MU(LS)2: Miami University Life Sciences Library Services

New NCBI Sequence Viewer Beta Available

2008-04-15T13:30:00.003-04:00

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

2008-04-15T12:32:00.004-04:00

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

2008-04-15T09:59:00.006-04:00

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.

NIH Public Access Policy Now in Effect

2008-04-09T18:07:00.000-04:00

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.

Faculty Learning Community for Improving Student Research Literacy

2008-04-02T09:23:00.004-04:00

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

ChemDraw/BioDraw Available for Download to MU Users

2008-03-31T20:23:00.006-04:00

(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:
http://scistore.cambridgesoft.com/sitelicense.cfm?sid=800

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

2008-03-31T20:17:00.003-04:00

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).

Access to ASM Journals, The Prokaryotes

2008-03-24T18:36:00.006-04:00

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

2008-03-24T18:22:00.003-04:00

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

2008-03-24T17:55:00.006-04:00

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

2008-03-24T17:47:00.003-04:00

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

Brill Science Library to Hold Orientation Event October 5

2007-09-16T18:29:00.000-04:00

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.

New Version of ISI Web of Science Available

2007-09-11T16:35:00.000-04:00

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

2007-09-11T16:08:00.000-04:00

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!

PRISM Anti-Open Access Lobbying Effort Launched

2007-09-08T18:16:00.000-04:00

"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).

Problems with Blackboard + E-Reserves

2007-08-22T16:37:00.000-04:00

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.)

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

2007-08-14T12:24:00.000-04:00

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

2007-08-14T07:40:00.000-04:00

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:
http://journals.ohiolink.edu/ejc/article.cgi?issn=00144827&issue=v313i0013&article=2766_domgaraamoad

Many Cell articles also contain supplementary files, for example:
http://journals.ohiolink.edu/ejc/article.cgi?issn=00928674&issue=v130i0002&article=323_sbfaotkkbscf

New Grad Student Orientations

2007-08-13T16:19:00.000-04:00

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/

RefWorks Import Guides for Life Sci Lit Databases Now Available

2007-08-09T10:10:00.001-04:00

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.

Workshops for Fall

2007-08-08T16:23:00.001-04:00

Registration is open for the Libraries' Technology and Information Management workshop series. Most workshops are 30-90 minutes long depending on topic, and introduce topics including database searching, citation management, as well as poster, web, podcast, and video design.

The RefWorks sessions (9/24, 10/5, 10/8) may be of particular interest. I'll also be giving a session on web-based bioinformatics resources (e.g. NCBI Entrez and Maps), coming up on Sept. 7. (Given the 1 hr time frame, this is primarily intended for users with little experience using the NCBI tools, e.g. students starting work in your lab.)

Workshop descriptions and registration are available at http://www.lib.muohio.edu/instruction/workshops/.

Library sessions for fall classes

2007-08-01T08:32:00.000-04:00

Course instructors, as you scramble to update syllabi for your fall classes, please let me know if you are interested in a library presentation for your class, particularly if your course involves a literature research and writing component. Depending on the class's needs, I can give a brief 15 minute spotlight session in your classroom on a particular topic (e.g. on a particular problem you've encountered in the class in previous years, like identifying "scholarly" or peer-reviewed materials), to a 2 hr session in the library computer lab with hands-on practice.

Topics can include: the basics of using the Miami Libraries; using literature indexes and databases; using bioinformatics databases and tools; finding print and electronic text in the library; identifying quality information on the Web; scholarly publication/peer review; properly citing sources; brainstorming topics, etc. -- let me know if you have something else in mind.

Bookmarking Electronic Journal Center Articles

2007-07-30T12:13:00.000-04:00

Now you can quickly bookmark articles found in the OhioLINK Electronic Journal Center to your del.icio.us, Google Bookmarks, Connotea, Digg, reddit, Spurl, or Windows Live Favorites account with just one click. Look for the icon for your favorite bookmarking tool on the abstract page of any article in the EJC.

See http://olc7.ohiolink.edu/whatsnew/archives/000197.html for more details.

