December 29, 2004

Nucleic Acids Research to go Open Access in 2005

Nucleic Acids Research, an Oxford University Press journal in press since 1974, has announced that it will switch to a full open access publication model in 2005. Under the open access model, each online issue of the journal will be made freely available to the public upon publication. Author charges of US $1500 per article accepted for publication have been set to recoup publication costs for OUP.

NAR has provided an option for institutions to purchase an institutional membership to the journal, which will reduce the publication charge for authors to $500. The Magrath Library will purchase the US $2855 institutional membership for UMTC (which comes with a print copy of the journal). University of Minnesota authors published nine articles in NAR in 2003, and three so far in 2004.

NAR was listed in 2003 by the Institute for Scientific Information (ISI) as one of the ten "hottest" journals in biology and biochemistry in the last decade. The journal currently ranks #27 out of 261 journals in Biochemistry and Molecular Biology on the ISI Journal Citation Reports Impact Factor list (which includes review-oriented journals as well as primary literature titles). It includes the popular annual Database and Web Server issues, which highlight developments in bioinformatics and computational biology resources.

Posted by Kevin Messner at 2:47 PM

December 15, 2004

Short Videos for Molecular Biology Education

The following short (<5 minutes) videos are a sampling of teaching materials for molecular biology available online. I compiled this list for a presentation I gave to the U Minn Bioinformatics Journal Club. For those of you who are course instructors, I hope some of these may be useful.

Exploring Our Molecular Selves -- an introduction to molecular biology and the "central dogma" for a lay or introductory audience. From National Human Genome Research Institute.

Biological Clocks tutorial on the period gene in Drosophila and the control of circadian rhythm at the molecular level. Good example of a multi-factor regulatory system. Video is done in five parts, each adding a layer of complexity to the system. From Howard Hughes Medical Institute's BioInteractive web site.

WEHI-TV Molecular Animations -- some of the most complelling animations of biomolecules I've seen. These raw videos have been incorporated into a number of larger media productions. Note: If you use these, you should consider downloading and saving them onto a local disk drive; I've had some trouble running them on the web page within a browser. Well worth the trouble of saving a copy, though.

Here are a few other biology education resources to know about; this list is at least one, probably two, orders of magnitude away from being comprehensive! These are just a few of the first places I look for materials.

ben: BiosciEdNet -- searchable portal site for biology education resources. Managed by AAAS.

Dolan DNA Learning Center -- part of Cold Spring Harbor Laboratories. Dolan produces a variety of high-quality online educational materials, as well as workshops and other resources, for molecular biology and genetics.

Shodor Foundation -- suite of both online and "wet lab" educational materials across the sciences and methematics.

Access Excellence -- range of materials, tutorials, graphics, etc. for biology and health education. From National Health Museum.

Posted by Kevin Messner at 7:49 AM

December 14, 2004

PubMed Bookmarklet and Toolbar Search Plugin Enhanced with U of M Find It Service

Frequent PubMed users may be interested in exploring two browser enhancements which allow users to initiate PubMed searches directly from a web browser window, and which are customized for University of Minnesota users.

Bookmarklets are short JavaScript applications contained in a web browser bookmark. They are often used to initiate a search in a web site database (e.g., in Google or For frequently searched sites, they are quicker to use than first loading the web site home page and then entering the search on that page.

Several bookmarklets have been written for PubMed. This U Minn PubMed search bookmarklet has the additional advantage of activating the U. Libraries' Find It service in PubMed. Find It helps users link from PubMed to full text articles available through the Libraries. (For more information on Find It, see the Find It FAQ or


You can add the bookmarklet to your list of bookmarks/favorites or to your bookmark toolbar as you would for any bookmark (e.g., right-click the link above and "Bookmark this link"). The bookmarklet works on current versions of Internet Explorer and Mozilla products, on both PC and Mac platforms.

For Mozilla Firefox users, Chad Fennell at the Bio-Med Library has also whipped up a PubMed toolbar search plugin with similar utility. This tool creates a Find It-enabled toolbar search box, for direct searching PubMed from the browser. (Firefox comes with toolbar searches for Google and several other databases pre-installed. See Firefox Central for more on toolbar search engines.)


Enabling the U. Minnesota PubMed toolbar search is a two-step process. First, go to and search for "NCBI PubMed" in the "Install search plugins" section. Follow the instructions to install. This will add the PubMed toolbar search to your browser.

Next, to enable the U Minn Find It function in your toolbar search, replace the file pubmed.src in Program Files/Mozilla Firefox/searchplugins/ with this version of the file.

Note that both the bookmarklet and toolbar search plugin tell PubMed to activate a web cookie (indicating you want U. Minnesota resources), so cookies must be enabled on your browser to use these tools.

Chad and I hope that one or both of these tools proves useful for you!

Posted by Kevin Messner at 8:18 PM