June 13, 2006

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) Upcoming Libraries Workshops:

2) "TreeView" of NCBI BLAST Results Now Available:

Posted by Kevin Messner at 1:06 PM

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 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

Posted by Kevin Messner at 11:47 AM

"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.

Posted by Kevin Messner at 10:18 AM

June 2, 2006

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.

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
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.


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

Posted by Kevin Messner at 8:07 AM