US House Approves Mandated Open Access to Funded Research Pubs

2007-07-25T13:17:00.000-04:00

Press Release from the Alliance for Taxpayer Access:

Washington, D.C. – July 20, 2007 – In what advocates hailed as a major advance for scientific communication, the U.S. House of Representatives yesterday approved a measure directing the National Institutes of Health (NIH) to provide free public online access to agency-funded research findings within 12 months of their publication in a peer-reviewed journal. With broad bipartisan support, the House passed the provision as part of the FY2008 Labor, HHS, and Education Appropriations Bill.

“The House has affirmed the principle that broad sharing of publicly funded research findings on the Internet is an essential component of our nation’s investment in science,” said Heather Joseph, Executive Director of SPARC (the Scholarly Publishing and Academic Resources Coalition), and a leader of the Alliance for Taxpayer Access (ATA). “This action paves the way for all scientists and citizens to access, use, and benefit from the results of publicly funded biomedical research.”

“We’re pleased by Congress’s recognition of the fundamental rationale for public access – that better-informed patients, clinicians, and researchers will mean better health outcomes,” said Sharon Terry, President of the Genetic Alliance and an ATA activist. “The time has come to sweep away unnecessary barriers to understanding and treating disease. The Genetic Alliance thanks and congratulates the House of Representatives for taking this vital step.”

The current NIH Public Access Policy, implemented in 2005 as a voluntary measure, has resulted in the deposit of less than 5% of eligible research by individual investigators.

In a recent letter to Congress, 26 Nobel Laureates called for enactment of mandatory NIH public access, noting that, "requiring compliance is not a punitive measure, but rather a simple step to ensure that everyone, including scientists themselves, will reap the benefits that public access can provide. We have seen this amply demonstrated in other innovative efforts within the NIH – most notably with the database that contains the outcome of the Human Genome Project.”

“The coalition of support for the NIH policy is extremely broad,” added Joseph. “This critical step was achieved as a result of the vision and collective effort of patient groups, scientists, researchers, publishers, students, and consumers who registered their support.”

A similar measure has been approved by the Senate Appropriations Committee and will be considered by the full Senate later this summer.

###

The Alliance for Taxpayer Access is a coalition of patient, academic, research, and publishing organizations that supports open public access to the results of federally funded research. The Alliance was formed in 2004 to urge that peer-reviewed articles stemming from taxpayer-funded research become fully accessible and available online at no extra cost to the American public. Details on the ATA may be found at http://www.taxpayeraccess.org.

SciFinder Scholar 2007 Now Available

2007-07-20T08:22:00.000-04:00

SciFinder Scholar, the major chemistry literature database, has released its 2007 version. To download, see the instructions at http://www.lib.muohio.edu/indexes/scifinder/. According to its producer, the Chemical Abstract Service (CAS):

SciFinder Scholar 2007 offers powerful new features:

Categorize references—this tool enables you to sort and evaluate information in your answer sets by creating a histogram for easy analysis. Categorize separates related references on the basis of their associated CA index terms. With categorize, you can reassemble the different subsets in unique ways creating opportunities for new insights.

Save answers—now you can save answer lists of references, substances, or reactions and re-use them later in other SciFinder Scholar sessions.

Combine answer sets—the combine tool makes it possible to focus on a particular research topic in new ways by combining the substances, reactions, and references in an active answer set with those in a previously saved one. By employing various options of Combine, Intersect, or Remove, you can manipulate and customize the information contained in these combined answer sets.

Export commercial chemicals records from CHEMCATS® into Excel—create reports listing your favorite commercial sources, including contact information and pricing, for substances of interest. Catalog information is exported into Excel spreadsheets for sorting, manipulation, and reference.

Explore from substance displays—become more productive by using a substance record display to launch a new search or refine a previous one.

Print structures in grid format—gain a unique comparative view of multiple chemical structures by printing them side by side in this handy grid arrangement.

Compatible with Windows VistaTM and Mac OS X

Visit www.cas.org to view examples that will show you the latest SciFinder Scholar 2007 features. If you have questions about downloading SciFinder Scholar 2007, please call CAS Customer Care at 800-753-4227, click on your Send Message to CAS button in your current SciFinder Scholar installation, or send e-mail to help@cas.org.

