Coming next month ...

I will be joining other Commons advocates, affiliates and experts next month at this year's Elevate Festival in Graz, Austria. For those of you in the area, I'll be speaking on Science Commons, as well as Creative Commons on Thursday, 6 November - as well as joining a podium discussion "Commons of the Mind" later that day. I hope you can attend.

The event's focus this year is the Commons, including four days of workshops and livened discussions from Creative and Science Commons to remix, History Commons etc. Each day is followed by an arts component, bringing together some of Europe's leading electronic musicians slightly out of the main stream, as well as multimedia performances of Good Copy, Bad Copy and shows by DJ Spooky (Paul Miller).

For more information on the festival and when/where I'll be, visit this page.

I have to say, I don't think I've ever had such a speaking engagement before or attended such an event ;)

Publishing in the New Millennium - Second Panel

(KT: My apologies for not getting these up on Friday. Due to technical difficulties, I'm just catching up now.)

Here are some notes from the second panel (out of two) at "Publishing in the New Millennium" at Harvard Medical School, entitled "Publishing 2.0". Each panelist gets five minutes to introduce themselves and to identify a few key issues.

The panelists:

John Wilbanks - Vice President of Science Commons at Creative Commons

Wilbanks kicked off his 5 minutes by distinguishing the difference between the "social web"/ Web 2.0 and the "research web". This provided a great segue into the Neurocommons work, an open source knowledge management tool. While Science Commons uses a few technologies that fall into the "Web 2.0" category - blogs, tags, comments and feeds - our focus is more on the research web, which Wilbanks succinctly explained.

He started by illustrating how bad the Web works for science. This is where you can start to focus on "research web", in hopes of bringing some of the power of the Web (think of what it did for commerce in terms of eBay, Amazon, etc) to the scientific research cycle. Our Neurocommons project works towards this goal.

His most recent post on Nature Network actually looks at this exact issue, echoing a number of points made on Friday. From his blog:

"We need to start talking about the Research Web, which is the reality of what we’re building here. Just as the Social Web uses, but is more than, AJAX), the Research Web will use the Semantic Web, RDF and other technologies and strategies to accomplish something we deeply care about: Making medical research more effective so that we can cure and relieve the suffering of patients.

We need the Research Web because the existing Web doesn’t work for research. Here’s what I mean: Googling a phrase like signal transduction genes in pyramidal neurons doesn’t get you a list of genes. It should get you a list of genes. No amount of collaborative filtering makes it easy to read 188,000 papers – and this is stuff where you tend to want experts moreso than the “wisdom of crowds” – advice from someone who doesn’t understand signal transduction tends to be less reliable than from someone who does.

The Research Web is about integrating lots of stuff that wasn’t designed to be integrated with anything. It’s about getting precise answers to complicated questions instead of a mess of Web pages. It’s about the move to industrialize the way scientists annotate data. The Research Web is about making the Web work in a complex data environment, where machines make and transmit terabytes of content that humans have to interpret."

Moshe Pritsker - Editor-in-Chief / Founder of the Journal of Visualized Experiments (JoVE)
video publication for biological research

Why did we start publishing this research in video? The idea comes from the lab.

The journal publishes "video articles", documenting how certain biological experiments are conducted. The goal is to make scientific publication usable, adding another layer of functionality to traditional publishing.

Hilary Spencer - Product Manager, Nature Precedings

Precedings is a pre-print server, for prepublication research, preliminary findings and other documents of scientific interest. Spencer provides a bit of background about the server, noting that Precedings does not publish materials regarding clinical trials since the material on the server is not peer-reviewed. Due to that, Precedings does not accept materials that make specific therapeutic claims.

"Web 2.0" technologies employed include a rating system for members of the community, relying on users to rate, filter and flag content of interest. Other 2.0 technologies: comments, "vote to promote", tagging, RSS feeds and e-mail alerts.

Why post research to a non-peer reviewed preprint server? Spencer touches on the following incentives for those in the research community: ability to record the provenance of an idea, Precedings serves as a permanent repository, enables authors to get pre-publication feedback, greater exposure, and authors retain copyright. Content is indexed, as well, in Google Scholar and BASE (an academic search engine).

Bora Zivkovic - Online Community Manager, PLoS One

PLoS One - now 10 months old. Bora shows some of the tools that PLoS One employs. This journal operates on Topaz software, allowing community members to add content / value to a scholarly work after it's published. This includes a rating system, comments and the ability to post annotations.

