Tag: open access

Wanted – input on topics for "open access" publishing discussion at #scio10

To all

I am posting this because I will be chairing a session this up coming weekend at Science Online 2010 on “Open Access” publishing.

And I would love input from everyone/anyone out there on what might be worth discussion at this session.  Possible topics include

  • why open and free are not the same thing
  • open access mandates
  • financial aspects of OA
  • educational uses of OA literature 
  • things that are slowing the inevitable spread of OA publishing

I am perhaps most interested these days in the last two on that list.  For example – it seems that OA publishing would spread even faster if we did not have some very conservative styles of tenure, promotion, hiring and grant review processes.

If anyone has some pressing topics that you think are worth bringing up in a discussion of OA publishing, please post them here.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Creative Commons Licenses adopted at Palo Alto High School

Cool – Creative Commons spreading even to Palo Alto High School – See Paly Voice – Creative Commons Spotlight.  According to the article, multiple Palo Alto High publications have adopted CC licenses and are the first high school publications to do so.  Good call I say.  Plus check out the article which discusses other diverse uses of CC including Nine Inch Nails, PLoS, Wikipedia, and others. Of course, this might have something to do with Lawrence Lessig being from the neighborhood, but that’s OK by me.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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US government seeks input on Open Access policies

Quick one here. For all interested in Open Access.  Below are some excerpts from an email I received from the folks at PLoS Computational Biology.  The main point: the White House Office of Science and Technology Policy is seeking input on broadening public access to publically funded research …

The White House Office of Science and Technology Policy has recently invited comment on broadening public access to publicly funded research and they want to hear from you. Contributions may be posted to their blog at: http://blog.ostp.gov/2009/12/10/policy-forum-on-public-access-to-federally-funded-research-implementation/

Their Request for Information (RFI) lasts for just 30 days and expires on 7 January 2010, so we’d like to inform you about this important effort and encourage you to get involved in the discussion. This is an opportunity for us to shape a broader public access policy – how it should be implemented, what type of technology and features are needed, and how to manage it.

There are 3 main topics where the administration would appreciate your input (they also welcome general comments) and each one is open for a set period of time:

1. Implementation – expires 20 December 2009 (i.e. on Sunday). Which Federal agencies are good candidates to adopt Public Access policies? What variables (field of science, proportion of research funded by public or private entities, etc.) should affect how public access is implemented at various agencies, including the maximum length of time between publication and public release?

2. Features and Technology – 21-31 December 2009. In what format should the data be submitted in order to make it easy to search and retrieve information, and to make it easy for others to link to it? Are there existing digital standards for archiving and interoperability to maximize public benefit? How are these anticipated to change?

3. Management – 1-7 January 2010. What are the best mechanisms to ensure compliance? What would be the best metrics of success? What are the best examples of usability in the private sector (both domestic and international)? Should those who access papers be given the opportunity to comment or provide feedback?

 Hat tip to Karla Heidelberg, Carl Beottiger, and many others who emailed me about this to suggest I post something …

Related things worth looking at:

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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#OpenAccess help needed – best way to publish conference proceedings in an OA manner?

To all Open Access fans or gurus out there.  I am writing at the request of a colleague who is looking into ways that one might switch from publishing papers for a conference from a closed access way to a more Open Access way.

Does anyone out there know if there are good Open Access publishing services that would enable one to do this?  Any information about possible publishers, costs associated with doing this, etc would be helpful.  Thanks in advance.

NOTE ADDED: Perhaps most importantly – we are looking for systems that would include the possibility of publishing printed versions of the proceedings …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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And the winner of ‘most nimble new science journal web site’ is mBio

Kudos to mBio the recently announced new open access journal from ASM. I posted a little bit about it a few days ago. There was some back and forth in the comments w/ people involved in the journal and, impressively, they have already modified some sections of the web site to clarify some of the things I and others felt were unclear. A pretty rare thing in the world of journals as far as I know, to make changes quickly. Normally there would be some sort of deliberative, painfully slow, and annoyingly conservative process in response to comments/feedback. Good job Barbara Goldman and ASM. And happy to have ASM moving a bit more towards an Open Access future.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Ted Kennedy in Pubmed Central #openaccess

For those interested in open access and/or Ted Kennedy, you might be interested to know that Kennedy has a few articles available in PubMed Central – all available for free …

Quality, Affordable Health Care for All Americans
Edward M. Kennedy

Am J Public Health. 2003 January; 93(1): 14.

PMCID: PMC1449947

Health care reform: workers beware.
E M Kennedy

Public Health Rep. 1996 Jan–Feb; 111(1): 11.

PMCID: PMC1381734

The congress and national health policy. Fifth Annual Matthew B. Rosenhaus Lecture.
E M Kennedy

Am J Public Health. 1978 March; 68(3): 241–244.

PMCID: PMC1653906

National leadership in confronting bioterrorism: 2.
E M Kennedy

Public Health Rep. 2001; 116(Suppl 2): 116–118.