Please note:
1) If you depend upon Discovery StudioTM Visualizer, third-party software from Accelrys, to view structures in 3D, please be advised that only DS Visualizer versions 1.5 or earlier work with SciFinder Scholar 2007. Installing DS Visualizer 1.7, the current version available from the Accelrys web site, will cause 3D viewing to stop functioning with SciFinder Scholar 2007.

To remedy any dysfunction with DS Visualizer 1.7: please install the ViewerLite software and the ViewerLite patch from the myCAS site or use an earlier version.

2) Effective with this release, CAS will no longer offer support of SciFinder Scholar 2007 with Mac OS X 10.2.

3) CAS will discontinue support for SciFinder Scholar Mac OS 9 on December 31, 2007. You will receive a reminder prior to discontinuation.

Out-of-Office Hours

2007-07-19T11:03:00.000-04:00

I'm currently at Pearson Hall in the alcove at the end of the 153 hallway, 1st floor, west side of the building. Will be here from 11AM -12N today. Stop by and say hi, and/or bring any questions you have about the library, our databases, finding books/journals, ILL, RefWorks, NCBI, etc!

Out-of-Office Hours

2007-07-16T13:02:00.000-04:00

I'm currently at Pearson Hall in the alcove at the end of the 253 hallway, 2nd floor, east side of the building. Will be here from 1-2 PM today. Stop by and say hi, and/or bring any questions you have about the library, our databases, finding books/journals, ILL, RefWorks, NCBI, etc!

Out-of-Office Hours

2007-07-12T11:04:00.000-04:00

I'm currently at Pearson Hall in the alcove at the end of the 341 hallway, 3rd floor, east side of the building. Stop by and say hi, and/or bring any questions you have about the library, our databases, finding books/journals, ILL, RefWorks, NCBI, etc!

Canadian Journal of Botany to be renamed "Botany"

2007-07-10T08:47:00.000-04:00

NRC Research Press has announced that, beginning January 2008, the Canadian Journal of Botany will be changing its name to Botany. This name change is intended to reflect the journal's position as an international journal for plant biology. The journal format and content is to remain consistent through the change.

See the full press release at http://pubs.nrc-cnrc.gc.ca/rp/rptemp/rp2_news4_e.html

Journal of Experimental Botany Announces Free Open Access for Authors at Subscribing Instititions

2007-06-21T08:56:00.000-04:00

Oxford Journals has announced that all primary research papers (i.e., not review articles) published in the Journal of Experimental Botany after 1 April 2007 are being published in an open access manner, without any open access charge to the author if the corresponding author’s institution has a current subscription to the journal.

OhioLINK subscribes to JXB, so this may be a consideration for you botanists when deciding where to submit manuscripts -- at root, open access to your paper means that a greater number of researchers will be able to read your work (e.g. those at smaller schools or underdeveloped parts of the world where journal subscriptions are a luxury). To their credit, Oxford Journals is currently experimenting with a number of open access models for various of their titles, notably Nucleic Acids Research which has gone to a full open access publishing model (OhioLINK will pay part of the publication charges for NAR).

See the Oxford press release at http://www.oxfordjournals.org/news/2007/06/19/journal_of_experimental_botany_a/journal_of_experimental_botany_a.html

'Science' and 'Nature' not to accept submissions in Office 2007

2007-06-19T10:43:00.000-04:00

I'll speculate that if these two journals have made this decision not to accept MS Office 2007 files, then other publishers are doing or thinking the same. If you've switched to Office '07, keep this in mind if you're starting to write now -- you may want to double-check the publication's guidelines.

From the KnowledgeSpeak Newlestter (scope@scopeknowledge.com):

"Academic journals Science and Nature have recently revised their publication guidelines and informed that Office 2007 file format documents will not be accepted for initial review or revision. According to recent notices posted on the websites of both these journals, the latest version of Word is no longer compatible with Mathematical Markup Language (MathML), the standard for writing equations in text documents."

