projects at OWW that you’re most excited by?

There are lots of examples, like our new one-click open lab notebook, but I’m especially excited about a project Julius Lucks is pursuing. He’s a post-doc at Berkeley who’s interested in publishing, and has written and published on OWW a paper on using Python for science. When I asked Julius if he’d be willing to write a full-length “Scientific Programming with Python” book on OWW as an experiment in open-access writing, he jumped at the chance. He now has an outline and two co-authors, and we’ve launched the OWW Open Writing Initiative. Wikis are designed for collaborative writing and editing, and I look forward to learning how the process will work on OWW.

What’s next for OWW?

We’re exploring ways that OWW can help make research easier, faster and more open. To that end, we’re looking very closely at where the problems and opportunities are within the traditional cycle of research. What tools and services can OWW develop or foment to help researchers move, for example, more swiftly from literature search to experimentation at the bench? Or from collecting data to writing a paper about what that data signifies? We also hope to grease the research pathways by providing tutorials on tagging data so it’s easier to search, or on choosing a research project, or when to stop working on a project. By using Web-based resources to help research move faster and more smoothly, we believe that it can’t help but become more open.

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