Depth-First: Category Open X

GlaxoSmithKline Donates Cancer Genomics Dataset to Public Information Network

Rich Apodaca — Fri, 27 Jun 2008 16:22:00 -0400

In a move likely to up the ante in the emerging Open Source Drug Discovery movement, GlaxoSmithKline have announced the donation of genomic profiling data for over 300 cancer cell lines to the National Cancer Institute's cancer Bioinformatics Grid (caBIG).

According to NCI's FAQ, caBIG is "an open-source, open-access information network enabling cancer researchers to share tools, data, applications, and technologies according to agreed-upon standards and identified needs." caBIG is comprised of publicly-available datasets and open source software tools designed to interact with them.

This move has potential significance on a number of levels:

Large pharmaceutical companies haven't generally made a habit out of donating their hard-earned raw intellectual property on this scale. For something this far outside the industry norm, nobody wants to go first; GSK's actions have made the practice a little more respectable.
caBIG is simultaneously a publicly-accessible database, a set of open data specifications, and an open source software platform. In other words, it's striving to become an end-to-end solution to the problem of open collaboration in the biological sciences.
Donating raw data directly into an open repository bypasses the established scientific publication model in which data are communicated only as part of a peer-reviewed publication. Should this new publication model continue to gain popularity, it would fundamentally change the way science is conducted.

Credit: Peter Murray-Rust, Peter Suber, and Wired.

ACS Responds to Request For Information on the New NIH Public Access Policy

Rich Apodaca — Tue, 03 Jun 2008 09:18:00 -0400

In case you haven't heard, a new law is now in effect that requires all recipients of NIH funding to deposit copies of their peer-reviewed manuscripts into PubMed Central. There's just one problem - if your work is published in an ACS journal, it's the ACS - not you - who owns the right to copy, reformat, and redistribute the manuscript.

Setting aside the issue of whether the new law (PL 110-161) is good public policy, PL 110-161 raises some difficult intellectual property issues. This site has highlighted some of them, and the resources section at the end of this article contains some leading references.

The NIH has solicited public comment on its implementation of PL 110-161, and the ACS has responded. To make the ACS comments more accessible, they have been reformatted and reproduced below in their entirety:

GENERAL OBSERVATIONS & OVERVIEW OF COMMENTS

In the Federal Register notice announcing the Request for Information (RFI) the National Institutes of Health (NIH) poses three questions regarding the new mandate. The American Chemical Society (ACS) is concerned that the questions posed are insufficient to garner the type of input necessary to lead to a comprehensive and meaningful evaluation of the mandate. Further, the format for submitting comments discourages the submission of comprehensive, cohesive and thoughtful input. An examination of input received at the NIH web-site as of the date of this submission seems to substantiate the fact that much of it is far from comprehensive and may be of limited use towards producing a meaningful analysis by NIH at the conclusion of the comment period on May 31, 2008.

The following ACS comments broadly cover all three questions posed by NIH but by extension also cover many issues attendant to a larger more expanded response to each of the questions.

In short, we believe that:

NIH missed an opportunity to make its 2005 voluntary initiative a success – and has failed to address the underlying problems associated with the voluntary policy and those impediments to success will now become exacerbated under a mandatory policy.

NIH has not implemented the mandate pursuant to Congressional intent to ensure consistency with copyright law, and instead is forcing the research community to divert time and effort away from advancing the frontiers of knowledge to perform this task in NIH’s place.

NIH should have followed the federal Administrative Procedures Act, not an RFI, to solicit public comment on the implementation of the mandate. The APA, the federal rule-making standard for over six decades provides a more structured and meaningful process and could have been accomplished within the same timeframe as the RFI.

NIH must proactively address a number of copyright, intellectual property, and other concerns raised by ACS and other publishers to make the mandate a success (as outlined on pages 5-9)

ACS AND SCHOLARLY PUBLISHING – WHY COPYRIGHT IS IMPORTANT

The ACS is the world's largest scientific society with more than 160,000 members. We care deeply about the advancement of scholars and scholarship and pursue these goals through advocacy, publishing, conferences, information resources and professional development efforts. We have been doing so ever since publishing our first journal – The Journal of the American Chemical Society – in 1879.

Our 36 peer-reviewed scientific journals are distributed globally in print and electronic media and showcase the world’s finest research in chemistry and related sciences. Articles that appear in our journals are widely regarded having received recognition of excellence and the visibility that content in ACS journals receives not only helps scholars achieve new scientific breakthroughs but also leads to practical applications that directly benefit human health and welfare and the world’s economy.