Read the full story at http://www.knowledgespeak.com/newsArchieveviewdtl.asp?pickUpID=4275&pickUpBatch=662#4275

Nature's Guidelines: http://www.nature.com/nature/authors/gta/index.html
Science's Guidelines: http://www.sciencemag.org/about/authors/

"Out of Office" Hours

2007-06-18T13:01:00.001-04:00

I'm currently at Pearson Hall in the alcove at the end of the 253 hallway, 2nd floor, west side of the building. Stop by and say hi, and/or bring any questions you have about the library, our databases, finding books/journals, ILL, RefWorks, NCBI, etc!

I'l be at Pearson through this summer Mondays 1-2pm and Thursdays 11am-12n.

Out-of-Office Hours

2007-06-14T11:04:00.000-04:00

I'm currently at Pearson Hall in the alcove at the end of the 153 hallway, 1st floor, east side of the building. Stop by and say hi, and/or bring any questions you have about the library, our databases, finding books/journals, ILL, RefWorks, NCBI, etc!

I'l be at Pearson through this summer Mondays 1-2pm and Thursdays 11am-12n.

RefWorks Demo Today

2007-06-13T09:34:00.000-04:00

I'lll be giving an (improptu) introduction to the RefWorks citation management software today at 2:30 in Pearson 218. Should be about 1/2 hour. Stop by if you're interested and can make the time. If you can't, drop me a line; I can certainly do another session later this summer or stop by to show anyone one-on-one.

Web of Science Access Now Extends Back to 1965

2007-06-12T13:38:00.000-04:00

The Libraries now have increased online access to the Thomson (ISI) Web of Science citation index backfiles. Our access to Science Citation Index now extends back an additional 15 years, to 1965. We're excited to be able to offer increased access to this important literature discovery and analysis tool. The additional years of access will provide more complete views of the citations of papers from this era, and will allow better connections between the recent literature and classic papers written during critical periods for fields like molecular biology and environmental science.

NIH Open Access Policy Nearing Vote in US House

2007-06-12T12:13:00.000-04:00

Lila Guterman, Open-Access Policy Would Be Strengthened in House Panel's NIH Spending Bill, Chronicle of Higher Education blog, June 12, 2007:

"The House Appropriations Committee will decide this week whether to strengthen the open-access publications policy of the National Institutes of Health. The shift, which appears in a 2008 spending bill for the Department of Health and Human Services, would make mandatory a policy that until now has been voluntary, according to Heather Joseph, executive director of the Scholarly Publishing and Academic Resources Coalition, which advocates for open access. The bill was approved last week by a House Appropriations subcommittee.

"The two-year-old policy requests but does not require that NIH grantees upload their research papers to an online repository no later than 12 months after publication. But not many scientists have made use of the repository. “Mandatory is a crucial element just because compliance is so low without it,” said Ms. Joseph."

Peter Suber (Open Access News) adds:

"There's still time for US citizens to ask their representatives to support this bill. See the details from the ACRL and the frequent updates from the ATA. The NIH is the world's largest funder of medical research, and its $28 billion budget results in about 65,000 peer-reviewed articles per year. Strengthening its public access policy from a request to a requirement is a critical goal for OA and medical research. "

"Out-of-Office" Hours in Pearson Hall Beginning Thurs 6/14

2007-06-12T11:21:00.000-04:00

I will be holding "Out-of-Office" Hours in Pearson Hall through this summer, beginning this Thursday, June 14. I'm hoping to catch more of your spur-of-the-moment questions and ideas about the literature and library services, by placing myself in situ (sorry, couldn't resist) near most of your labs.

I'll be at Pearson Mondays 1-2pm and Thursdays 11am-12n. I'll generally plant myself in one of the alcoves at the ends of the x53 hallways on the 1st, 2nd, or 3rd floors; I'll post my exact location for a given day on my web site. Stop by and say hello! As always, if these times are poor for you, feel free to drop by my office in Brill or email me at messnekr@muohio.edu.