A few questions to highlight ...
Q: How much of the community comments on material (directed towards PLoS One and Precedings)?
A: Spencer: Commentary on Precedings is actually quite low. Not sure why. Precedings does not allow anonymous posts, which could be why the numbers are so low. But not sure.
Zivkovic: PLoS One has quite a bit of commentary, 1,000 back in July and growing since then.

Q: There was a considerable amount of work done on the Semantic Web years ago, talk of it being a "cool" technology. What makes you think this will work now?
A: Wilbanks: The SW allows for one to add context to links between two things. The difference this time is that this is a public effort, bringing the power of Metcalfe's and Moore's Law to science. Wilbanks thinks this (being the NC and our SW work at Science Commons) is useful enough to justify the pain of working with RDF. This provides a single point of access to the public domain and information.

Q: Generating and editing all of that video seems like an expensive ambition. What's JoVE's business model?
A: Pritsker: It is expensive and even more so - it's difficult. JoVE employs a distributed production network, minimizing some of the cost through a network of contractors in certain areas. Each of these contractors have not only the skills to film the experiments but backgrounds in the sciences, giving them the knowledge to accurately and thoroughly document the experiments.

Q: I'm curious about the age groups for who uses these services / sites?
A: Wilbanks: The majority of people who use our SW work / NC project are hardcore systems biologists, making this not about the age per se, but more about the willingness someone has to take a risk with a new technology. This skews our demographic.
Spencer: Anecdotally, it's across the board. No formal surveys of the users have been done to date.
Zivkovic: PLoS One is working currently on surveying users to gain a better understanding of the demographic.

"Publishing in the New Millennium" - First Panel

"What publishing model best serves us as we move forward?" - Emilie Marcus

Time for the first panel (out of two) at "Publishing in the New Millennium" at Harvard Medical School, examining the state of scientific publishing. Each panelist gets five minutes to introduce themselves and to identify a few key issues.

The panelists:
Emilie Marcus - Editor-in-Chief, Cell Press; Editor, Cell -- here to offer her thoughts on changing publishing models and peer review, subscription based business models v. author pays (a model often employed by OA journals).

Stuart Shieber - Professor, Harvard University - OA advocate

Shieber posits the following questions: Would it be a "good" thing for all journals to be Open Access journals? Two separate questions , he identifies: Which of the two scenarios are better (subscription based / journals funded through publication charge)? Even if you thought it'd be better for the majority of journals to be OA, would the disruption, dislocation, costs, etc. that would overwhelm the benefits of getting there?

Can we get from here to there in a way that doesn't cause a massive disruption? Shieber thinks this is where we should focus our attention / discussions, rather than OA as a static notion.

Address notion of threatening editorial independence - vanity press (take money to reduce its standards), since quality / standards vary on payment, with higher payments correlated with lower standards.

Robert Kiley - Head of Systems Strategy, Wellcome Trust - a veteran of OA meetings.

Kiley starts off with providing a bit of background on Wellcome's OA policy. All research papers funded by the Wellcome Trust must be made freely available in either of the PubMed Centrals in 6 months of less. Two ways to comply, 1) Make it the publisher's responsibility to deposit the article, 2) Some publishers don't have such a model, but do allow for authors to self-archive their work, often after an embargo. If a publisher offers neither, authors can suggest the journal's copyright agreement, or ... worst case scenario, find another publisher.

Making this research available, helps improve the research process by maximizing the impact of the research output. Can programmatically search, use bots etc, taking advantage of text mining and SW technologies. This can only be done if the full-text, I repeat FULL-TEXT is made available.

Wellcome, like Howard Hughes Medical Institute (HHMI), sometimes shoulders the cost for the publisher to deposit the scholarly work in PMC or UKPMC.

In order to promote OA to the research community, need to better articulate sharing mandates, consider linking OA policy to data sharing policies, provide the infrastructure for papers to be deposited, reassure the community that its the intrinsic value of what they have published that's mroe important than where the article is published.

Asked to comment on the relationship between OA and peer-review - Terry doesn't believe there is a relationship. Peer review is a function that the publisher organizes.

Issac Kohane - Director, Countway Library

95% of our output, output that we as scientists are allowed to submit, is being put into PubMed Central. Kohane says one would not get any pushback from the publishers for submitting to PubMed Central, so why don't people do it? People just do not have the time (KT: among other reasons).

As a librarian - friendly librarian will help. In a relatively short amount of time, matter of a few years, make sure that the only barrier is "us" - working to ease the transition.

