An alert Depth-First reader pointed me to the new ACS policy for authors receiving NIH funding. The details are contained in a document outlining two ways authors can choose to comply with the new law requiring recipients of NIH funds to deposit a copy of their peer-reviewed manuscripts into PubMed Central. The choices are:

1. Publish the article under ACS Author Choice by paying a fee. The ACS will then automatically deposit the article on behalf of the author.

2. Publish the article using the standard procedure, but with the ACS granting authors the right (and responsibility) to deposit their manuscripts in compliance with the NIH Public Access Policy.

Under Option 2, copyright remains with the ACS - authors are simply granted an exception to enable them to comply with federal law. This means, among other things, that ACS retains the right to prevent third parties (including authors themselves) from creating derivative works of deposited manuscripts, and from redistributing them.

For better or worse, the federal government is now in the scientific publishing business. What remains to be seen is the extent to which this new publisher has the power and ability to deliver on the high expectations of many in the scientific community.

Source: blip.tv via Chemists Without Borders

The NIH heard public comments yesterday on its plans for implementing PL 110-161 Section 218, a new law that grants the agency broad powers to intervene in the scientific publication system.

Scientific publishers were out in force. According to The Scientist, Jack Ochs of the American Chemical Society (ACS) was first in line to offer comments:

He started out by saying that a brief meeting was no substitute for the formal comments on rulemaking process like the one the NIH held when they were implementing the voluntary submission program in 2005. He was the first of several to call a halt to implementing the mandate so the details could be worked out.

A lot is riding on the outcome. The new law requires NIH grant recipients to deposit peer-reviewed manuscripts of their publications into PubMed Central, in apparent opposition to the policies of many leading scientific publishers - including the ACS.

NIH has given its grant recipients until April 7 before compliance will become mandatory. It remains unclear what steps, if any, ACS will take to enable authors to comply.

Unless ACS policy changes, NIH grant recipients face the possibility of losing one of the most prestigious publication options in chemistry.

Also see Peter Suber's comments.

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.