Entrez Version 2.0 Now Running PubMed, Other NCBI web sites

2007-06-10T12:12:00.000-04:00

The NCBI databases, including PubMed, have recently transitioned to a new database system/structure. The web interface is visually the same; you may notice some differences such as more descriptive web page titles when viewing search results, a new placement for the OhioLINK full text button on PubMed abstract pages. More information is available on the change from NCBI at http://www.nlm.nih.gov/pubs/techbull/ma07/ma07_ncbi_new_titles.html.

You may come across some other quirks and problems if you maintain links to or from PubMed. I have also noticed that Nature's Connotea social bookmarking service is not capturing citation information (e.g. journal title, page numbers, etc) from PubMed following the transition. The citation would have to be recorded by hand. A link to the PubMed record is still captured.

Moly Bio Search

2007-06-08T14:44:00.000-04:00

This is an experimental search engine I'm working on, using Google's Custom Search. Custom Search allows you to build a search engine that searches particular web sites. We are searching a series of major bioinformatics/molecular biology web sites. If you input the name of your favorite gene/protein/cell type, the hope is you'll get back some useful/novel information.

We have the search set up so that it DOES NOT return PubMed results. When PubMed is included, it seems to overwhelm all other results. We may try to tinker/finesse this in the future.

Let me know what you think -- do you find relevant info using this? Things you would not have found elsewhere? I'm interested in your experience to inform how we can improve this. We'll also be exploring building a similar tool looking more at ecological/environmental biology. Drop me a line at messnekr@muohio.edu

Access to Springer E-books Now Available

2007-05-20T12:25:00.000-04:00

Through OhioLINK, Miami now has access to most books published by Springer in online format from 2005 to present, including a large number of sci-tech titles. OhioLINK is currently working to build a platform to contain and present this data on the Web. Until then, you are able to access the e-book content through the Springer web site at http://www.springerlink.com/home/main.mpx. From on campus, you should be able to access items labeled as "Books" with copyright dates from 2005 onwards. The search engine on Springer's site has some problems, so we are eagerly awaiting OhioLINK's forthcoming platform as a cleaner way to search this content.

Encyclopedia of Life to Document All Named Species

2007-05-13T12:07:00.000-04:00

Many of the world’s leading scientific institutions announced on May 9 the launch of the Encyclopedia of Life, an unprecedented global effort to document all 1.8 million named species of animals, plants, and other forms of life on Earth. For the first time in the history of the planet, scientists, students, and citizens will have multi-media access to all known living species, even those that have just been discovered.

Read the full press release at http://www.eol.org/press_release.html. The Encyclopedia of Life web site is http://www.eol.org.

Publication Fee Waivers/Reimbursement for BMC, PLoS, NAR journals

2007-04-23T11:04:00.000-04:00

"Open Access" publishing continues to gain ground in the scholarly publications world, and some Miami authors are starting to seek publication in open access venues. The standard open access model relies on publication charges made to authors to publish in a journal, rather than on subscriptions charges to libraries and individuals to receive the journal. This business model allows the content of the journal to be made available to all interested parties, not just to those who can afford a subscription.

To promote the open access model, OhioLINK provides financial assistance to authors to pay publication charges from three major publishers of open access titles: BioMed Central (BMC), Public Library of Science (PLoS), and Nucleic Acids Research.

OhioLINK provides an institutional membership to BioMedCentral for all 84 OhioLINK members. This allows authors from OhioLINK institutions to publish in BioMed Central's open access titles free of additional charge. (For those with interests spanning the physical sciences and mathematics, BMC has also recently launched a sister site, PhysMath Central for those fields.)

For authors who publish in a PLoS journal, OhioLINK will provide assistance by directly reimbursing the author for 1/2 of the publication fees the author is charged by PLoS. This same arrangement is in place for authors publishing in Nucleic Acids Research (now published in an open access model by Oxford U Press). If you are planning to publish in PLoS or NAR, please contact me (messnekr@muohio.edu) for details on reimbursement.

Miami U LibX Firefox Browser Toolbar Now Available

2007-04-12T10:53:00.000-04:00

A search toolbar is now available for users of the Firefox browser.

