Table of Contents - Eccles Health Sciences LibraryMLA Releases Web-based Health Information Literacy Tutorial Introducing Todd Vandenbark Welcome Kathleen Amos Cool Tools -- Gliffy

Table of Contents

From the Director - Welcome!

Jean P. Shipman

Library Champion -- Grant W. Cannon

Medical Library Association Awards Given to Directors

Looking Up - Ceiling Project Planned for Eccles Library

MLA Releases Web-based Health Information Literacy Tutorial

Introducing Todd Vandenbark

Welcome Kathleen Amos

Cool Tools -- Gliffy

Todd Vandenbark

Tools for Data Mining

New Resources Available for Scholarly Research

Wimba Virtual Consultation with a Health Sciences Librarian

Open Access Week: Expanding Research and Increasing Impact

J. Williard Marriott Library Rededication!

Farmers Market Comes to the Health Sciences

4/19/2015 Shipman

http://ojs.med.utah.edu/index.php/esynapse/rt/printerFriendly/93/164 1/1

Jean P. Shipman, Director,Eccles Health SciencesLibrary

eSynapse, Vol 24, No 3 (2009)

From the Director -- Welcome!

A lot of things in life are cyclic and this time of year,I reflect on the start of another fall and the return ofstudents to campus. We at the Spencer S. EcclesHealth Sciences Library welcome you to enjoyanother year of learning and intellectual adventure!We encourage you to stretch your imagination andto challenge yourself to approach your learning innew ways!

We will be doing the same this year ourselves, aswe embrace a renovation of our ceiling andinstallation of a safety sprinkler system. In order toreduce costs, acquire faster networking, andachieve complete removal of asbestos from ourceiling, we will be closing the physical librarybuilding for a period of time this year. That does notmean however that the library will be unavailable to

you. Instead it means that we will be offering services in creative ways,mostly virtually, so that you will still be able to easily ask questions, gethelp with your research, and order materials from our collection as well asmany other libraries across the country.

We will be distributing staff throughout the campus as well to be better ableto assist you when needed. And yes, we will still be offering terrific classes,lectures and seminars to inform you of ways to use new and existing tools,resources, and technology.

Will this be a challenge - you bet! But one that is going to enable us toreally understand your information needs as well as what services andresources you rely upon to accomplish your learning, research, and patientcare. Watch our website for construction details as they unfold and do enjoythe beginning of a new academic year!

We welcome you and look forward to working with you in the coming year!

JPS-August 16,2009

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Grant W. Cannon, M.D.,FACP, FACR


Library Champion -- Grant W. Cannon

The Spencer S. Eccles Health Sciences Librarysalutes our Library Champions. This month wefeature Grant W. Cannon, M.D., FACP, FACR. Dr.Canon has appointments at both the University ofUtah and the VA Medical Center in Salt Lake City. Atthe George E. Wahlen VA Medical Center Dr. Cannonis the Associate Chief of Staff for AcademicAffiliations; at the University of Utah he is aProfessor of Medicine and the Thomas E. andRebecca D. Jeremy Presidential and Endowed Chairfor Arthritis Research, in the Division ofRheumatology, Department of Internal Medicine andSchool of Medicine. Dr. Cannon graduated from theUniversity of Utah School of Medicine in 1979 anddid his residency and fellowship training here as

well.

We asked Dr. Cannon to tell us, in his own words, why he is an EcclesLibrary Champion.

Tell us why the Eccles Library is your best friend.Throughout my career, first as a medical student and then as a clinician andresearcher, the Eccles Library has been there with the resources andservices that I need. The library compliments the work I do but also fills aspecial niche. It's not just about literature searching and access to journalarticles, but also teaching and information management. The library facultyand staff have helped me learn to use WebCT for course presentation,taught me EndNote, provided student materials, placed readings and examson electronic reserves, and planned, developed and taught courses for themedical students.

Why do you support the library?I support the library because they support me. The library faculty and staffare committed to providing a range of information services and resourcesthat help me get my job done.

How has the library helped you do your job?First, the library has provided information support for my various researchendeavors. If they don't have a journal article I need, they will get it for methrough the Interlibrary Loan service. In addition, the library faculty haveworked closely with me to develop informatics instruction for the third year



medical student during the OB/GYN and Pediatric rotations. Library facultyhave helped plan, develop, implement, teach and evaluate these importantsessions that have the goal to help the students become life-long learners.By helping the students, the library faculty have helped me help thestudents become successful users of information resources and services.

What are the top three library services you use?

1. Library faculty and staff as instructors.2. Electronic reserve.3. On-line examinations.

What will the library look like in the near and distant future? The library of the future will provide a virtual consulting service withresources to provide real time on-site information needs. When I firststarted to use the library in the mid-1970's it was all about books andfinding the books and journals I needed; I spent hours in front of the printIndex Medicus trying to locate journal articles of interest. Now the library isabout providing access to information online. I can locate the information Ineed without leaving my office or by using my home computer or PDA. Thelibrary of the future will be more about information access and providingconsultations. You don't necessarily need a big physical space for thelibrary; you just need a computer with remote access to library subscriptionresources to locate the information you need now.