PMCID: PMC1497282
| Summary | PDF–32K |

Discussions
Edward M. Kennedy

Bull N Y Acad Med. 1972 January; 48(1): 146–156.

PMCID: PMC1806655

1974 Yale Medical Student Council Lectureship: Partners or protagonists-Congress and the Academic Medical Centers.
E. M. Kennedy

Yale J Biol Med. 1975 March; 48(1): 1–7.

PMCID: PMC2595194

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Why endosymbionts rule – see #PLoS Genetics paper on origin of an alternative genetic code

ResearchBlogging.org

Way way way cool new paper in PLoS Genetics from Nancy Moran’s lab. The paper (Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont). The paper discusses the use of genome sequencing and proteomics (as well as a variety of bioinformatic analyses) of a bacterial symbiont (Hodgkinia) of cicadas.

And for those not in the know, this is an Open Access paper using a broad Creative Commons license (since it is in a PLoS journal) so anyone can reuse material from it as long as the source is cited. This image to the left is from their paper so I am citing the source here: McCutcheon JP, McDonald BR, Moran NA (2009) Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont. PLoS Genet 5(7): e1000565. doi:10.1371/journal.pgen.1000565

The study has some interesting things including:

  • the genome of the symbiont has a much higher GC content than other small bacterial genomes for which the sequence is available
  • the symbiont is member of the alpha proteobacterial group, which is somewhat unusual since most other insect endosymbionts that have been studied are from the gamma proteobacterial group and/or the bacteroidetes clade
  • the UGA codon in this species is used to encode tryptophan and not as a stop codon

Taken together these things are very interesting since other species that have been found to have the UGA codon reassigned to code for an amino acid all have low genomic GC content. This correlation led people to conclude that the codon reassignment was directly related to the low GC content. However, the authors suggest here that the UGA reassignment in many species might be due to the genome reduction (loss of genes) seen in endosymbionts and not to low GC content.

Anyway the paper is worth a read …

McCutcheon, J., McDonald, B., & Moran, N. (2009). Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont PLoS Genetics, 5 (7) DOI: 10.1371/journal.pgen.1000565

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Another reason to publish as Open Access – libraries hurting big time financially and they will be cancelling many subscriptions

If you need any more incentive to publish a paper in an Open Access manner if you have a choice – here is one. If you publish in a closed access journal of some kind, it is likely fewer and fewer colleagues will be able to get your paper as libraries are hurting big time and will be canceling a lot of subscriptions. (e.g., see this page from UC Davis system Library Collections: A Forum – About the Libraries – University Library – UC Davis).

From Friendfeed

http://friendfeed.com/treeoflife/05393084/another-reason-to-publish-as-open-access?embed=1

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Who should have acess to publications supported by federal money? Well, everyone. See Federal Research Public Access Act

Well, this is good news. Here is some information on the Federal Research Public Access Act S. 1373 introduced by Sen. Lieberman and Sen. Cornyn (information is mostly from this site: Alliance for Taxpayer Access | Federal Research Public Access Act). This is really important as it will expand the accessibility of papers to agencies outside NIH (e.g., NSF are you listening, DOE are you listening). To help with this see Call to action: Tell Congress you support the Federal Research Public Access Act

Every federal agency with an annual extramural research budget of $100 million or more will implement a public access policy that is consistent with and advances the federal purpose of the respective agency. Each agency must:

  • Require each researcher – funded totally or partially by the agency – to submit an electronic copy of the final manuscript that has been accepted for publication in a peer-reviewed journal.
  • Ensure that the manuscript is preserved in a stable digital repository maintained by that agency or in another suitable repository that permits free public access, interoperability, and long-term preservation. Agencies have the flexibility to choose the best suitable location for their repository.
  • Require that free, online access to each taxpayer-funded manuscript be available as soon as possible, and no later than six months after the article has been published in a peer-reviewed journal.

To whom this policy applies:

  • Any researcher employed by a federal agency with an annual research budget exceeding $100 million who publishes an article based on the work done for the funding agency in a peer-reviewed journal.
  • Any researcher funded by a federal agency with an annual research budget exceeding $100 million who publishes an article based on the funded research in a peer-reviewed journal.

What is not covered by this legislation:

  • The public access policy does not apply to laboratory notes, preliminary data analyses, author notes, phone logs, or other information used to produce the final manuscript.
  • The policy does not apply to classified research. Research that results in works that generate revenue or royalties for the author (such as books), or patentable discoveries are exempt only to the extent necessary to protect copyright or a patent.

Also see below from the Congressional Record (and Hat Tip to Heather Joseph from SPARC for pointing all of this out).

From June 25 Congressional Record:          By Mr. LIEBERMAN (for himself and Mr. Cornyn):

S. 1373. A bill to provide for Federal agencies to develop public access policies relating to research conducted by employees of that agency; or from funds administered by that agency to the Committee on Homeland Security and Governmental Affairs

Mr. CORNYN. Mr. President, I rise to introduce the Federal Research Public Access Act. I am very pleased to be joined again by my good friend and colleague, Senator Joe Lieberman, who has remained dedicated to seeing this important legislation passed. This bipartisan bill is the same legislation we introduced in the 109th Congress. The purpose of this legislation is to ensure American taxpayers’ dollars are spent wisely, which is even more important now in this time of fiscal tension.

