Molecular Biosciences Virtual Library

Google Accelerator and Library Resources

Google Web Accelerator (GWA) is a product from Google Labs that uses the Google network to allow one to surf the Web faster than before. This sounds like a good idea at first. Recently, staff in the University Libraries have discovered a downside to using Google Web Accelerator while using library-licensed resources such as electronic journals and online databases.

GWA creates a dynamic IP address for any of its users within the Google IP range. Therefore, if you are trying to access an e-journal via GWA, it will appear to the journal provider that you are coming to this resource from Google and not from the University of Minnesota's IP range. Consequently, you'll be denied entry into this library-licensed resource.

According to the GWA's FAQ, there are ways to disable GWA or to tell it not to "accelerate" a particular website, but in practice we've found this to be problematic. For the near future, we recommend not using GWA when using the University Libraries' licensed resources.

Health Sciecnes Libraries Open House

Please visit the Bio-Medical Library, Tuesday, October 24th from 10:00-2:00 for our Open House (http://www.biomed.lib.umn.edu/openhouse.html). Enjoy refreshments, learn about library collections and services, and meet your librarian liaison.

Regards,

Jim Beattie
jbeattie@umn.edu

BioMed Central Changes

The Health Sciences Libraries has supported open access publisher BioMed Central (BMC) through a membership fee which, until 2006, permitted unlimited waivers of the submission fee for University of Minnesota authors. Many of our faculty have taken advantage of this venue to share their research results with a world-wide audience.

This past year, BMC changed its membership accounting which is now based on the number of published articles. They assess us the entire submission fee, which averages $1350 per article in most categories (some types of non-research articles don’t assess author fees). Our membership for 2006 was for $10,000, which has now been exhausted. Going forward, our membership subscription will not accommodate payment of the submission fee, but rather a 15% discount on the fee; the remainder is the responsibility of the author, similar to page charges of other types of journals. Most of our colleagues around the country have taken a similar step, or did not renew at all, believing that the reporting of results through journal publication is an integral part of research that should be supported by funding sources as just one part of the cost of doing research.

We regret the late notice of this change, and that the transition wasn’t smoother. If you have any questions, please contact Katherine Chew at chewx002@umn.edu.

New Version of SciFinder Scholar for Mac OS X Available

There is a new version of SciFinder for Mac OS X now available for download at http://www.lib.umn.edu/slog.phtml?url=http://sciweb.lib.umn.edu/subject/software/.

CAS didn't specify a date for ending support of the previous version, so to our knowledge anyone using the Mac version that came out last fall should be fine for now.

This Week's University Libraries Update for the Molecular Biosciences

This University Libraries update is being sent to members of the Depts of BMBB, GCD, Microbiology, Neuroscience, Pharmacology, and Physiology. Others are welcome to sign up to receive the update -- please email me at messn006@umn.edu.

1) Libraries subscribing to Nature Protocols:
http://blog.lib.umn.edu/messn006/molbiolibrary/048647.html

2) Libraries orientations, guest lectures, web pages for fall classes:
http://blog.lib.umn.edu/messn006/molbiolibrary/048646.html

3) Print Journal Reduction at Bio-Medical Library:
http://blog.lib.umn.edu/messn006/molbiolibrary/048642.html

Libraries subscribing to Nature Protocols

The U Libraries are now subscribing to Nature Protocols, a new resource from Nature Publishing Group. Nature Protocols is an online resource for experimental protocols, primarily in biology and chemistry, including authoritative, peer-reviewed 'Nature Protocols' and an interactive 'Protocols Network'. The two create a dynamic forum for scientists to upload and comment on protocols.

Libraries orientations, guest lectures, web pages for fall classes

If you are working with new students or staff starting at the U, or planning a fall course which includes a writing or research paper component, the Libraries offer a number of services which may be of interest. For new students or staff members, we're always available to provide an overview orientation to U Libraries services and systems. Similarly, we can offer basic orientations to particular classes as they start to use the library for their coursework or research. Beyond that, I speak to various classes on topics such as crafting a good research paper, how to select high quality information sources on the web, keeping organized while conducting literature research, and more.

