As discussed by Peter Suber, Peter Murray-Rust and others, President Bush signed H.R. 2764 into law yesterday. Among the many items in this bill is one that proponents argue could change the nature of the Open Access debate. Does this new law represent a fundamentally changed game, or just the next inning of the old one?

The text of the new law spells out what is now required:

SEC. 218. The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

IANAL, but the provision requiring the policy to be implemented "in a manner consistent with copyright law" offers publishers (and scientists) all the flexibility they need to continue business as usual.

The reason is simple. Transfer of copyright from the author of a scientific paper to the publisher is usually one of the first things to happen "upon acceptance" of a manuscript for publication. And the new law makes it perfectly clear that copyright law takes precedence over deposition into PubMed Central.

Most of the journals in question will be hostile to the idea of having their copyrighted material deposited into PubMed Central and so understandably won't allow it to be done by the authors of papers or anyone else.

Take this hypothetical scenario for example: Professor Gross at California University gets his manuscript approved for publication in the Journal of Nanoscale Devices (JND). Professor Gross is fully aware both of HR 2764 and JND's refusal to deposit manuscripts into PubMed Central - the reasons why Professor Gross would choose JND anyway are interesting, but not relevant here. Along with the acceptance letter, JND requests prompt return of a signed copyright transfer agreement. Professor Gross sends in the signed form and from that point on, all rights to his article belong to JND. As is their policy, JND refuses Professor Gross permission to deposit a copy of his paper into PubMed Central within 12 months after publication.

Unless I'm missing something, neither Professor Gross nor JND have violated any laws. The assumption made by proponents of the new law seems to be that to implement the new policy, the Director of NIH will forbid publication by grant recipients in journals that don't allow deposition of articles into PubMed Central.

How many influential scientist do you know of who would tolerate the government telling them which journals they can and can't publish in? The minute such a misguided policy is put in place, the national scientific outcry would more than overwhelm anything Open Access proponents could muster.

Neither HR 2764 nor any form of government intervention will bring widespread Open Access into being. The only things that will change the status quo are: (1) the availability of tools for making it happen; and (2) the realization by individual investigators that continuing to give away their hard-earned copyright makes them far less competitive than their peers who don't.

Open Access proponents should forget about getting the Federal Government to fix the mess that modern scientific publication has become. Instead, they should focus on making Open Access-like options more attractive to scientists.

Image Credit: mayr

How does open source software happen? Although many factors come into play, the majority of answers seem to revolve around a simple theme: developers building solutions to fill their own needs. Yet only a fraction of these solutions end up becoming open source software. And only a fraction of those end up being used by a wider audience. What's the key ingredient? There's still a lot to learn from studying individual cases.

Readable discussions about the origins of specific open source projects are pretty rare, but those dealing with the origins of open source cheminformatics software are more uncommon still. So it was with great interest that I came across Ivan Tubert-Brohman's account of how PerlMol was created.

PerlMol is an open source "collection of Perl modules for cheminformatics and computational chemistry." Many software packages fit into this category, and some of them are open source, so why write another? For Tubert-Brohman, the deciding factor was being able to work in his preferred environment, Perl:

I was surprised that CPAN [The Comprehensive Perl Archive Network] was sorely lacking in terms of modules for chemistry. The only available modules were Chemistry::Element, which allows you to convert between atomic number, element symbol, and element name and store other elemental information; and Chemistry::MolecularMass, which calculates the mass from the molecular formula. There were no modules that actually dealt with the structure of molecules. While some of the options in other languages are not bad, I was looking for something with the simplicity and conciseness of Perl that could allow me to write "chemical one-liners" to solve small problems very quickly, without having to compile anything. Hence, PerlMol was born.

The elimination of the need to compile, and relaxed syntaxes that promote succinct code are two of the biggest reasons to try a cheminformatics scripting environment.

There's a lot of great software still to be written in cheminformatics, and some of it will be open source. Although open sourcing that side project you've been working on may not be the best option for your career or your company, studying case studies like that of PerlMol gives plenty of food for thought.

SMILES is one of the most widely-used line notations in cheminformatics. Yet until very recently, there has been no concerted attempt to develop open SMILES encoding standards.

OpenSMILES aims to change that. By providing a forum in which concerns from the SMILES user community can be voiced, peer-reviewed, and addressed, OpenSMILES introduces a new way for the SMILES language to become better.