To put things in perspective, the Federal Government spends upwards of $55 billion on investments for basic and applied research every year. There are approximately 11 departments/agencies that are the recipients of these investments, including: the National Institutes of Health, National Science Foundation, NASA, the Department of Energy, the Department of Defense, and the Department of Agriculture. These departments/agencies then distribute the taxpayers’ money to fund research which is typically conducted by outside researchers working for universities, health care systems, and other groups.

While this research is undoubtedly necessary and is beneficial to America, it remains the case that not all Americans are capable of experiencing these benefits firsthand. Usually the results of the researchers are published in academic journals. Despite the fact that the research was paid for by Americans’ tax dollars, most citizens are unable to attain timely access to the wealth of information that the research provides.

Some Federal agencies, most notably the NIH, have recognized this lack of availability and have proceeded to take positive steps in the right direction by requiring that those articles based on government- funded research be easily accessible to the public in a timely manner. I am proud to report that the NIH’s public access policy has been a success over the past few years. By the NIH implementing a groundbreaking public access policy, there has been strong progress in making the NIH’s federally funded research available to the public, and has helped to energize this debate.

Although this has surely been an encouraging and important step forward, Senator Lieberman and I believe there is more that can and must be done, as this is just a small part of the research funded by the Federal Government.

With that in mind, Senator Lieberman and I find it necessary to reintroduce the Federal Research Public Access Act that will build on and refine the work done by the NIH and require that the Federal Government’s leading underwriters of research adopt meaningful public access policies. Our legislation provides a simple and practical solution to giving the public access to the research it funds.

Our bill will ask all Federal departments and agencies that invest $100 million or more annually in research to develop a public access policy. Our goal is to have the results of all government-funded research to be disseminated and made available to the largest possible audience. By speeding access to this research, we can help promote the advancement of science, accelerate the pace of new discoveries and innovations, and improve the lives and welfare of people at home and abroad.

Each policy that these departments and agencies develop will require that articles resulting from federal funding must be presented in some publicly accessible archive within six months of publication. In doing so, the American taxpayers will have guaranteed access to the latest research, ensuring that they do not have to pay for the same research twice–first to conduct it and then again to view the results.

This simple legislation will provide our government with an opportunity to better leverage our investment in research and in turn ensure a greater return on that investment. All Americans stand to benefit from this bill, including patients diagnosed with a disease who will have the ability to use the Internet to read the latest articles in their entirety concerning their prognosis, students who will be able to find full abundant research as they further their education, or researchers who will have their findings more broadly evaluated which will lead to further discovery and innovation.

While a comprehensive competitiveness agenda is still a work-in- progress, this legislation is good step forward. Providing public access to cutting-edge scientific information is one way we can encourage public interest in these fields and help accelerate the pace of discovery and innovation. In promoting this legislation, I hope to guarantee that students, researchers, and every American can access the published results of the research they funded.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Elsevier, fake medical journals, and yet another reason for #openaccess

For those of you not in the loop on this there is a bubbling story going around the web and in some news sources about Elsevier publishing fake science/medical journals for hire. First reported by The Scientist (as far as I can tell), the story just seems to get worse and worse. Basically, it seems one branch of Elsevier published a series of journals that were little more than advertisements for Merck products while pretending to be independent journals.

The whole thing is pretty sad. The head of Elsevier as well as multiple people that have worked at Elsevier seem to have not been aware of that these were being used to pretend they were real journals. But I think one this is abundantly clear – we can cross of the list of criticisms of Open Access publishing that the costly non open access journals and publishers are protecting the world from bad science. Instead, it seems like they are in fact explicitly and purposefully pushing bad science and medicine in order to make extra money. Lovely.

For more informaiton on the story see for example, Kate McDonald in the Australian Life Scientist (see Elsevier published fake medical journals – Elsevier Australia, Merck, Vioxx – Australian Life Scientist). In this article she reports:

The CEO of Elsevier’s Health Sciences division in the US, Michael Hansen, has now issued a statement admitting the company’s Australian office published six journals paid for by pharmaceutical companies.

Also see for example Forbes (via AP). The best source on this has been the Bloggosphere where there were a large number of discussions including

My favorite source so far has been Bill Hooker at Open Reading Frame who did some really useful digging into the details of what was being published. After his posting there has been an interesting discussion on FriendFeed (see embed below)

http://friendfeed.com/billhooker/6907bac6/no-bottom-to-worse-at-elsevier?embed=1

There also has been some other discussion on FriendFeed including the following from a Graham Steel posting:

http://friendfeed.com/mcdawg/9b919af7/statement-from-michael-hansen-ceo-of-elsevier?embed=1

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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