NCBI has released a beta version of a new Sequence Viewer, a tool that provides a graphical view of Entrez Nucleotide (aka GenBank) and Protein records. The direct link to the tool is http://www.ncbi.nlm.nih.gov/projects/sviewer/
There are some nice example views linked from this page.
At first glance, the tool is a considerable improvement over the previous viewer. They've mercifully gone to a horizontal viewing mode, and the labeling seems more intuitive (IMO). There's a mechanism to customize a page view (to show a particular section of a gene, or series of genes, for example) and then create a link to that view, that you can (for example) bookmark, send in an email, or post on a web site.
Help for the product is available at http://www.ncbi.nlm.nih.gov/projects/sviewer/help/, or click the question mark in the upper right of the Viewer page. I'm told the Sequence Viewer shares code base with the NCBI Genome Workbench, if any of you use that downloadable software package.
Showing posts with label News/FYI. Show all posts
Showing posts with label News/FYI. Show all posts
Tuesday, April 15, 2008
Protein Data Bank Hits 50,000 Structures
The Protein Data Bank (PDB) archive of biomacromolecule structures recently reached a significant milestone in its 37-year history: the holdings now contain more than 50,000 current experimental structures. The worldwide Protein Data Bank (wwPDB) has seen the archive double in size since 2004, and is expected to reach 150,000 by 2014.
For the full story, go to http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2008.html#20080408
For the full story, go to http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2008.html#20080408
Springer Changes Copyright Transfer to comply with NIH Public Access
Those looking for journals offering a reasonably straightforward route to compliance with the NIH Public Access mandate may want keep Springer journals in mind as a possibility. Their default copyright transfer has been altered to be (minimally) workable with the mandate. From the Springer web site:
"As of 7 April 2008, Springer has adapted its standard Copyright Transfer Statement (CTS) for new articles to ensure compliance with new guidelines from the US National Institutes of Health (NIH).
"An author may self-archive an author-created version of his/her article on his/her own website. He/she may also deposit this version on his/her institution's and funder's (funder-designated) repository at the funder’s requesthttp://www.blogger.com/img/gl.link.gif or as a result of a legal obligation, including his/her final version, provided it is not made publicly available until after 12 months of official publication. He/she may not use the publisher's PDF version which is posted on www.springerlink.com for the purpose of self-archiving or deposit. Furthermore, the author may only post his/her version provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The original publication is available at www.springerlink.com"."
This policy means that authors will not have to negotiate with Springer to maintain minimal copyrights to submit to PubMed Central. Note though that the author/grantee must still push the manuscript to NIH -- Springer does not do this automatically under this policy. Note also that the release is given only to the final manuscript, not the publication-formatted article.
Alternatively, as an even more hassle-free method, NIH provides a list of journals which automatically deposit the paper in PubMedCentral within the 12 month post-pub window -- there's no further action required on the author's part following acceptance for these titles. See http://publicaccess.nih.gov/submit_process_journals.htm for details.
"As of 7 April 2008, Springer has adapted its standard Copyright Transfer Statement (CTS) for new articles to ensure compliance with new guidelines from the US National Institutes of Health (NIH).
"An author may self-archive an author-created version of his/her article on his/her own website. He/she may also deposit this version on his/her institution's and funder's (funder-designated) repository at the funder’s requesthttp://www.blogger.com/img/gl.link.gif or as a result of a legal obligation, including his/her final version, provided it is not made publicly available until after 12 months of official publication. He/she may not use the publisher's PDF version which is posted on www.springerlink.com for the purpose of self-archiving or deposit. Furthermore, the author may only post his/her version provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The original publication is available at www.springerlink.com"."
This policy means that authors will not have to negotiate with Springer to maintain minimal copyrights to submit to PubMed Central. Note though that the author/grantee must still push the manuscript to NIH -- Springer does not do this automatically under this policy. Note also that the release is given only to the final manuscript, not the publication-formatted article.
Alternatively, as an even more hassle-free method, NIH provides a list of journals which automatically deposit the paper in PubMedCentral within the 12 month post-pub window -- there's no further action required on the author's part following acceptance for these titles. See http://publicaccess.nih.gov/submit_process_journals.htm for details.