Collectively our peer-reviewed journals form an informal but widely recognized hierarchy used by funding bodies and the academic community itself to assess research quality, impact, and priority—key factors used to allocate funding resources, evaluate levels of personal achievement, and determine professional advancement.

We believe that it is in the public interest to foster this beneficial publishing activity and toward that end we invest heavily in staff and technology resources required to be successful in this endeavor. Copyright creates the opportunity for us to do this by sustaining our publishing enterprise. This is why, we trust, Congress directed NIH to implement its Public Access Policy in a manner consistent with copyright law and respect for its underlying principles and why the Senate Appropriations Committee, in Report 110-107, directed NIH to “seek and carefully take into account the advice of journal publishers on the implementation of this policy” and “to ensure that publishers’ copyright protections are maintained”. We also believe that Congress considers, as we do, that the integrity of intellectual property is an essential criterion for the advancement of science as well as for innovation and creative activity.

IMPEDIMENTS TO THE SUCCESS OF THE VOLUNTARY POLICY STILL EXIST UNDER THE MANDATE

The American Chemical Society supports public access to the results of federally funded research but asserts that the implementation plan for the NIH Public Access Policy mandate does not abide with the law creating the mandate or with the sentiment and direction of the U.S. Congress, particularly as outlined in the Senate Appropriations Committee report that directed NIH to work with scientific journal publishers in implementing the new policy mandate.

The NIH missed an opportunity to make its May 2005 voluntary public access policy a success by not proactively including scientific journal publishers as it developed its procedures and policies for the deposit of manuscripts reporting on NIH-funded research into PubMed Central. Consultation with publishers is critical in 2008 to prevent the agency from embarking on a similar collision course as it proceeds to implement the new mandate. Key to success will be NIH taking an active role, one based on openness and inclusiveness, to resolve the outstanding copyright and intellectual property issues that cut across a very broad and deep swath of the scientific journal publishing community.

The ACS publishes annually approximately 4,000 articles that acknowledge NIH as a research funding source. ACS has tried to resolve outstanding copyright and intellectual property issues with NIH in connection with the Society’s efforts to deposit manuscripts directly with NIH PubMed Central on behalf of ACS authors who have elected to “opt in” to have the Society do so on their behalf. Despite ACS’ efforts, the NIH instructed ACS in December 2005 to suspend article deposition into PubMed Central; that prohibition has prevented the Society from depositing more than 3,000 manuscripts on behalf of ACS authors. During the 2005-2008 time period, NIH PubMed Central has accepted unauthorized postings of ACS copyrighted material, and repurposed and openly displayed such postings without adhering either to NIH’s own policy guidelines, or terms and conditions as set forth to NIH by ACS as rights holder. Issues of concern to ACS remain unresolved and will continue to be problematic and exacerbated under the new mandatory policy as outlined in NIH’s implementation plan issued on January 11, 2008.

ACS hastens to point out that the vast majority, if not all, the Society’s copyright and intellectual property concerns could be resolved if NIH would abide the original intent of the Public Access policy and post without alteration or modification the unedited author versions of peer-reviewed manuscripts on PubMed Central—without any reformatting, repurposing or modification or any mirroring of content to third-party websites—and simply link back to the final published article as the authoritative version for readers on the Society’s own website.

NIH HAS NOT IMPLEMENTED THE MANDATE PURSUANT TO CONGRESSIONAL INTENT

The American Chemical Society (ACS) expresses concern that NIH has not abided by the law in creating the new mandatory public access policy as stipulated in Division G, Title II, Section 218 of Public Law 110-161 (the Consolidated Appropriations Act of 2007)

In enacting Section 218, ACS believes that Congress was aware that flawed implementation of a mandatory public access policy could create serious problems for the scientific publishing community which is why it included the statutory proviso directing “That NIH shall implement the public access policy in a manner consistent with copyright law.”

In its implementation plan published on the NIH website on January 11, 2008, NIH placed the burden of ensuring copyright compliance on the individual researcher or institution, a directive that ACS asserts does not comport with the Congressional intent or guidance.

Shortly after P.L. 110-161 was enacted, ACS submitted a letter to NIH Director Zerhouni wherein we proposed a constructive path forward for implementation of the new mandatory policy in consultation with publishers as rights holders. That letter, sent several hours before NIH posted its implementation plan, asked that NIH seek broad input into the formulation of its implementation plan, and recommended the appropriate method to do this is through the rulemaking procedures under the Administrative Procedures Act (APA), an Act that has guided federal regulatory activities for over 60 years. Following the APA would assure that all stakeholders have an opportunity to provide input into the implementation process and the oversight of NIH’s administration of the policy.