Additionally, if there is a set of articles, books, journals, web sites, or other resources which you'll use in your class, the Libraries can prepare a CourseLib web page to help provide access and maintain links to these materials.

Drop me a line if you're interested in having me or a colleague in the Libraries speak to your class or put together a web page for your class. We're happy to work with you to suit your needs.

Print Journal Reduction at Bio-Medical Library

The Bio-Medical Library is assessing our print journal collections this summer, trying to find journals which we can switch our print subscriptions to online format, or if we currently receive both formats, cancel the print subscription. The hope in reducing print subscriptions is to find cost savings to allow subscription to additional titles not currently received by the Libraries.

To be clear, we will not be cancelling any journal subscriptions outright during this project -- any journals which we stop receiving in print will be received electronically instead.

Also, we don't want to cancel print journals which are still important to users. If there are any particular journal titles which you use in print at the Bio-Medical Library and feel it is important that the library continues to receive in print, please feel free to drop me a line at messn006@umn.edu. It's most helpful if you can specify particular titles.

By the same token, if there are any journals which we only subscribe to in print and you want online access, let me know. (In some cases, we've been unable to obtain online access; but there may be some titles which we can try to readdress.)

This Week's University Libraries Update for the Molecular Biosciences

1) Upcoming Libraries Workshops:
http://blog.lib.umn.edu/messn006/molbiolibrary/047478.html

2) "TreeView" of NCBI BLAST Results Now Available:
http://blog.lib.umn.edu/messn006/molbiolibrary/047483.html

Upcoming Libraries Workshops

The following workshops are being offered by the University Libraries for resarchers and students in the sciences through the remainder of June. To register, and for a complete list of workshops being offered through August, go to http://www.lib.umn.edu/registration/

Basics of Database Searching: PubMed
Learn the basics searching MEDLINE, the premier health science citation database, through PubMed using Medical Subject Headings (MeSH) and other tools.
Time: Thursday, June 22, 2006 10:00 AM -- 11:00 AM
Location: AHC Learning Commons, 535/545 Diehl Hall

Beilstein Basics
Beilstein offers deep coverage of the literature of organic chemistry and the ability to search structures, properties, and reactions. This workshop offers an introduction to fact and structure searching in Beilstein with hands-on time at the end of the class.
Time: Wednesday, June 21, 2006 10:00 AM -- 11:30 AM
Location: Walter 310

Finding Electronic Full Text: Tips and Tricks
This class will cover the various ways that University students, staff, and faculty can access electronic full-text resources from MNCAT (the University online catalog) and from various University subscribed databases.
Time: Monday, June 19, 2006 10:30 AM -- 11:45 AM
Location: AHC Learning Commons, 535/545 Diehl Hall

Introduction to SciFinder Scholar
Covers the basics of using the SciFinder Scholar database including hands-on time at the end of the class.
Time: Monday, June 19, 2006 1:30 PM -- 3:00 PM
Location: Walter 310

Keeping Current in the Sciences
This is an overview of the alerting services in the science & engineering fields. The databases will send weekly updates of current literature references which meet the criteria you specify. We will help you define your interests in a search profile and set up an alert in the appropriate database.
Time: Wednesday, June 14, 2006 10:00 AM -- 11:00 AM
Location: Walter 310

Literature Search Techniques and RefWorks
Is doing research for your paper or literature review leaving you frustrated? We will show you a few simple strategies to make your literature searches focused and sophisticated. We’ll give you tips on the research process, and show you how to use RefWorks to organize your references and automatically create your bibliography. There will be time at the end of the class for you to work on your own project.
Time: Tuesday, June 20, 2006 10:30 AM -- 12:00 PM
Location: AHC Learning Commons, 535/545 Diehl Hall