Tuesday, April 8, 2008
NIH Public Access Policy Now in Effect
The new NIH Public Access Policy came into effect this week. The revised policy requires authors funded by NIH arrange for public access to their research manuscripts via PubMed Central within a year following publication. For many journal publishers, this requires negotiation away from the default copyright transfer agreement authors enter with the publisher.
The policy and how to comply with it is addressed at http://publicaccess.nih.gov/. If you are NIH-funded and expect to apply for NIH funding in the future, it's well-worth making sure you understand the new demands.
The policy and how to comply with it is addressed at http://publicaccess.nih.gov/. If you are NIH-funded and expect to apply for NIH funding in the future, it's well-worth making sure you understand the new demands.
Wednesday, April 2, 2008
Faculty Learning Community for Improving Student Research Literacy
Just a reminder to consider applying for next academic year's Faculty Learning Community for Improving Student Research Literacy. The deadline for applications has been changed to April 14. More information is available at http://www.units.muohio.edu/celt/flcs/miami/flc-LibraryLiteracy.php
Sunday, March 30, 2008
Short Video on Author Rights
Does the recent NIH policy on public access have you thinking about how to make sure you can publish your work where you want to, and comply with the access policy? Have you wanted to post your own articles on your web site, but are (rightfully) concerned that your publisher doesn't allow this? This two-minute video presentation is available at http://blip.tv/file/743274. It explains in simple terms the potential for wider exposure of scholarly articles when authors retain key rights. Inspired by the SPARC Author Rights initiative, the presentation offers three steps to effective rights management. These include scrutinizing publication agreements, negotiating with the publisher, and retaining the rights you need. The video was produced by The Scholarly Publishing and Academic Resources Coalition (SPARC), the Association of College and Research Libraries (ACRL) and the Association of Research Libraries (ARL).
Sunday, March 23, 2008
Initial content for the Encyclopedia of Life Project Unveiled
The first 30,000 pages of the online Encyclopedia of Life (EOL) were recently unveiled. The EOL seeks to catalog and describe in one location the estimated 1.8 million species of life on Earth. See an example record.
In addition to its strong potential for use in comparative biology and as a general taxonomic reference, The EOL will be a foundational resource for helping to conserve species already known and to identify millions of additional species that haven’t yet been described or named. At its core is the knowledge about the world’s species that has been discovered by scientists over the last 250 years. By putting this information all together in one place, EOL hopes to accelerate our understanding of the world’s remaining biodiversity.
In addition to its strong potential for use in comparative biology and as a general taxonomic reference, The EOL will be a foundational resource for helping to conserve species already known and to identify millions of additional species that haven’t yet been described or named. At its core is the knowledge about the world’s species that has been discovered by scientists over the last 250 years. By putting this information all together in one place, EOL hopes to accelerate our understanding of the world’s remaining biodiversity.
NIH Public Access Policy will go into Force Soon
As many of you know, the National Institutes of Health (NIH) recently announced a revision to its Public Access Policy. The policy now *requires* eligible researchers to deposit copies of final manuscripts upon acceptance into a peer-reviewed journal so that they may be made publicly available within 12 months of publication. This policy applies to any journal articles resulting from research supported in whole or in part by direct funds from NIH. The manuscript is defined as the final version accepted for journal publication and includes all modifications from the publishing and peer-review process. The policy is set to go into place in April 7 2008.
The NIH access policy is an important step in making taxpayer-funded research literature available to as broad a community as possible.
Please note that there is real potential for conflict between adherence to the NIH policy and the common practice in the review and publication process of signing away all copyright for a journal manuscript to the publisher. It will be crucial for authors to ascertain whether a journal you seek to publish in allows author retention of copyright and permission to post to PubMed Central, or to negotiate this during the publication process. On the other hand, a fair number of journals automatically submit their content to PubMed Central and so require no further action on the authors' part -- see http://publicaccess.nih.gov/submit_process_journals.htm for a list of these titles. The policy has potential to affect eligibility for future research grants from NIH. For more information on the NIH policy please see http://publicaccess.nih.gov/.
The NIH access policy is an important step in making taxpayer-funded research literature available to as broad a community as possible.