ACS asserts that following the APA would be consistent with Senate Committee Report 110-107 which conveyed with P.L. 110-161. The report directed NIH to take the following course of action when implementing the new mandatory policy. The Report reads, in part:

“…The Committee highly encourages collaborations with journal publishers that would enable them to deposit manuscripts on behalf of the funded investigator, if all parties agree. The committee directs the NIH to seek and carefully take into account the advice of journal publishers on the implementation of this policy.

In particular, the Committee directs the NIH to ensure that publishers’ copyright protections are maintained…”

Following an APA process would also have been consistent with the approach NIH followed when it published its proposed voluntary public access policy on September 17, 2004, in the Federal Register and the public was invited to offer comment. NIH noted in publishing its final voluntary policy in the February 9, 2005 Federal Register that it was not required to follow the APA because of the voluntary nature of the policy, but had done so in order to obtain public comment on the proposed policy. NIH noted that it received over 6,000 public comments at that time. The public comments received were quite thoughtful and provided value to the process, as NIH modified its original proposal and increased the timeframe for manuscript deposition into PubMed Central from 6 to 12 months, citing the need to “ensure that peer review of scientific articles is preserved.”

It would only seem logical and fair that since the policy is now mandatory, and carries with it full enforceability of federal law that its implementation should now be subject to the APA process. That process would allow comment from all concerned parties to ensure the policy is implemented fairly and comports with the Congressional intent of complying fully with the protections that rights holders are afforded under copyright. It is hard to see how NIH’s implementation announcement on January 11, 2008 – 16 days after enactment – followed either the statutory language or the above referenced Senate Committee report language. ACS is unaware of any scientific journal publishers that were consulted in this 16 day window.

By contrast, the RFI process initiated by NIH on March 31, 2008 is a much more informal process than the APA and has only attracted about 1% of the responders to the NIH notice seeking public comment on its voluntary policy as outlined above. ACS believes that the lack of response to the RFI is due primarily to the fact that NIH has already gone ahead and fully implemented the mandate on April 7, 2008 just seven days after announcing the RFI leaving scores of potential responders wondering what value their time and effort in offering thoughtful input might yield.

ACS is unaware of any other federal mandate being implemented in such a disjointed fashion. A policy as important as this should be initiated only after a period of public comment and those comments have been carefully weighed and considered and any amendments found necessary have been made. ACS believes that an APA process would best abide the Congressional intent in both that statute and committee report and does not feel that the RFI will yield the input that an APA process could generate. In fact, an examination of input received at the NIH web-site as of the date of the ACS submission seems to substantiate the fact that much of the input is far from comprehensive and may be of limited use towards producing a meaningful analysis by NIH at the conclusion of the comment period on May 31, 2008.

COMMENTS AND CONCERNS RELATIVE TO COPYRIGHT AND INTELLECTUAL PROPERTY

Since 2005, ACS has made voluntary and good-faith efforts to facilitate the deposit of NIH-funded research into PubMed Central in a manner consistent with the Society’s interests in copyright. We have been prevented from doing so by NIH-generated intellectual property and process-related roadblocks that remain unaddressed by the agency to this day.

We are concerned that such problems will remain unaddressed, and may even be exacerbated under the new mandatory policy. By way of example, ACS has in excess of 3,000 unedited peer-reviewed author manuscripts pending deposit with PubMed Central, as a consequence of NIH’s having refused to accept such deposits from ACS. NIH has rejected ACS’ right, as copyright holder, to establish reasonable safeguards on use of this material.

Instead, NIH has sought to appropriate copyright for itself - reformatting and altering submitted author manuscripts; “repurposing” deposited manuscripts in connection with their display in PubMed Central; and expatriating versions of that repository to countries elsewhere around the globe. In our view, implementing the Public Access Policy in a manner consistent with copyright law, and the intent of that aspect of its Congressional mandate, would mean that:

A. NIH would respect the integrity of the copyrighted content it receives and ensure that any revisions to copyrighted materials such as reformatting, enhancing, linking or otherwise changing the articles are undertaken only when consistent with copyright. Not only are there no mechanisms in place to do this, but also the range of uses outlined in NIH’s terms and conditions for manuscript deposit take substantial liberty with content to create unauthorized derivative works. ACS questions how NIH can proceed in this manner, as doing so would seem to disregard the intent of Congress.