The MiamiU LibX toolbar is a Firefox extension that provides direct access to many Miami University Library resources. With this toolbar, you can search the Miami U. Library catalog, the OhioLINK catalog, the OhioLINK Articles and Books Quick Search, Online Journal Titles, and other resources directly from the LibX toolbar or using the right-click context menu.

For more information or to download, go to http://www.lib.muohio.edu/libx/.

Species 2000 and Catalogue of Life Project Reaches 1M Species Milestone

2007-04-11T09:11:00.000-04:00

The Species 2000 and Catalogue of Life project, a collaborative program to catalog all known species of organisms by 2011, has reached at last count 1,008,965 entries. By the project's estimate, this is about half of the world's total number of species.

The present catalog is compiled with information from 47 different taxonomic databases around the world. The catalog's development is led by the Integrated Taxonomic Information System (ITIS), a partnership of U.S., Canadian, and Mexican organizations and government agencies; and Species 2000, a federation of taxonomic database custodians.

More information about the project is available at http://www.catalogueoflife.org/info_about_col.php.

Brill Now Offering ChemOffice Pro, Including BioDraw Drawing Software

2007-04-02T12:06:00.000-04:00

Brill Library has upgraded our license to the the CambridgeSort ChemDraw chemical drawing program for the PC. The new version, ChemOffice Pro 2006, includes a range of drawing tools called BioDraw, particularly for biochemistry and molecular biology. These tools provide an easy way to draw presentation-quality diagrams of metabolic pathways, membrane bilayers, enzymes and signal transduction effectors, and more. It may be a useful tool for researchers and students in preparing presentation slides and figures for publication.

ChemOffice Pro is only available on a set of public computers at Brill Library. Please ask at the reference desk (or drop me a line) if you'd like to try using it.

Birds of North America Online

2007-04-02T11:52:00.000-04:00

The Libraries have begun a subscription to Birds of North America Online, from the Cornell Laboratory of Ornithology. This site is a comprehensive reference covering the life histories of each of 716 North American birds (i.e., species nesting in the U.S. and Canada). Brill Libraries held previous editions of the title in print, and the move to online has enabled this work to incorporate several new types of information, including image, video, and audio galleries for many of the described species, as well as site search capabiities. The work will also be updated on a rolling basis.

Access to Nature Online Now Extends to 1987, Nature Genetics Now Received Online

2007-04-02T10:21:00.000-04:00

I'm pleased to report that we have been able to extend our newly acquired online access to the journal Nature back to 1987, with the Libraries' purchase of an archive segment from NPG.

We are also now receiving Nature Genetics in online format, rather than in print.

I'd like to encourage you to make use of our new Nature online subscription, which began at the start of 2007, and this archive of the journal, as well as the several Nature Reviews titles we've recently acquired online. As I'm sure most of you know, NPG journals are quite expensive, and moreso in online format than in print, and so it is through active classroom and research use of these titles that we justify our subscriptions.

What'd You Say? Construction Begins Below Brill Library

2007-03-31T13:26:00.000-04:00

It bears mentioning that if you use Brill as a quiet spot for reading or study, at the present time you may be best off using the north side of the facility, that is, the side facing High St./Pearson Hall. Construction (well, more demolition at this point) has begun on the Chem and Biochem Department's new NMR facility beneath the library on the south side of the building, and it's been intermittently loud-to-teeth-grinding directly above.

Fortunately the noise doesn't seem to carry too badly up to the third and fourth floors, and there's no problem on the north side (at least so far!).

(Alas, the librarians' offices are all directly above the construction space. So far I haven't fled, but if you're looking for me at Brill and I'm not in my office, ask at the front desk. I may have taken temporary refuge in a study room upstairs...)

Petition for Public Access to Publicly Funded Research in the United States

2007-03-31T12:38:00.000-04:00

Recent good news about journal subscriptions at Miami aside, here's a reminder that our access to the scientific literature remains tenuous, as prices steadily rise and budgets bob in an uncertain fiscal sea. Most of you have some familiarity with the open access publishing movement, NIH's access requirements for publications emerging from NIH-funded research, and related legislation and activity. Scholarly Publishing and Academic Resources Coalition and the Alliance for Taxpayer Access have recently put forth a petition in support of the Federal Research Public Access Act.

