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2013 August 3

University of California faculty commit to open access

Filed under: Uncategorized — gasstationwithoutpumps @ 15:06
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According to the press release, The University of California faculty have just endorsed an open-access publication policy.  The policy does not require publication in open-access journals, but deposit of articles in  eScholarship (UC’s open access repository).  There are supposedly opt-out mechanisms, which will undoubtedly see heavy use, both because many major journal still don’t allow deposit in university repositories, and because depositing in the UC repository will probably be a bureaucratic hassle that is easier to opt out of than to comply with.

Of course, I haven’t seen the details of the policy—it has not been distributed to the faculty yet.  Once again, I find out UC changes of policies first from the news media, not from any internal communication with the faculty.

I’m basically in favor of open-access publishing, but not in favor of author-pays funding of it (as an unfunded researcher, I can’t afford $2000–3000 per article).  Having a UC-based respository is basically a good idea, as long as it isn’t as much hassle to deal with as the NIH repository was (and maybe still is—I’ve not had NIH funding for a while).  I don’t know how good the indexing is going to be, either—whether people will be able to go from a standard journal citation to the UC copy of the article easily, without having to go to the eScholarship site explicitly looking for the article.

2012 November 29

PeerJ, open-access done reasonably

Filed under: Uncategorized — gasstationwithoutpumps @ 10:28
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There is a new open-access journal—what could be less newsworthy than that?  I get dozens of spam messages a week from open-access vanity journals eager to take my money.  Most of them get discarded quickly, as being not worth the time it takes to figure out what the scam is for this one.  As an unfunded researcher who has gotten tired of chasing after grants, I can’t afford the $2000–3000 an article cost of publishing in open-access journals like PLoS Computational Biology.

So why am I writing about yet another open-access journal? One with a crummy name like PeerJ, at that?

Well, it seems that the creators of PeerJ have recognized that publishing an online academic journal need not be expensive, and that the lower costs of production can be turned into lower costs for the authors (rather than into high profits for the nameless owners of the journal).  Their model is a subscription model, but it is a subscription for authors, not for readers. For a one-time fee of $99 you can publish one paper a year; for $199, two papers a year; and for $299 an unlimited number of papers per year.  (They charge a little more if you wait until your first paper is accepted before publishing.)

There are a few gotchas: every author must pay (well, only a dozen for papers with more than 12 authors), and every author must do a review each year in order to retain their membership (they can restart a membership for $99 if it lapses for lack of reviews).  There are institutional discounts, which might be useful for a company or university, if they are reasonably priced (institutional pricing is not on their web page, just an email address to discuss it with them).

This looks to me like a reasonable model for open-access publishing, if they can make it work.  Note that unlike high-fee open-access journals, there is little incentive for them to become a bottom-fishing vanity press. They have the same sort of incentive that a subscription journal has to keep the number of papers down, as they don’t make a lot more money by publishing a lot of papers.  This leads me to hope that their editorial policies will concentrate on publishing quality papers.  They do have substantial incentive to seek out new authors, though, so they won’t fall into the trap of only publishing papers from an old-boy network, the way some traditional journals do (I’m looking at you, PNAS).

I’m even considering finishing up one of my long-neglected drafts, just so I have something to try submitting to them.

Thanks to Iddo Friedberg, whose blog post on PeerJ alerted me to its existence.

2012 April 15

University of California open access

Filed under: Uncategorized — gasstationwithoutpumps @ 09:20
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The faculty of the University of California are once again attempting to formulate an open-access policy: Reshaping Scholarly Communication: 2012 UC Open Access Policy Proposal.

They thought things through a little better than the last time they attempted this, making the proposed new policy be a mandate that faculty have to deposit their papers with the California Digital Library or another open-access repository. I can see potential for problems there, with some faculty submitting to open-access repositories that disappear—I think that there should be a maintained list of repositories that are acceptable. If I were making such a list, I would limit it to repositories with exchange agreements with the California Digital Library, to ensure that CDL could have a copy, no matter which upload portal faculty chose.

The papers will be open access by default, but faculty can opt out for specific papers (opt out of the open-access, that is, not out of the deposit requirement).  The access is a transferable non-exclusive license to exercise copyright.  I’m not sure legally exactly what that exact wording entails, and the description (which is not an official part of the proposed policy) seems a bit vague, as if the authors of the policy were not sure exactly what rights they were giving the University, or did not want the faculty to know exactly what they were giving up to the University.

I’ve written about open access several times, and my feelings on the matter are pretty clear now:  I’m basically in favor of open access journals, I believe that the papers resulting from tax-payer-funded research should be open access, and I fear the suppression of publication of non-funded research if an author-pays model becomes dominant.

The NIH PubMed repository accepts open-access submissions directly from several of the journals I have published in, which is much easier than trying to navigate their direct submission system. I particularly disliked NIH’s insistence that authors proofread their mangling of submitted materials. It is bad enough having to proofread articles once—having to proofread them again anytime a library wants to archive the article is unacceptable (I regard the NIH repository as more akin to a library than a journal—I hope CDL sees their role as a library, not as a an alternative journal that reformats articles.)

The policy that the University of California faculty is proposing is compatible with several different business models for open access, including the one I favor, that allows subscriber-only access for a limited time, followed by open access (with the author having the option to pay for immediate open access).  That model allows journals to continue to be paid for a combination of author fees from authors with government or non-profit funding and subscription fees to support publication for authors without funding.  I also support models in which publication is directly funded by support from government agencies or non-profits, without author or subscriber fees—the proposed policy is compatible with that model also.

