Tuesday, April 15, 2008

New NCBI Sequence Viewer Beta Available

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.

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

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.

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.

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

ChemDraw/BioDraw Available for Download to MU Users

(REVISED 4/16/2008) Miami has purchased an annual site license for ChemDraw and some related software through CambridgeSoft. If you have an @muohio.edu email, you are now able to download this software and have access to related online databases.

The MU license is for the products “ChemOffice Ultra” (for PC) and “ChemDraw Ultra 11.0” (for Mac). There are unfortunately some differences between the two products: ChemOffice for PC contains (amongst other tools) ChemDraw and BioDraw for creating high-quality drawings (cartoons) of an assortment of chemical and biological objects. However, ChemDraw Ultra for Mac only includes the chemistry tools (and some runt biology tools that aren't much use).

To download, go to:

ChemDraw and BioDraw together provide an easy way to draw presentation-quality diagrams of chemical structures and reactions, metabolic pathways, membrane bilayers, enzymes and signal transduction effectors, and more. They can be a useful tool for researchers and students in preparing presentation slides and figures for publication. We previously had a few copies of these tools on our computers at Brill (and still do for those who don't have ready access to a PC), but the University-wide purchase is an obvious step ahead.

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

Access to ASM Journals, The Prokaryotes

We now (read: finally...) have stable online access to the American Society for Microbiology journals. BOT and ZOO folks, before you stop reading, this includes the titles "Microbiology and Molecular Biology Reviews," and "Molecular and Cellular Biology." You should now be able to access online recent articles published in these journals via links from PubMed, the Libraries' catalog, e-journal list, etc.

Somewhat related, I've had a few people recently express interest in the microbiology reference set "The Prokaryotes." We do have access to this work online, via the OhioLINK Electronic Book Center. The EBC is a relatively new project and unfortunately its content is not yet well-reflected in the Libraries' catalog, so access through the EBC works best.

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.

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/.

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

Saturday, September 15, 2007

Brill Science Library to Hold Orientation Event October 5

Brill Science Library will hold an orientation event for students and interested faculty and staff on Friday October 5 from 12:30-4:30 pm. During the event, participants will explore several different stations devoted to research, information, and literature on the topic of global climate change. Stations will also provide information about services available at the library.

Faculty may consider offering extra credit in the courses to participating students. Students will be given a "passport" and must be documented at six stations to be eligible for prizes and extra credit. If you are interested in offering extra credit in your class, please contact Eric Resnis (resnisew@muohio.edu) as soon as possible.

More information is available at http://www.lib.muohio.edu/gaia.

Monday, September 10, 2007

New Version of ISI Web of Science Available

Thomson ISI has released a new version of the Web of Science literature citation database. It can be accessed on campus through the existing Web of Science web site -- once in Web of Science click the button reading "Access the New Version" at the top of the page. Note that at present the new version is only available on campus; for off-campus use, you'll need to continue to use the old/current version.

The changes to the interface are not profound, mostly cosmetic. Linking to citing and cited papers is essentially unchanged. One can search within a set of existing results, and the analyses one can perform on a set of search results are more straightforward -- so one can ask, e.g., "for a given set of results on a topic, which authors wrote the most of these papers?"

As always, feel free to address any questions or problems using this tool to my attention!

Try the New Libraries Catalog

The Libraries are pleased to announce a new experimental interface for the Libraries' catalog. This interface enables users to refine their initial search results based on a menu of choices of subject, format, media, location (e.g., just the science library), or geographical area. The catalog also presents a cleaner interface than our current production catalog site.

The new catalog is at http://beta.lib.muohio.edu/drupal5/. More info available at http://www.lib.muohio.edu/spotlight/story.php?id=271. Feedback is welcome and encouraged!

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).

Tuesday, August 21, 2007

Problems with Blackboard + E-Reserves

The start of a new semester always comes with its share of hiccups. One item that's come to our attention regards course electronic reserves. Several instructors have reported that their e-reserves are not showing when accessing within Blackboard.

The e-reserves are actually being processed as the library receives them, and they are in fact available through the Libraries e-reserves web site: http://www.lib.muohio.edu/reserves/. The data from the Libraries isn't currently being captured properly by University IT Services. IT services is working to resolve the problem with Blackboard -- for the moment, though, please direct your students to access through the Libraries' site. (Students can go directly to http://www.lib.muohio.edu/reserves/; or in Blackboard click on the name of the class that appears in the Blackboard popup window. That will take them directly to the Libraries site where they can get the most up to date article listing.)

Tuesday, August 14, 2007

OhioLINK Adds Thousands of Scholarly E-Books, Opens E-Book Center

Thousands of new scholarly e-books, published by Springer, are now available to students, faculty and staff at OhioLINK member institutions. These are recent (2005-2007), high-quality scientific, technological and medical books. Students can use these books to do research anytime, anywhere. Faculty can use the books for research or as course materials. Faculty can assign particular readings and link to relevant chapters or sections from course pages or Web sites. New Springer e-books will be added regularly. These recent additions bring the total number of e-books offered by OhioLINK to 25,000.

These new e-books are available as part of the new Electronic Book Center. Similar in concept to the Electronic Journal Center, the E-Book Center will allow you to find and utilize e-books from multiple publishers using one common interface. Currently, the E-Book Center contains 5,000 e-books from Oxford University Press and Springer. Additional e-books and e-book collections will be added, including the Electronic Reference Books collection. Links to OhioLINK’s other e-book collections are available from the E-Book Center’s home page.

Books in the E-Book Center will also be accessible from the OhioLINK Library Catalog. Records are being added for the new e-books.

Supplementary files in OhioLINK journals

Part of the gradual shift we're seeing towards more data and computation intensive and media-rich science is the greater use of supplementary files as adjuncts to primary research articles. The OhioLINK Electronic Journal Center now displays any accompanying material included in Institute of Physics and Elsevier articles as "Supplementary Files" below the abstract. The available files include videos (.mov, .avi and .mpeg formats), PDFs and PowerPoints. All files sent to OhioLINK by publishers are made available.

Here's a good example:

Many Cell articles also contain supplementary files, for example:

Sunday, August 12, 2007

New Grad Student Orientations

The Miami University Libraries are pleased to welcome our newest graduate students at these upcoming orientation sessions:

* Thursday, August 23, 7-9 p.m. OR
* Friday, August 24, 2-4 p.m.

These sessions will include a question and answer session on new and existing library services and resources, a quick tour of King Library, and an opportunity to meet informally with liaison librarians who coordinate library services to individual academic programs.

We hope that you can join us for one of the sessions, which will be held at King Library, Room 110. For online registration, please visit http://www.lib.muohio.edu/registration/graduate/

Thursday, August 9, 2007

RefWorks Import Guides for Life Sci Lit Databases Now Available

Step-by-step guides for importing citations from PubMed, BIOSIS, Agricola, and Google Scholar into RefWorks are now available at the MU(LS)2 blog, http://miamiulifescilib.blogspot.com/

Some of you will note that Web of Science (Science Citation Index) is conspicuously absent from the list above. Thomson ISI has indicated that they will be releasing a new version of Web of Science "soon," so I'm awaiting the new version to see how it handles exporting and will make a guide accordingly. We'll also tackle a few other databases (e.g. SciFinder Scholar); please let me know of any others you use regularly.