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.
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
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