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.

During the last few years, there have been a few occasions when I've been at a computer but without immediate access to a periodic table. My standby is Web Elements, a site that seems to have been around forever.

I recently happened onto Jorge Goncalves' Triple Point, which summarizes the best 55 online periodic tables. Although some of the links are broken, there's plenty to choose from if Web Elements doesn't do the job.

The various forms of elemental periodic tables are in many ways the ultimate chemical information systems. They summarize what's already known and even after a century still light the way to new areas of discovery. Periodic tables demonstrate, like perhaps nothing else in chemistry, the power of organizing information.

Image Credit: Mike Mertz

You know something's gone mainstream when chemistry's flagship magazine, Chemical & Engineering News, recommends it. The current issue contains an article offering five tips for a better job search. And right there at number three is "Connect through blogging."

What specifically should job-seekers be doing with their blogs? The article suggests:

• writing short summaries of your presentations at meetings

• inviting comments to create an interactive environment

• posting fresh content regularly

("Writing summaries of your most recent publications" is not one of the suggestions. Perhaps certain unpleasant copyright issues are best avoided altogether).

I could be dead wrong about this, but the day may well come when not having a professional online presence outside of standard publications will be a competitive disadvantage to chemists. Regardless of whether you're still an undergrad or in your third decade in industry, blogging does something for you as a candidate that is impossible to achieve by other means.

Let me explain.

I've interviewed numerous job candidates, but I find it very difficult to do. No matter how good a company is at pre-screening and structuring the on-site interview, and no matter how skilled the interviewers, the process is fundamentally flawed. Here are some of the things I always looked for but was rarely able to fully address during an interview:

• How passionate is the candidate about their field? Clock-punchers have a tendency to stay in an organization for a long time.

• How does the candidate deal with criticism? The better the working environment, the more likely it is the candidate will be exposed frequently to one form of scientific criticism or another. Dealing with it is not always easy, especially when money and promotions are involved.

• How does the candidate work with potential competitors? Most academic programs in chemistry do very little to prepare chemists for the reality they face in flat, efficient organizations oriented around teams of equivalently-trained peers.

• Can the candidate generate enough new ideas to sustain themselves and anyone who might work with them? A chemist who runs out of good ideas quickly, or who doesn't dig deeply enough when the project is failing will have a very hard time thriving professionally.

• How does the candidate try to persuade others? Persuasion plays a deciding role in getting things done within organizations. Integrity, humility, and tact are incredibly powerful persuasive tools that are only taught by the very best mentors and professors.

• How willing is the candidate to stand against established dogma? Dogma kills innovation. But going against dogma is often very unpleasant, especially for the person doing it. People with the skill and courage to challenge orthodoxy while keeping their cool are worth every penny they earn.

Sadly, no matter what you ask a candidate, you will rarely get good answers to questions like these. For one thing, interviewing is very stressful for candidates, and as surprising as it might sound - it can be equally so for interviewers. For better or worse, what you see during an interview may not be what you would get in a colleague. Another factor is the interview schedule itself and its dampening effect on in-depth discussions.

Blogging, on the other hand, has the unique potential to give insights into all of these questions.

How many blogs do you read by authors you respect but whom you've never met? How many of those blogs offer insight into one or more of the questions listed above? If one of these respected authors were interviewing at your company or university, how would your expectations differ from a candidate you knew less about? How would the quality of the interview differ?

Of course, the effect works in the opposite direction as well. We're just starting to come to grips with the idea that it's literally possible for ordinary people to reach a world-wide audience for virtually zero cost with content that stays around for a long time. The concept is simultaneously liberating and terrifying.

The payoffs can be large for those willing to take the risk, stay creative, focus, and persevere. Which, of course, are exactly the kinds of talents your next employer may be looking for.

Image Credit: blakie

The graphical language of 2D structures has served chemistry well for the last 100 years. Ironically, this language which is so useful for human communication is extraordinarily difficult for machines to understand. Heroic efforts at digital raster image recognition such as OSRA and those recently summarized by Egon Willighagen, in addition to a handful of others, have tried to tackle this problem with varying degrees of success.

The problem remains unsolved, and continues to be one of the most difficult technical challenges in cheminformatics. But the pace at which non-machine readable images are generated has accelerated dramatically in the last two years with the emergence of numerous free chemical databases.

What if 2D structure images simply contained all of the information needed for machine processing in the first place?

This idea isn't as far-fetched as it may sound initially. As discussed in a recent D-F article, both GChemPaint and ACD ChemSketch have been claimed to be capable of encoding machine-readable structure information.

Previous D-F articles have described "Firefly", the codename for a new lightweight 2D structure editor designed specifically for the Web. With major work on the editor's user interface complete, more recent efforts have focused on implementing a 2D rendering toolkit, and with it a mechanism to encode structural information within 2D molecular images.

As a demonstration of what is now possible, consider the structure of GlaxoSmithKline's diabetes treatment rosiglitazone (Avandia), depicted as a PNG image at the beginning of this article. At first glance, the image appears to be just like any other image of a 2D molecular structure. But it is not, for embedded within it are the connection table and 2D atom coordinates of rosiglitazone encoded as an industry-standard molfile.

Given the right software, a computer can interpret the structural information encoded in the rosiglitazone image and precisely re-create the original molecular representation. A graphical diagnostic tool bundled with Firefly was equipped with code for precisely this purpose.

This tool can work with molfile-encoded PNG images just as easily as it can with molfiles; they can be opened and the resulting molecule can be further edited, saved in another format, or re-written as a embedded-molfile PNG image.

The first step is to select the PNG image from a local hard drive:

Opening this image produces a fully-editable version of the original molecule:

Obviously, nothing limits this technique to molfiles. InChI, SMILES, CML, or any other molecular encoding scheme would work just as well.

Using molecular-encoded PNG images as a Web-ready replacement for the Word/Chemdraw OLE technology may be one application of this approach. With a large corpus of these images, chemical Web spidering and data mining would be possible on a scale unimaginable today. As always, these possibilities reinforce the desperate need for high quality tools that chemists actually want to use, and which simultaneously yield machine-readable output.