Visit http://www.publicaccesstoresearch.org/ to sign.

From the web site:

This petition builds on the 24,000+ signatures collected from around the world in support of free and open access to European research and for the recommendations proposed in the EU's 'Study on the Economic and Technical Evolution of the Scientific Publication Markets of Europe' as well as the 132 higher education leaders who have written of their explicit support for public access to publicly funded research.

Sign this petition to register your support for free and open access to research funded by the U.S. Federal government. For more information on current policies and legislation for taxpayer access to federally funded research – including the Federal Research Public Access Act – visit the Alliance for Taxpayer Access Web site.

Discover Magazine Debuts New Web Site

2007-03-26T13:25:00.000-04:00

Discover, a monthly magazine which covers science, technology and the future, has launched a newly redesigned website to deliver science news through the latest innovative technology. The newly named discovermagazine.com will feature a video front and centre on its homepage, allowing readers to watch science in action.

Read the full article at http://www.knowledgespeak.com/newsArchieveviewdtl.asp?pickUpID=3776&pickUpBatch=598#3776

A Few More New E-journals

2007-03-19T14:18:00.000-04:00

We now have online access to the journals Limnology and Oceanography, Limnology
and Oceanography: Methods and Limnology and Oceanography Bulletin from ASLO.

Also, our access to ESA's Frontiers in Ecology and the Environment has been fixed. Access is currently available on campus at http://www.esajournals.org/esaonline/?request=get-archive. The title will be added to the library catalog and e-journals list ASAP to allow off-campus access.

The problem with online access to the new FEMS Microbiology journals has also been resolved with the publisher.

Changes to NCBI BLAST in Beta Release

2007-03-19T14:01:00.000-04:00

NCBI has recently released a new BLAST web site with a number of useful updates. If you use BLAST on NCBI's site for research or courses, you'll want to take a look at the new version. Changes/enhancements include:

Reorganization of links on the BLAST home page for the various query forms

A list of search results performed within the past 36 hours

Search strategies can be saved to MyNCBI

Redesigned BLAST forms with usability enhancements

A documentation directory

A consistent, tabbed user interface across the BLAST site

The list of prior search results will be particularly handy, as it will eliminate the need for users to store BLAST RID numbers to retrieve a search.

Try the "MU2PubMed" Bookmarklet for PubMed Searches

2007-03-15T16:39:00.002-04:00

Frequent PubMed users may be interested in trying this small browser enhancement, called a bookmarklet, which allows you to initiate a search of PubMed directly from any web browser window. I've built the MU2PubMed bookmarklet to additionally tell PubMed that you have Miami's library privileges.

Bookmarklets are short JavaScript applications contained within a web browser bookmark. They are often used to initiate a search in a web site database (e.g., in Google or Amazon.com). For sites you search frequently, they are quicker to use than navigating to the search engine's home page, and then entering the search on that page.

Several generic bookmarklets have been written for PubMed. MU2PubMed also activates the MU Libraries/OhioLink "OLinks" service in PubMed, so that an OLinks button appears on article records you find within PubMed. OLinks can help you link from PubMed to full text articles available through Miami's Libraries and OhioLink.

You can add this bookmarklet to your list of bookmarks/favorites, or to a bookmark toolbar, and use as you would a regular web browser bookmark. To add to your browser, right-click this MU2PubMed bookmarklet link and select "Bookmark this link"). The bookmarklet works on current versions of Internet Explorer, Firefox, and Safari, on both PC and Mac platforms.