So aside from wanting greater clarity, I basically favor the proposed policy.

I want greater clarity in the policy itself, not just commentary, about

  • exactly what rights are being given to the University,
  • what defines an acceptable repository,
  • what defines a “scholarly article” to which the policy applies,
  • whether faculty are expected to proofread or otherwise verify submissions, and
  • what the time frame is for making the deposits in the repository (would it be acceptable for CDL to get the articles a year after initial publication, when the journal makes them open access, or would faculty have to submit drafts, then resubmit when the edited article becomes available).

2012 February 25

PLoS Computational Biology: Bioinformatics: Starting Early

The Public Library of Science has a a service where they group together open-access articles from their journals to make  PLoS Collections: Article collections published by the Public Library of Science.

One collection that might be particularly interesting to readers of this blog is PLoS Computational Biology: Bioinformatics: Starting Early, which has articles from PLoS Computational Biology about getting bioinformatics into high-school courses.  So far, there are only 4 articles, all from the 27 October 2011 issue of the journal, but I expect that more will come out in the next year.

2012 January 30

F1000 Research—yet another open-access publisher

Filed under: Uncategorized — gasstationwithoutpumps @ 21:38
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F1000, who publish the extremely pricey “Faculty of 1000″ reviews of scientific literature are now throwing their hat in the open-access publication ring with F1000 Research.

They are planning to do post-publication review,which is the current darling of the open-access advocates, as it pretty much guarantees that anything someone wants to publish will appear—the only barrier being the price the author has to pay to get it published. F1000 has been doing post-publication review (of work from any scientific journal) for years, so they have some ideas about how that should go.

I’ve written some Faculty of 1000 reviews, and I found their editorial constraints rather limiting.  They never wanted any negative comments about a paper, just superlatives.  Even the very good papers I read generally had a few flaws, and they kept wanting to remove mention of those parts from my reviews.  I’ve pretty much given up doing reviews for Faculty of 1000 for several reasons:

  • Their subscription prices are so high that the University of California Library has come close to unsubscribing a couple of times, and I don’t want to be providing free content to a company then charging so much for the content.
  • Their editorial policy of “superlatives only” does not match my more balanced (or perhaps just more negative) reviewing style.
  • I’ve lost interest in the field for which the originally recruited me. I find it very difficult these days to read most papers on protein structure prediction and related fields.  Mostly people are rehashing ideas that have been around for a decade or more, rarely improving on them.  There are probably only a handful of good papers a year in the field, and I don’t have the patience to find them.  (That is the job of F1000 reviewers, and if I were eagerly reading dozens of papers I’d be glad to share the occasional gem, but I’m not eagerly reading papers, so I almost never encounter the good ones.)

Given F1000’s history, I’m worried that the new F1000 Research will be very expensive and will quickly become a repository for trash papers. In a standard open-access journal that problem can be avoided with strong editorial control (PLoS Computational Biology generally publishes decent papers, for example), but with only post-publication review, the venue is likely to get clogged with stuff too bad to be published elsewhere.

Who is going to want to do post-publication review of a stream of junk?  It is hard enough reading the mediocre papers that have already been through peer review already—reading the ones that even the authors think would fail peer review would be excruciating.  If no one competent is reading and critiquing the papers, then the junk will not be filtered out and the whole process will degrade into a vanity press.  There are already dozens of vanity open-access journals that will print any sort of s**t if the author pays the fee (even going through a pretense of peer reviewing), and I did not see anything in the F1000 Research announcement that suggested that they would avoid this trap.

Note that what F1000 is proposing is very different from the open access in arXiv, the (mostly) pre-publication archive heavily used by the physics community. “Open access to 731,853 e-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics.”  The arXiv site does not provide discussion forums, but many researchers put papers into arXiv for pre-publication discussion before submitting them to peer-reviewed journals.  There are enough respected scientists doing this that people do regularly look through arXiv for interesting material in their field. Because depositing a paper in arXiv gets it read by a few people, but does not count as publication for promotion and tenure, there is little incentive to clog arXiv with junk.

People do sometimes stick papers in there to establish that they got an idea first, even if the paper needs some work still before it is publishable, and sometimes the early drafts of a paper have flaws that are revealed before publication, but most of the papers in arXiv are published in peer-reviewed journals eventually.

Also, note that the fields most rife with sloppy research and outright fraud are not covered by arXiv (medical research seems to have the lion’s share of scientific fraud, probably because of the amount of money involved). Although there are some crackpot papers in arXiv, for the most part it is real science. I believe that F1000 wants to cover a wider swath, including fields in which fraud and crackpot theorists are a more common problem.  Relying on post-publication review seems a risky endeavor.

Disclaimer: as an unfunded researcher, I have mixed feelings about open-access publication. I like getting papers for free, and I like the idea of distributing scientific papers as freely and cheaply as possible. But most of the business models call for the author to pay for publication, which is fine for those who have grants that can pay publication charges, but deadly for those of us without funding.  Open-access publishing may, in fact, restrict publishing to a smaller group of authors than the traditional publication model—those with money.  Requiring those with grants to publish in open-access venues makes some sense to me as a taxpayer, but if it results in the loss of subscriber-pays journals, many researchers will be excluded from publication, and everyone will need to spend even more time writing grant proposals instead of doing research.

What I’d like to see are more things like arXiv, which provide free access funded neither by the authors nor the readers, but by organizations with an interest in free distribution of scientific literature (granting agencies, governments, and research libraries, for example).  I doubt that F1000, as a for-profit company, plans anything like that.

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