What are the other information inefficiencies?

OA will create a shift in our ecology, Kohane believes.

A few questions to highlight (My fingers can only type so fast :) )
Q: Does OA provide any solutions to publishing negative data?

A: Kohane - Only cure he can think of is create a journal, such as PLoS One, where those studies can live.
Marcus - Science is an evolving pursuit. Fine line between saying something is wrong and something has changed. It's hard to isolate out papers to say specifically that an idea is wrong without saying that something is right, shedding light on the direction that one should go in. Issue with negative data - difficult to make a case out of negative data - high barrier. Confidence that something exists because you cannot see it is much different / more difficult than saying something exists because you can see it.

Q: Varmus - Want to address the question "Can authors be hurt if they post their article in PMC?"
Would argue that journals need their authors and dont have much ammunition for their reprisal, but authors need the editors and need them to smile favorably on them. The point is that the number of journals have sent out notes basically threatening their potential authors / discouraging them from participating in this effort ("this effort" being contributing their article to PMC and adhering to NIH's request for submission).

Marcus - Cell does make its content accessible on PMC 12 months after submission.

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Next: The final panel - "Publishing 2.0" - featuring Moshe Pritsker (JoVE), Hilary Spencer (Nature Precedings), John Wilbanks (Science Commons / Creative Commons), and Bora Zivkovic (PLoS One) ...

Conference round-up -the speed round

I've been remiss in writing about the series of meetings I've had over the past few weeks.

// slaps self on wrist.

So instead of going through all of my notes and posting 15 posts here in rapid succession, I'll resort to summarizing in bullet-point fashion. Hopefully this can adequately encapsulate the basic gist of each gathering.

First, Berlin 5 Open Access Conference in Padova, Italy:
- best summarized by PMR's posts in real-time (accessible, here). Wonderful to see him again and others from the open access circuit, as well as touch base with those more engaged in international discussions on access issues. Fabulous crowd.
- the event not only spurred (and somewhat ignited) a dialogue about policy (mandates, data-sharing best practices, funding, etc) but also looked at the status of OA in a smattering of countries and leading organizations - from France, Italy, and the UK to India, CERN, and Japan. Also pushed into the successes and obstacles of extending OA into the humanities and social sciences - which presents a world of issues not commonly found in dealing with scientific publishing.
- how to move a step beyond solely green access (granting the author the ability to self-archive) to gold (making the material "free" or freely available at the point of access). Not that the two cannot coexist, since they often do, but how to focus on getting publishers to make the material available free at the time of publication, whether that's paid for by a research agency or by the author.
- one of the most valuable components of this conference for me was learning about what the European Commission, the European Science Foundation, CRUI, DFG, Max Planck Society etc. were doing about OA. As well as meeting the key players from each of those organizations.
- my personal favorites, talk-wise: Alma Swan's compelling closing session, Ilaria Capua's session on Avian Bird Influenza and data, and of course, PMR's discussion on Open Data.
- there is so much more to write about this event, but I'm running out of steam. so, with that said, conference program and submitted abstracts can be found here.

Next, a joint workshop with CODATA, GBIF and Science Commons on common use licensing for scientific data products.
- this was a closed meeting, so I can't say provide an actual record of the meeting, but can say the following things.
(personal views, of course. in case you needed another disclaimer)
- data sharing is hard. It's an issue I've been engrossed in for the past few weeks, due to work-related research and discussion, paired with my own fascination with the nuances / complexities of this issue. There's certainly a drumbeat swelling for an answer to how to best make data "open". Now, I'm not a lawyer, nor a scientist, though I deal with issues regarding both regularly. Clearly, in terms of this kind of data, and data in general when speaking of taxpayer-funded research and that in the sciences, I tend to join the "more open the better" camp. The benefits of sharing data, be it of high-value or little worth to the researcher, are vast. Especially with modern day advances in how that data is queried / put into publicly integrated databases, etc etc etc. Even with that, there are serious implications for certain jurisdictions and types of data - say, indigenous knowledge or sensitive information.

You can see how this could be problematic for an absolutist, pushing for "all" data to be freely accessible. I'm still learning more about all of the implications, through SC and on my own. There are myriad things to consider ... many of which don't immediately come to mind if you're not involved in the debates.

Also attended the first organizational meeting for iGEM in Europe (another Paris meeting).

Since this post is already weeks late and far too long, I'll leave it at that. Phew, finally. :)