Yale University has ended it's financial support of BioMed Central's Open Access Membership program effective July 27, 2007. Under the program, Yale libraries paid an annual fee to cover the costs of submissions by Yale authors to BioMed Central (BMC) open access journals. Yale authors can continue to submit manuscripts to BMC, but must pay for all charges themselves.

According to the August 3, 2007 statement by Yale,

... Starting with 2005, BioMed Central page charges cost the libraries $4,658, comparable to single biomedicine journal subscription. The cost of page charges for 2006 then jumped to $31,625. The page charges have continued to soar in 2007 with the libraries charged $29,635 through June 2007, with $34,965 in potential additional page charges in submission.

As we deal with unprecedented increases in electronic resources, we have had to make hard choices about which resources to keep. At this point we can no longer afford to support the BioMedCentral model.

Apparently, Yale is not alone in its decision. In a refreshing act of openness, BMC lists both current members and former members. A surprisingly large number of universities have canceled their memberships, including over 80 in the United States alone. In effect, these cancellations represent a version of the journal deadpool, but in reverse.

Cost increases pose a real threat to the viability of scientific publication. Journals rely heavily on network effects to attract readers, authors, citations, and ultimately, subscribers. A journal can remain viable for some time in the face of canceled subscriptions. But each cancellation brings a journal that much closer to destroying its network, its only real value.

Open access by itself doesn't solve scientific publishing's most serious problem - it simply changes the paths through which ever-increasing sums of money flow.

Thanks to Wendy Warr for her alert on this story posted to the CHMINF-L mailing list.

I realize that being the U.S. Government has its advantages, but the copyright notice at the bottom of a recent J. Chem. Inf. Model. paper caught my attention:

This article not subject to U.S. Copyright. Published xxxx by the American Chemical Society

As far as I can tell, this article is not part of the ACS AuthorChoice program.

In a recent interview, Peter Murray-Rust offers some very interesting comments on Open Access in chemistry. Beilstein Journal of Organic Chemistry remains the only widely-available Open Access option for chemical publication backed by a major publisher. With these thoughts in mind, I offer an update to my previous compilation of their statistics.

Greg Beaver has written an interesting set of ten golden rules for running open source projects. Many of these rules apply to running (or working on) anything. My favorite rule is "3. Despite the evidence, it's probably your fault." Greg develops the popular Open Source project PEAR, a packaging tool for PHP that looks similar in concept to RubyGems.

Cheminformatics, like all vertical markets, has is own peculiarities when it comes to Open Source. Most importantly, cheminformatics software has a limited, but captive audience. When done well, it is both highly profitable and expensive to develop. For insightful perspectives on Open Source software as it applies to cheminformatics and vertical markets, see Matt Stahl, Warren DeLano, Craig James, and Eric S. Raymond.

The minimum level of disclosure that Nature Methods requires depends on how central the software is to the paper. If a software program is the focus of the report, we expect the programming code to be made available. Without this code, the software - and thus the paper - would become a black box of little use to the scientific community. In many papers, however, the software is only an ancillary part of the method, and the focus is on the methodological approach or an insight gained from it.

-Nature Methods Editorial, March 2007

It's refreshing to see Nature Methods publicly acknowledge the importance of software availability in the sciences. On the other hand, the editorial still leaves wriggle room for an author determined to keep his or her source code private.

For example, consider the term "programming code." Does this mean "source code", or does it also include "object code"? The rest of the editorial makes it clear that both are acceptable to Nature Methods, although source code is preferred. Releasing binaries only "... may be acceptable if the operations performed by the software are sufficiently clear." Can any amount of description ever substitute for source code itself?

Over twenty years ago, John Figueras made the case that authors wishing to keep their source code private fundamentally misunderstood the difference between science and advertising. This may be a distinction lost on certain authors, but journals play along at their own risk.