B. NIH would respect ACS’ right, as the copyright holder, to stipulate what it will or will not allow related to third-party use of its works. Instead, NIH has rejected ACS terms and conditions, designed to protect the integrity of the scientific record and, without permission or consultation, has linked content to a variety of online resources (or seeks the latitude to do so). For example, nothing in NIH’s implementation guidelines explicitly prohibits the licensing, selling, or distributing of links or access to content deposited within the PubMed Central database.

C. NIH would acknowledge and support ACS as the copyright holder in the works deposited. Instead, the NIH website directs users to information which we assert undermines ACS’ copyright. In some cases, ACS’ copyright notice is not displayed or NIH’s site links to its own copyright information rather than that of ACS as rights holder.

D. NIH would respect the trademarks and branding of the ACS. Not only has there been no affirmation of these markers of quality, but all too often branding information is missing ? potentially misleading users to the erroneous conclusion that the NIH is claiming copyright, or that the content is in the public domain.

E. NIH would take steps to ensure copyright compliance for material deposited into PubMed Central. No mechanisms to do this are in place, even for content that that has been erroneously deposited by authors without authorization, or that does not fall within the scope of the NIH Policy, and thus should not have been made publicly available. This causes potential economic harm to ACS as publisher.

F. NIH would provide a mechanism to incorporate the concerns of publishers as the policy evolves over time. No mechanisms to do this are in place or have been proposed ? indeed, the implementation guidelines in connection with the mandated Public Access Policy were announced almost immediately after enactment of P.L. 110-161, without consultation with publishers, even as the NIH proceeded to inform other stakeholders.

G. NIH would respect ACS’ right, as copyright holder, to decide how its content will be disseminated. Instead, NIH, without permission or consultation, has made arrangements to mirror ACS content deposited on its site. A mirror site for PubMed Central has been established in the United Kingdom, and our understanding is that other mirror sites are planned or proposed to be located internationally. This raises important questions and concerns regarding copyright protections that would prevail in such circumstances for content located outside the borders of the U.S. We question also how such international mirror sites serve the needs of the U.S. taxpayer and the intended purpose of the NIH Public Access Policy as directed by Congress.

H. NIH would support the integrity of the scientific record. Instead, NIH has declined to use a link to the final published article at a specified URL on the ACS’ own website as an alternative to the deposit and display of the unedited author’s version on PubMed Central. Furthermore, NIH has also chosen to use its own system of article identification (PubMed Identifiers) rather than adopt the widely- accepted Digital Object Identifier (DOI) as a means of identifying authoritative material and associating it with the rights holder of record. This adds to reader confusion as to the definitive version of the article, and by diverting web traffic from ACS’ final published article, poses economic harm in the process. It is unclear to us how NIH will manage and maintain such an identifier system, or the value that this system adds on behalf of the taxpayer.

I. NIH would seek only the deposit of final, peer-reviewed manuscripts upon acceptance for publication. Instead, under the scope of the policy NIH allows, and even encourages, the deposit by authors of the final published version (article) ? without any provision for distinguishing the two versions, or for compensation in recognition of this federal taking of the publisher’s investment in the peer-reviewed version of the manuscript. In so doing, NIH is placing authors in potential conflict with publishers and their copyright or other publishing policies, or (at worst) steering authors to favor journals with policies consistent with a particular business model. ACS questions whether the intent of Congress was to enable NIH to engage in this interference with the private sector and authors’ right to assign and transfer their copyrights in an unfettered manner.

In addition to the issues summarized above, we note that the NIH has not implemented its current voluntary Public Access Policy in a manner consistent with its own self-created guidelines.

For example, articles, including those from ACS, falling outside the NIH Public Access Policy implementation date of May, 2005 have been posted on the PubMed Central repository. Those and other posted articles are made openly available that should have been embargoed for 12 months. Final published articles in journal formal and with content copyrighted by ACS have been converted into NIH’s XML format and posted regardless of publication date. One of our own journal editors has expressed surprise that PubMed Central includes open access to articles he published prior to the policy implementation date ? articles that were posted by others without his knowledge. These experiences indicate that NIH lacks adequate control over the posting of manuscripts on its own website. This must be addressed.

Mindful of these unaddressed implementation problems that affect protections provided under copyright, ACS is concerned that the new mandatory NIH Public Access Policy leaves key policy and implementation questions unaddressed, such as:

By what process will NIH establish criteria to ensure that publishers’ copyright protections are maintained? Why has NIH refused to engage in a notice and comment rulemaking that would help to assure publishers that such protections can be put in place?