New Journal Subscriptions for 2007

2007-02-25T23:00:00.000-05:00

Last fall the Libraries were able to allocate some additional monies towards new journal subscriptions. Many of you have already discovered some of our new titles; for those of you who have not, I'm pleased to write that we were able to add subscriptions to the following life science titles as part of this project:

Nature (with backfile to 1997)
Nature Reviews Genetics
Nature Reviews Immunology
Nature Reviews Microbiology
Nature Reviews Nolecular Cell Biology
Nature Reviews Neuroscience
Heredity
Cold Spring Harbor Protocols
RNA
American Journal of Physiology (including APS backfile)
Ecology
Ecological Monographs
Ecological Applications
Frontiers in Ecology and the Environment
FEMS Immmunology and Medical Microbiology
FEMS Microbiology Ecology
FEMS Yeast Research

Most of these titles were added as online-only subscriptions. In a few cases we canceled our previous print subscription to the title to help afford online access (in general, we can't afford to purchase duplicate subscriptions to a single title).

Most of these titles are now set up in our catalog and e-journals list. A few (Frontiers, FEMS) are still having kinks in access worked out with publishers and vendors. As I learn of progress on these I will post.

To be sure, there are other journal titles that we would like to have online access to, or just to have a subscription of any kind. Please feel free to let me know of titles that are a priority for you. I make no pomises, but hearing from you helps me to develop my wish list for possible future purchases.

Book Purchase Possibilities

2007-02-25T19:09:00.000-05:00

Want Brill Science Library to purchase a book? Please, just drop me a line with as much on the title as you know: messnekr@muohio.edu. We'll do our best to acquire the book titles you and our students need for research, teaching, outreach, and professional development.

If you like to browse what's available in the book world, I invite you to take a look at my available title lists. Most of my book buying for Brill is through a vendor called Yankee Book Peddlers. I sort through the vendor's weekly lists of newly released titles for books relevant to biologists and biology students on our campus; I purchase titles mostly from these lists.

I'm now making these lists of biology titles available online, for anyone interested to glance through at your convenience: http://www.users.muohio.edu/messnekr/bookpossibilities/. (Department representatives to the Libraries John Kiss, Kelly Abshire, and Tom Dockendorff will continue to get a hard copy of the lists, though I'm moving away from the stacks of yellow slips some of you may have seen in the past.)

The lists are short and sweet, usually between 5-30 titles; I invite you to have a look to see if there are titles we should have for your class, lab group, etc., and let me know if we should buy a copy!

"Biomolecule of the Month" Contest at Brill

2007-02-20T19:01:00.000-05:00

Brill Science Library is running a display and contest throughout this semester, called "Biomolecule of the Month." Each month we are featuring a nutrient, drug, or other chemical compound with a biological relevance and an interesting story. A chemical model of the compound is shown in the display, along with several clues as to its identity.

If a student can guess what the compound is and find the answers to two questions about it, they can enter a monthly drawing for a $10 gift certificate. The contest is open to all current Miami students (including grad students). The displays are designed so that even students with little experience in chemistry or biology should still be able to use the clues provided to do a little research and figure out the mystery compound. The display is on the second floor of Brill Library, near the reference desk. An image of the molecule is also available at href="http://www.users.muohio.edu/messnekr/botm/">http://www.users.muohio.edu/messnekr/botm/

In honor of Black History Month, February's exhibit features the work of Julian Percy, a chemist who persevered against bigotry throughout his life and remarkable career. The current display and contest runs through March 9, and this month's winner will receive a $10 certificate to Kofenya Coffee Shop.

"Wikipedia" Not an Acceptable Source, says Middlebury College Dept. of History

2007-02-18T11:52:00.000-05:00

The History Dept. at Middlebury College (VT) has created a formal policy disallowing students from citing Wikipedia articles as a source for academic papers. See the story at Yahoo News: http://news.yahoo.com/s/ap/20070213/ap_on_hi_te/wikipedia_ban.

As a science librarian, I use and recommend Wikipedia to researchers on a fairly regular basis. In the natural sciences and technology, at least, much of the content is excellent and provides a good introduction to huge array of topics. But the recommendation always comes with a caveat emptor: since Wikipedia's articles can essentially be edited anytime by anyone in any way, it's unwise to rely exclusively on Wikipedia as an authoritative source for important or controversial information.

It a nutshell, Wikipedia is oftentimes a good place to start research, but rarely the source a student should end with or actually cite in a paper. This is the crux of the Middlebury policy, and I think it equally applicable for the sciences as it is for history.