A draft OpenSMILES specification is now available for review. For now, the best way to raise issues and otherwise get involved is through the OpenSMILES mailing list.

Few would argue against small companies using open source software - indeed many owe their very existence to it. But what real, tangible good can come from a small company releasing open source software?

Signal to Noise, the company blog of 37signals, offers a worthwhile perspective on this issue. To summarize the business case:

• Certain kinds of software, like infrastructure software, take vast amounts of time and resources to get right - something that few small companies can afford. Open sourcing can accelerate the process.

• Open sourcing provides a public arena in which your own company's developers can learn from other great developers.

• That public arena provides unique access to a pool of smart, motivated developers - and offers a way to evaluate their work before even deciding to interview them.

• Open source generates press attention and goodwill from potential customers.

And about the elephant in the room:

A big fear that a lot of people have is that they’ll somehow be giving away their secret sauce. Unless your actual product is what you’re open sourcing, it really doesn't matter (and there are even plenty of examples of that working well). It’s unlikely that the piece of code that’s only seen internal development is such a silver bullet that you’re going to outshine your competition by its use alone.

The distinction between infrastructure software and a company's secret sauce is particularly important.

By just about any standard, 37signals is a leader in the deliberate use of open source software to achieve business objectives. We can all learn from them.

A gem of a chemistry blog has been operating for some time - apparently without much notice. ChemBlogs is Sigma-Aldrich's Web answer to their Aldrichimica Acta print magazine, and it's packed with mini-reviews on synthetic chemistry with links to the primary literature. This approach to scientific marketing has so much potential, I can't imagine why others aren't doing it.

Nevertheless, there are some small things that could be done to make ChemBlogs a lot more effective. Here, in no particular order, are some suggestions:

• Submit the RSS feed to Chemical Blogspace. Chemical Blogspace is perhaps the most widely-read aggregator of free chemistry content on the Web. And it's one of the best ways to get your chemistry blog noticed, bookmarked, and linked to.

• Make it easier to discover and use a post's permalink. If I see an article I like in ChemBlogs, such as this one on gold catalysis, there's no obvious way for me to link to it in my own blog. Standard practice is that all titles on the front page are hyperlinked to the article's permalink. This article discusses the importance of permalinks.

• Don't moderate comments - use reCAPTCHA instead. Nothing stifles online discussion like moderated comments. The Web is about immediacy. Make a change and see it live instantly. Everything else is so 1999. If spam is the concern, reCAPTCHA is a wonderful tool for the job.

• Drop the company group when identifying authors. No reader cares whether Sharbil J. Firsan is part of the Marketing Group or not. In fact, it's a bit of a turn-off to have the word "Marketing" appear at all.

• Each author should have an online bio that links to their name. Although titles and company divisions are not useful, other information about authors is. In a multi-author blog like ChemBlogs, the byline should hyperlink to a bio of the author, or a collection of their writing. This makes it easier for readers to follow authors they like.

• Link to the primary literature via DOI. ChemBlogs cites many articles appearing in journals, which is a great thing. Unfortunately, there's no way for a search engine to know that this is happening. The simple fix is to hyperlink a literature citation to the DOI entry, like this one for Chem. Rev. 1994, 94, 2483-2547.

• Include InChIs for all important structures. Free tools like InChIMatic can then be used to quickly find articles dealing with those molecules.

• Post more frequently and/or regularly. More content means more eyeballs. When it's regularly posted, readers know when to expect it.

• Invite some working scientists to write articles. If recent experience with Wikipedia and Chemistry is any guide, there are plenty of capable scientist more than willing to create free, high-quality compound monographs and other chemical content. Invite some of them to contribute very short articles for ChemBlogs in their area of expertise and see what happens.

• Release all content under a Creative Commons License. Information wants to be free - why not make it free? Allowing ChemBlogs' content to spread far and wide just makes it that much more visible. For example, at last count, Depth-First content was reproduced on about a dozen other Web sites, including one in Korean. This matches my goals exactly, and it's all perfectly legal thanks to the way the content is licensed.

With a little tweaking, Sigma-Aldrich's experiment in Permission Marketing could pay off - for everyone. Readers would conveniently get useful bits of information to make them more productive. The Internet would get new, high-quality chemical content - free to use and link to. Who knows - this might even become an Open Access business model that actually works.

And Sigma-Aldrich would have a far more effective marketing tool than anything else they currently use. With the possible exception of the Handbook, but even that could change.

Image Credit: angela7