By what process will NIH seek and take into account the advice of journal publishers in determining if it is implementing its Public Access Policy in a manner consistent with protections under copyright law, and the spirit of NIH’s Congressional mandate?

If deposited content will be “mirrored” to other sites outside the U.S., what process will be entailed for the establishment of such sites, and how would national and international copyright considerations be addressed to protect rights holders?

What limitations, if any, would be imposed on PubMed Central as an “aggregator” of content from sources such as HHMI, Wellcome Trust, other U.S. government agencies, etc?

Will NIH negotiate terms and conditions with publishers for the use of NIH grant funds to enable the deposit of copyrighted works on behalf of authors? Will NIH make such payment directly to publishers on behalf of its grantee authors?

How will NIH identify grant funds allowable to be used for the payment of publication fees? Will supplemental funds be made available to support author compliance with the mandate?

What steps will NIH take if it is found that its Public Access Policy is harming publishers?

Why has NIH refused to work with publishers to gather and share PubMed Central usage statistics on copyrighted content? Should this information not be considered as in the public domain, as it is funded with taxpayer monies? Why should articles be freely available, but information about the usage of those same articles be hidden?

How will NIH ensure that articles on PubMed Central meet ACS requirements, such as the access-control period, and that the policy actually applies to the articles that it is posting?

How will NIH prevent piracy of the articles from PubMed Central? At present, publishers are not protected from systematic downloading that could occur from the NIH website; pirates also could disseminate paper copies of article content, and undermine publishers’ economic interests. What will happen if piracy is discovered as a result of downloading of content from PubMed Central?

What provisions will be made to evaluate whether the policy is effective in achieving its intended purpose of promoting public access by US taxpayers to NIH-funded research? As announced, the policy makes no mention of mechanisms for oversight of NIH’s implementation efforts, to ensure that the policy’s scope and operational costs are contained. What “sunset” provisions will be made so that the policy mandate may be amended or phased out if it proves to be ineffective, too costly to maintain, or too disruptive to the peer-reviewed scientific publications on which ultimately it relies?

Regardless of the questions and serious nature of the issues raised above, we choose not to believe that NIH is willfully disregarding copyright law and Congressional intent in the implementation of its Public Access Policy.

However, ongoing consultation with publishers such as ACS is needed to ensure that NIH does not misapply its Congressional mandate and do irreparable harm to the very fabric of scholarly publishing that supports scientific research and our nation’s competitiveness. ACS is willing and able to work with NIH and other key stakeholders to establish the kind of productive ongoing dialog that we feel will truly maximize the sustainable dissemination and discoverability of knowledge in chemistry and the allied sciences, and fulfill the intended purpose of the Congressional mandate in serving the public interest.

Thank you for this opportunity to share the views of the American Chemical Society with you.

Brian Crawford President, Publications Division NIH RFI Comments Results

Resources

Open Access: Think Globally, Act Locally Short video explaining the core issue.
A New Beginning or More of the Same? Be careful what you wish for.
NIH Hears Publisher Feedback on Open Access Mandate A preview of the ACS position.
Crunch Time: Can NIH Grant Recipients Still Publish in ACS Journals? Something's gotta give.
ACS and the NIH Public Access Policy: Clarification at Last Policy enabling ACS authors to comply with PL 110-161.

ACS and the NIH Public Access Policy: Clarification at Last

Rich Apodaca — Thu, 10 Apr 2008 10:27:00 -0400

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:

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

Open Access: Think Globally, Act Locally

Rich Apodaca — Mon, 24 Mar 2008 09:24:00 -0400

Source: blip.tv via Chemists Without Borders

NIH Hears Publisher Feedback on Open Access Mandate

Rich Apodaca — Fri, 21 Mar 2008 18:17:00 -0400

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.

A New Beginning or More of the Same?

Rich Apodaca — Thu, 27 Dec 2007 16:02:00 -0500

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

PerlMol: A Case Study in Open Source Cheminformatics Software

Rich Apodaca — Thu, 15 Nov 2007 09:49:00 -0500

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.

Making the Case: OpenSMILES

Rich Apodaca — Wed, 14 Nov 2007 09:42:00 -0500

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.

The Business Case for Open Source and the Small Company

Rich Apodaca — Fri, 09 Nov 2007 09:37:00 -0500

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.

Open Access Business Models That Can Actually Work: Sigma-Aldrich's ChemBlogs

Rich Apodaca — Thu, 11 Oct 2007 12:49:00 -0400

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