Please note that there is real potential for conflict between adherence to the NIH policy and the common practice in the review and publication process of signing away all copyright for a journal manuscript to the publisher. It will be crucial for authors to ascertain whether a journal you seek to publish in allows author retention of copyright and permission to post to PubMed Central, or to negotiate this during the publication process. On the other hand, a fair number of journals automatically submit their content to PubMed Central and so require no further action on the authors' part -- see http://publicaccess.nih.gov/submit_process_journals.htm for a list of these titles. The policy has potential to affect eligibility for future research grants from NIH. For more information on the NIH policy please see http://publicaccess.nih.gov/.
Faculty Learning Community for Improving Student Research Literacy
Applications are now being accepted for the 2008/09 session of the Faculty Learning Community for Improving Student Research Literacy. More information is below, and more information about FLCs is available at: http://www.units.muohio.edu/celt/flcs/miami/flc-LibraryLiteracy.php
Description: The purpose of this community is to provide a forum for collaboration among faculty and librarians across disciplines to discuss concepts and applications for integration of information literacy into the curriculum. Broadly defined, information literacy is the ability to locate, evaluate, and use information ethically while fostering the development of critical thinking skills. Participants in this community will discuss the philosophy and theories of information literacy and explore methods/approaches for incorporating these concepts into the learning environment.
Support: Each participant has available up to $1,000 to support his or her efforts, for example, purchase of hardware or software, travel to conferences, on-line courses, etc.
Eligibility: Full-time faculty and librarians at assistant rank or above are eligible. Applications from both early career and seasoned faculty are encouraged.
Selection: Librarians and faculty will be selected to create a community representing a variety of disciplines and teaching styles by a subcommittee of CELT.
Submission: Please send an electronic copy of your application to Melody Barton and one original application with your signature page via campus mail to Melody Barton, CELT.
Due date: April 7. Awards will be announced in late April.
Consponsors: The Center for the Enhancement of Learning and Teaching (CELT) and University Libraries
Description: The purpose of this community is to provide a forum for collaboration among faculty and librarians across disciplines to discuss concepts and applications for integration of information literacy into the curriculum. Broadly defined, information literacy is the ability to locate, evaluate, and use information ethically while fostering the development of critical thinking skills. Participants in this community will discuss the philosophy and theories of information literacy and explore methods/approaches for incorporating these concepts into the learning environment.
Support: Each participant has available up to $1,000 to support his or her efforts, for example, purchase of hardware or software, travel to conferences, on-line courses, etc.
Eligibility: Full-time faculty and librarians at assistant rank or above are eligible. Applications from both early career and seasoned faculty are encouraged.
Selection: Librarians and faculty will be selected to create a community representing a variety of disciplines and teaching styles by a subcommittee of CELT.
Submission: Please send an electronic copy of your application to Melody Barton and one original application with your signature page via campus mail to Melody Barton, CELT.
Due date: April 7. Awards will be announced in late April.
Consponsors: The Center for the Enhancement of Learning and Teaching (CELT) and University Libraries
Friday, September 7, 2007
PRISM Anti-Open Access Lobbying Effort Launched
"PRISM – the Partnership for Research Integrity in Science and Medicine" (http://www.prismcoalition.org) is an anti-open access advocacy organization recently launched with development support from the Association of American Publishers.
From Heather Joseph, SPARC:
"The organization specifically targets efforts to expand public access to federally funded research results – including the National Institute of Health’s Public Access Policy.
"The messaging on the PRISM Web site, which is aimed at key policy makers, directly corresponds to the PR campaign reportedly undertaken by the AAP earlier this year. As Nature reported in January, AAP publishers met with PR 'pit bull' Eric Dezenhall to develop a campaign against the 'free-information movement' that focuses on simple messages, such as 'public access equals government censorship,' and suggested that 'the publishers should attempt to equate traditional publishing models with peer review' (http://www.nature.com/news/2007/070122/full/445347a.html). News of this proposed campaign met with immediate and heavy criticism in the academic community. See http://www.taxpayeraccess.org/media/blogs.html.
"The new PRISM Web site closely tracks with the recommended PR strategy, highlighting messages that include:
- Public access/open access will destroy the peer review system
- Public access equals government censorship
- The government is trying to expropriate publishers’ intellectual property
"This campaign is clearly focused on the preservation of the status quo in scholarly publishing, (along with the attendant revenues), and not on ensuring that scientific research results are distributed and used as widely as possible."
