The OpenHelix Blog

Five universities, Harvard, Cornell, Dartmouth, UC Berkeley and MIT, have compacted to support open-access publishing by funding publishing fees. Many open access journals, because the do not charge readers, use the model of charging for publication. This could be a barrier to publishing in an OA journal, so the compact:

…supports equity of the business models by committing each university to the timely establishment of durable mechanisms for underwriting reasonable publication fees for open-access journal articles written by its faculty for which other institutions would not be expected to provide funds.

Open access isn’t free, someone has to pay for it.. the provider, the user or some other model. I, personally, like the idea behind open access publishing of research. I believe it can be one model, among several, to make access to research free and available to help advance further research. Two years ago, the Consolidated Appropriations Act made it a requirement that NIH-funded research be published in such a manner that it was open after a certain period of time, a boon to open access publishing. Publishers of all stripes are attempting to develop ways to make research available to researchers, and pay for it.

I look forward to seeing how these universities underwrite those fees and which other universities join the compact.

A new open access journal, Ideas in Ecology and Evolution, has, well, opened. It’s published at Queen’s College in Canada.

“So?” you ask, “there are lots of journals up starting all the time”.

This one is different. It’s experimenting with a lot of things (ok, so there seem to be a lot of journals experimenting with the model lately). The subject matter is not research per se, but ideas. Having been to my share of ecology and evolution conferences and discussion, I can see this journal has opened itself up to some quite lovely discussions.

As explained by Bob O’hara, there are some interesting review process experiments going on here too. Authors pay to get their ideas published, reviewers are paid, reviewers are not anonymous and they get to publish their views of the article as a companion piece. Bob discusses the issues we’ve all heard about the pros of anonymity (and they are valid ones), but this might work in this case. I also agree with Bob on one point, this structure (reviewers publishing their views) will indeed increase discussion, but I’d too like to see some mechanism for a broader discussion. As it is designed now, it will be like watching TV pundits arguing the finer points of health policy, which I guess is informative, but I’d like to see some mechanism that allows a broader discussion of the article. Something like PLoS has, which I think would actually work better in a journal of ideas like this.

Well, we’ll see. Right now there is nothing there but the editorial. I’ll be watching though.

hat tip: Coturnix

If you haven’t already seen it, open-access publishing either just made a jump backward or forward. The not-so-open access Springer publisher bought Biomed Central, the open access publisher recently. Open access publishing took a huge leap with the passage of a law last year that requires NIH-funded research to be open access and deposited in PubMed central within 12 months of publication. The law hasn’t not met resistence though. Perhaps Springer saw the writing on the wall, so to speak, and decided that buying BioMed Central was a good move in a world were open-access publishing seems to be gaining ground. Or…?  According the BioMed Central FAQ about the buy, BioMed Central publishing will remain 100% open access.

According to this BioMed Central blog, tomorrow is Open Access day – how shall we celebrate? Maybe read an extra open access article or two? Attend one of the events? Your blog on Oct 14th about the importance of open access to you could win you a ‘bag of swag’ PLoS ‘Synchroblogging competition – get writing this weekend’ competition. Another option is to join the BioMed Central Facebook fan club. As you can see there are LOTS of ways to support OpenAcess – let us know what you do to celebrate this important movement.

We train on publicly available databases and resources. For our purposes on deciding when to develop training, the definition is relatively straightforward: Can the academic researcher access the data without cost or license restriction? If the answer is yes, our next step is to determine if we can develop training materials based on the resource without cost or license restriction and to ask the providers specifically for permission to do so. We ask permission for several reasons: let the developer know what we are doing, verify the restrictions or lack there of, build good relationships, etc.

That first decision, “is it publicly available?”, would seem a relatively clearcut criteria, but we have found that it isn’t always. There are several problems. Often, the ‘terms of use’ or copyright documentation is difficult to find on the web site or non-existent. Even when it available, the terms, language and restrictions can vary quite a bit across databases, countries and even within a resource at times. Determining what “publicly available” is and which resource fits that definition can be less than simple, to say the least.

There is an attempt to offer a definition of “open” using the Creative Commons license.

Dr. Eisen at UC Davis has started a new blog theme on his “Tree of Life” blog called “Open Evolution” (open access publications, open source programs, etc) and has started with open access journals. He has listed a few open access journals (and there’s a good discussion in the comments about the difference between ‘open access’ and ‘free online access’ journals) and is asking if anyone knows of any others. He hasn’t asked for it yet, but I’ve got some ideas for open source/access phylogeny analysis programs and/or databases. I’ll post a few of those in the coming week or so, but for now here is a link to a list of such programs (some on this list I’m not sure are open source, I’ll cull these later too).

We have a slide we like to present at some trainings showing the rise in the amount of raw sequence data and number of complete genomes over the last 18 years. There is another slide we show that indicates the rise of the number of databases and analysis tools over the years as listed in the annual database issue of NAR. The number has been doubling every 4 years.

Well, there is another slide we can show too, and this shows the growth of the number of abstract entries into PubMed over the last 20 years (from Hunter and Cohen, 2006). Like data and databases, the number of research articles published and indexed just keeps getting larger. This increase in number is both a bane and a boon to researchers. Well, of course not only the number of papers indexed is growing, the amount of text is growing (open access, etc) and is about to grow even more with the signing of the new open access act. Searching, mining and making sense of all this literature is going to be a challenge, it is a challenge now.

The Public Library of Science was founded in 2001 and published a letter urging publishers to open access to research published in their journals (I remember this letter being presented at an ISMB conference then). PLOS launched a series of open access journals when the response wasn’t particularly enthusiastic from the publishers. Those PLOS journals have had some success since, as have those at Biomed Central, another open access publisher.

There has been resistance from scientific publishers to the open access movement. Some fully opposing it, others like Nature Publishing Group’s official opinion is that it has no position, but that the business model is unproven and peer review an expensive endeavor. Nature has been experimenting with open source models though through the Molecular Systems Biology (an open access Nature journal) supporting self-archiving through public repositories, making an exception for papers reporting genomes and their open text mining initiative.

And now a new development: Wednesday, President Bush signed the Consolidated Appropriations Act of 2007 (H.R. 2764), which requires all NIH-funded published research to be deposited into PubMed Central (and thus open access) within 12 months of publication.