As part of the Bioinformatics@HSL workshop series, the Health Sciences Library is providing hands-on computer workshops  for the UCSC Genome Browser resource and a short course in NCBI BLAST during the Fall 2011 semester.

UCSC Genome Browser

The Health Sciences Library is hosting a FREE  full-day, hands-on UCSC Genome Browser workshop provided by OpenHelix instructors.  Registration is required. The workshop will be offered on the Buffalo Niagara Medical Campus, Sept. 21, 2011, and on the UB South campus,  Sept. 22. Topics covered include searching genomes via text or sequence, creating and manipulating the Browser’s multitude of “data tracks” ( e.g., variation and repeats, phenotypes and disease, mapping and sequencing), exporting and importing both public and user-generated data and much more. Read the full description and register for the workshop  here.

NCBI BLAST Short Course

A three-part, interactive  hands-on computer NCBI BLAST “short course”  will be offered on both the North and South campus in September 2011. The first workshop , BLAST, covers the fundamentals of the BLAST algorithm and the BLAST interface. The second workshop, Intermediate BLAST, concentrates to tailoring   and editing BLAST searches effectively to call-out only those sequences of interest. Topics covered will include working with short sequences, masking sequences, aligning sequences,and more. The third workshop, Advanced BLAST, covers three advanced BLAST strategies: PSI-BLAST, PHI-BLAST and augmenting BLAST searches with the simultaneous use of the Entrez search engine. Register for all three or just what you need. The instructional portion of the workshops run 2-2.5 hours with an additional 0.5-1.0 hours appended to each workshop to permit participants to practice with their own sequences. For full description and links to register, visit the Health Sciences Library workshops web page, scrolling to the Bioinformatics@HSL section.

It is often difficult to search for bioinformatics articles in literature databases. Authors typically use a wide range of different bioinformatics vocabulary terms to describe the same thing. If you are not using the exact same search term as an author, or are not familiar with the vocabulary of bioinformatics, you will not be able to retrieve many of the articles available to you from any given database.

The way around this problem is to switch to using Medical Subject Headings, or MeSH, as search terms. The varying terms for the same concept are collapsed into one single “controlled” MeSH search term.  When you search with any one of these varying terms, MeSH automatically compiles all the variant search terms and adds them to your results lists. The trick is knowing how to command the database to use MeSH and knowing which MeSH terms you should use for bioinformatics.

The UB Libraries subscribes to several literature databases which exclusively use MeSH. These are MEDLINE via OVID, MEDLINE via EBSCO, and CINAHL (nursing literature). In addition, the free PubMed database also has it available.

Visually described below is how to run a comprehensive search for bioinformatics in each of these databases using MeSH terms. You can use the exact same MeSH search string to retrieve bioinformatics articles from all four databases.

PUBMED

Copy/paste (without the quotes)  “computational biology[mesh] OR genomics[mesh] OR proteomics[mesh]” into the PubMed search box as follows.

In PubMed, anything in closed square brackets following a search term is a command. If you want to search only these terms in the title to the article,  type without the quotes “computational biology[title]“:

PUBMED

MEDLINE via OVID

Once you login to MedLine at UB Libraries , first click on the link for the “Multi-Field Search”, then input the search terms of computational biology, genomics and proteomics each into their own separate search box, and then configure the search interface as follows:

MEDLINE via OVID

MEDLINE via EBSCO

The UB Libraries version of the EBSCO interface of MedLine already opens to the multi-field search interface. Pulling down the  menu to specify the  “MH Exact Subject Heading” is the way you call for a MeSH search in the EBSCO interface.

CINAHL

Configuring a search for bioinformatics in CINAHL is similar to the MEDLINE interfaces. Leave the “suggest subject terms” unchecked because you specifying them in the “MH Exact Subject Heading”pull-down menu next to each search term:

CINAHL