"The reaction to the launch of PRISM by the academic research community has been immediate and quite strong. Of particular note are reactions by these important constituencies:
1) Some publishers have called for the AAP to post a disclaimer on the PRISM Web site, indicating that PRISM does *not* represent their views on the issues of open access and public access. (See the open letter from Mike Rossner, Executive Director of Rockefeller University Press at https://mx2.arl.org/Lists/SPARC-OAForum/Message/3941.html).
James D. Jordan, president and director of Columbia University Press, resignation from the Executive Council of the AAP’s Professional and Scholarly Publishing division, in protest of PRISM's message. See Chronicle of Higher Education story.
2) Some journal editors have also expressed displeasure with the initiative. For example, Tom Wilson, Editor (and Founder) of the International Journal of Information Management, resigned from that editorial board in protest of Elsevier's involvement with PRISM. (See http://www.free-conversant.com/irweblog/879).
Others, including Peter Murray Rust of the University of Cambridge (UK), have written to publishers with which they are affiliated as author or editor and asked them to take action to publicly disassociate themselves with PRISM. (See http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=525).
3) Researchers are also questioning how their choices may result in unwanted association with PRISM. Some are calling for colleagues to register displeasure over publishers’ involvement with PRISM by reconsidering submitting work, reviewing, or editing for publishers who support the coalition (See http://network.nature.com/blogs/user/smount/2007/08/29/prism-distorts-our-view-of-the-open-access-debate). Others are going even further, calling for a boycott of those publishers (http://phylogenomics.blogspot.com/2007/08/calling-for-boycott-of-of-aap.html).
From Heather Joseph, SPARC:
"The organization specifically targets efforts to expand public access to federally funded research results – including the National Institute of Health’s Public Access Policy.
"The messaging on the PRISM Web site, which is aimed at key policy makers, directly corresponds to the PR campaign reportedly undertaken by the AAP earlier this year. As Nature reported in January, AAP publishers met with PR 'pit bull' Eric Dezenhall to develop a campaign against the 'free-information movement' that focuses on simple messages, such as 'public access equals government censorship,' and suggested that 'the publishers should attempt to equate traditional publishing models with peer review' (http://www.nature.com/news/2007/070122/full/445347a.html). News of this proposed campaign met with immediate and heavy criticism in the academic community. See http://www.taxpayeraccess.org/media/blogs.html.
"The new PRISM Web site closely tracks with the recommended PR strategy, highlighting messages that include:
- Public access/open access will destroy the peer review system
- Public access equals government censorship
- The government is trying to expropriate publishers’ intellectual property
"This campaign is clearly focused on the preservation of the status quo in scholarly publishing, (along with the attendant revenues), and not on ensuring that scientific research results are distributed and used as widely as possible."
"The reaction to the launch of PRISM by the academic research community has been immediate and quite strong. Of particular note are reactions by these important constituencies:
1) Some publishers have called for the AAP to post a disclaimer on the PRISM Web site, indicating that PRISM does *not* represent their views on the issues of open access and public access. (See the open letter from Mike Rossner, Executive Director of Rockefeller University Press at https://mx2.arl.org/Lists/SPARC-OAForum/Message/3941.html).
James D. Jordan, president and director of Columbia University Press, resignation from the Executive Council of the AAP’s Professional and Scholarly Publishing division, in protest of PRISM's message. See Chronicle of Higher Education story.
2) Some journal editors have also expressed displeasure with the initiative. For example, Tom Wilson, Editor (and Founder) of the International Journal of Information Management, resigned from that editorial board in protest of Elsevier's involvement with PRISM. (See http://www.free-conversant.com/irweblog/879).
Others, including Peter Murray Rust of the University of Cambridge (UK), have written to publishers with which they are affiliated as author or editor and asked them to take action to publicly disassociate themselves with PRISM. (See http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=525).
3) Researchers are also questioning how their choices may result in unwanted association with PRISM. Some are calling for colleagues to register displeasure over publishers’ involvement with PRISM by reconsidering submitting work, reviewing, or editing for publishers who support the coalition (See http://network.nature.com/blogs/user/smount/2007/08/29/prism-distorts-our-view-of-the-open-access-debate). Others are going even further, calling for a boycott of those publishers (http://phylogenomics.blogspot.com/2007/08/calling-for-boycott-of-of-aap.html).
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