OVID vs. PubMed
Want to know the differences between searching MEDLINE using Ovid versus PubMed? Are there any similarities? Learn how to effectively use each search interface to retrieve the citations you are looking for.
Time: Friday, June 30, 2006 11:00 AM -- 12:00 PM
Location: AHC Learning Commons, 535/545 Diehl Hall

RefWorks
RefWorks is a web-based bibliographic management service which allows students, faculty, and staff to create personal databases of references. RefWorks allows you to import directly from databases and formats papers in various styles.
Topics Covered include:
* Setting up an account
* Direct exporting
* Searching MNCAT/PubMed directly
* Saving citations and importing
* Intro to working with MS Word and creating bibliographies
Prerequisites: Emphasis on health sciences and using Medline.
Time: Thursday, June 15, 2006 10:00 AM -- 11:00 AM
Location: Bio-Medical Library: 2nd Floor Computing Area

RefWorks Basics
Learn the basics of using RefWorks, the Web-based citation manager that is available to all U of M Faculty, students and staff. Adding references to RefWorks will be covered, as well as exporting them to Word, and selecting a style (MLA, APA, etc) for your bibliography. See http://www.lib.umn.edu/refworks/ for more details about RefWorks.
Time: Wednesday, June 14, 2006 2:00 PM -- 3:15 PM
Location: Magrath Library Instruction Room - St. Paul

Setting Up AutoAlerts: PubMed, Web of Science, Science Direct
This workshop will demonstrate how to set up (or revise) an auto-alert, whether it is for receiving email alerts for selected journal Table of Contents (TOC), subject search updates, or receiving notifications when targeted articles are cited in the literature. The workshop will be especially helpful if you were a Current Contents user and need to re-establish your alerts. Databases covered will include PubMed, ISI Web of Science, ScienceDirect.
Time: Thursday, June 22, 2006 2:00 PM -- 3:00 PM
Location: AHC Learning Commons, 535/545 Diehl Hall

"TreeView" of NCBI BLAST Results Now Available

BLAST results may now be shown using a new "TreeView" dendrogram, clustered on the basis of BLAST score. Either of two methods, "Fast Minimal Evolution" or "Neighbor Joining" can be used to construct the tree. To see a "TreeView", run a BLAST search from the NCBI BLAST page using the default 'pairwise' formatting option and click on the "TreeView" link on the results page. The NCBI BLAST page is found at: http://www.ncbi.nlm.nih.gov/BLAST/

For a fun sample sequence to BLAST, see http://blog.lib.umn.edu/messn006/blastit/

While BLAST results are highly heuristic and should not be construed to constitute an accurate sequence phylogeny, the graphic representation provided by TreeView may be helpful in analyzing similarity patterns in one's BLAST results.

Last Chance to Register for NCBI Field Guide, June 8-9

Just a reminder that the NCBI Field Guide, a short course taught by bioinformatics help staff at NCBI, will be held at the U of M next Thursday and Friday, June 8-9. Please let grad students and others who may be interested know. Registrations will be accepted through Tuesday June 6. Complete details on the course and registration are available at http://www.biomed.lib.umn.edu/services/instruction/ncbifieldguide

Related, the Mayo Clinic is hosting a longer, two full day version of the NCBI course, called "Field Guide Plus" on July 6-7. Space is limited, but they have kindly offered to host some participants from U of M. If you would be interested in travelling to Rochester for the Field Guide Plus course, please drop me a line at messn006@umn.edu. See further details on the Field Guide Plus course below.

CLASS DETAILS
Title: Field Guide Plus
Date: July 6th - 7th, 2006
Time: 8:00 AM - 4:00 PM
Location: Charter House, room 1-160/162
Instructors: NCBI Staff
Prerequisites: Basic molecular biology
Description:
This course is intended for biologists who desire more detailed coverage of NCBI molecular databases and tools. The focus will be on effective use of the Entrez system and sequence similarity searching with NCBI BLAST. The course will give special emphasis to genomic information and molecular structures. The hands-on portions are more extensive and incorporate the "Exploring 3D Molecular structures" and "Identification of Disease Genes" courses.

SCHEDULE

Day 1: July 6th
AM Session
* 8:00 NCBI Databases and ENTREZ
* 9:00 BREAK
* 9:15 Hands-on ENTREZ Practice
* 11:30 LUNCH (on your own)
PM Session
* 12:30 NCBI Web BLAST
* 1:15 Alternatives to BLAST
* 2:00 BREAK
* 2:15 Hands-on BLAST Practice

Day 2: July 7th
AM Session
* 8:00 NCBI Structures - Part 1
* 8:45 Hands-on Structures Practice 1
* 9:30 BREAK
* 9:45 NCBI Structures - Part 2
* 10:30 Hands-on Structures Practice 2
* 11:30 LUNCH (on your own)
PM Session
* 12:30 Identification of Disease Genes
* 2:00 Hands-on Disease Genes Practice
* 3:00 BREAK
* 3:15 Additional Hands-on Practice

This Week's University Libraries Update for the Molecular Biosciences

This update is being sent to members of the Depts of BMBB, GCD, Microbiology, Neuroscience, Pharmacology, and Physiology. Anyone is welcome to sign up to receive the update -- please email me at messn006@umn.edu.

1) NCBI Field Guide Coming to Campus June 8-9:
http://blog.lib.umn.edu/messn006/molbiolibrary/046020.html

2) Trial Subscription for Faculty of 1000 Biology, Medicine Underway:
http://blog.lib.umn.edu/messn006/molbiolibrary/045924.html

NCBI Field Guide Coming to Campus June 8-9

Please help spread the word! On Thursday June 8 – Friday June 9, the Bio-Medical Library is sponsoring a short course, including a hands-on workshop, taught by bioinformatics specialists with the NCBI User Services staff. The course, “NCBI Field Guide to GenBank and Molecular Biology Resources,�? discusses effective use of tools including the Entrez databases and search service, the BLAST similarity search engine, genome data, Map Viewer, NCBI’s structure visualization software, and the conserved domain database.

The course consists of a 3 hour lecture the morning of June 8, followed by a 2 hour hands-on computer workshop, several duplicate sessions of which will be held the afternoon of June 8 and all day June 9.

Registration for the workshop will open on Monday, May 15, and is required. Please note that seating is limited, and registrations will be handled on a first-come, first-served basis. Please visit http://www.biomed.lib.umn.edu/services/instruction/ncbifieldguide for more information on the course and complete registration information.

Trial Subscription for Faculty of 1000 Biology, Medicine Underway

The Libraries are currently conducting a trial of BioMedCentral’s "Faculty of 1000 Biology" and "Faculty of 1000 Medicine" products. These literature tools "highlight and review the most interesting papers published in the biological sciences and medicine, based on the recommendations of a faculty of well over 1000 selected leading researchers in each field." Currently 24 U of M faculty are F1000 reviewers. The trials are available at www.f1000biology.com and www.f1000medicine.com through June 8.

Current users have found the Faculty of 1000 products useful in prioritizing their reading of the literature, particularly researchers entering interdisciplinary areas where they may be less familiar with "what’s important" in the crossover field. The products can also be a valuable tool in graduate and undergraduate education, helping to steer students towards high quality and/or novel articles for journal club presentations, class research papers, and other needs. The reviewer comments can also be helpful in demonstrating the peer review process, traditionally out of view of students and trainee scientists until they author papers.

In addition to searching for articles on the F1000 web sites, PubMed can now be set up to activate F1000 linkouts for articles which have been reviewed by F1000. For example, see this sample record. Use this link to PubMed to activate the F1000 links during your search session: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?otool=umnbmlib&holding=f1000

Please take a look at www.f1000biology.com and www.f1000medicine.com from on campus, and let us know what you think. Comments can be submitted to Kevin Messner at messn006@umn.edu.

(One access caveat – there have been some troubles accessing our trial of F1000 through a VPN over U of M wireless. Certainly this is something that would be hammered out if we purchase the product; for now, though, you may save yourself some trouble by accessing the trial site over a hard line on campus.)