How do you describe the Eccles Library to others?The library is a wonderful resource with dedicated staff who can help youmeet your objectives related to clinical care, research, and education.Library faculty and staff quickly respond to requests for the purchase or loanof materials, teach classes like EndNote, PowerPoint and Photoshop, and canhelp you develop curriculum integrated training programs. The librarymanages the Health Sciences Education Building and while there is alogistical component to running the building, it meshes quite nicely withlibrary services and teaching. One example is the Audience ResponseSystem (the clickers). The tech support team ensures that the software andthe receivers operate as they should in the individual classrooms; while thestaff provides instruction on how to create a polling slide and use thegathered statistics.

What information seeking/using advice would you offer to today'shealth sciences students?Get to know library faculty and staff by name! Get them to help younavigate the information maze. Libraries are more than just books; they canhelp you learn about appropriate technologies and tools that will make yourtime in school more efficient and productive.

What's the best information advice you ever got?"It's only money." If you want to do something that requires an expenditureof monies you don't have, don't let that stop you. There are teaching grants,technology grants and folks out there who can help you get the money youneed to do the project you want to do. In working with the library faculty to



incorporate the use of PDAs into the 3rd year Pediatrics rotation, we wereable to find the funding we needed to purchase 20 devices and software. Besure to talk to the people and experts who can move your ideas fromconcept to reality.

What do you do for fun? Spend time with my family, plan vacations, and take vacations. Always havea vacation planned.

Grant and Sandra Cannon on vacation.

GC/JML August 16, 2009



Jean P. Shipman, Director Eccles Health SciencesLibrary


Medical Library Association Awards Given to Directors

The faculty and staff of the Spencer S. Eccles Health Sciences Library arepleased to announce that two prestigious awards were given to both thecurrent Library Director, Jean P. Shipman and Emeritus Director Wayne J.Peay at the Medical Library Association annual meeting, May 18, 2009 inHonolulu, Hawai'i.

Jean Shipman received the MLA Fellows Awardfrom the Board of Directors in recognition of hernotable leadership, outstanding achievement,significant scholarship and professional reputation.Jean was president of the Medical LibraryAssociation in 2006-2007, a member of the MLABoard of Directors from 1999-2002, a DistinguishedMember of the Academy of Health InformationProfessionals and has long served the association inmany capacities. She is particularly noted for herrole in health information literacy and is the co-principle investigator for MLA's recently completedHealth Information Literacy Research Project.

Jean has also been awarded Honorarymembership in the Southern Chapter of theMedical Library Association which will be

presented at the Annual meeting in Memphis, TN.

Jean has presented over 50 papers and presentations all over the countryand will be travelling to Milan this month to present a paper entitledTeachers of Health Information Literacy - Future roles for librarians assupported by the Medical Library Association/National Library of Medicine'sHealth Information Literacy Research Project Jean P. Shipman (University ofUtah, Salt Lake City, USA) and Carla Funk (Medical Library Association,U.S.A.)

Wayne Peay was awarded the Marcia C. Noyes Award, the highestprofessional distinction of the Medical Library Association. The award wasestablished in 1947, recognizing a career that has resulted in lasting,outstanding contributions to the field of health sciences librarianship. Waynewas named a Fellow in MLA in 2000 and was asked to deliver theassociation's Janet Doe lecture in 1998. He served on the MLA Board ofDirectors, as president of the Association of Academic Health SciencesLibraries, and was elected as Fellow of the American College of Medical



Wayne J. Peay Emeritus DirectorEccles Health SciencesLibrary

Informatics. From his earliest days as a librarian,Wayne has promoted the use of technology inlibraries and been viewed as an innovator of newand creative ideas. An introduction of Wayne as hereceived this award can be found on YouTube.

JMS-8/17/09



Todd Vandenbark, Web ServicesLibrarian.

Twitter logo.

Twitter logo.


No Hard Hat Required: Keeping Current during Library CeilingProject

As the semester winds down the Spencer S.Eccles Health Sciences Library Ceiling Projectis ramping up. Books have been moved tothe lower level while library staff membersare being relocated to adjacent buildings. Asthe date for closing the building approacheshow is one to keep track of all the changes?In addition to posting large colorful signsaround the library we are leveraging thepower of Web 2.0 applications to make up-to-date information available to you online.

Eccles Library has recently begun hosting itsown blogging service using the free, open-source software Wordpress MU. A blog (which

is a contracted version of the earlier term weblog) is a kind of website withregular entries that are typically listed in reverse-chronological order. Theentries are often news or commentary in nature and can include othermedia such as images, audio and video. To blog or blogging refers to the actof writing for and maintaining a blog, and a single entry is a blog post. Manyblogs allow followers (readers) to comment on its content, creating a dialogbetween author and audience. The entire collection of blogs on the Internetis often referred to as the blogosphere.

Eccles Library has created two blogs to provide patrons and fans withcurrent information. The first, EHSLibrary, is the general news andinformation source for the library. The second, Eccles Library Ceiling Project,was created to provide up-to-date information on our current renovationsand their effects on service. Generally both blogs are updated 1-2 times perweek and include pictures and other media of interest whenever available.Comments are welcome and moderated for inappropriate content.

A recent change to blogging is the advent of micro-blogs, themost popular and familiar form being Twitter. These blogsallow the user to post short updates of 140 characters or lessas well as pictures, audio clips, etc. Both kinds of blogs can beopen to anyone or restricted to a certain group as determinedby the owner of the blog. An update or post on Twitter isreferred to as a tweet; the act of writing tweets is referred to

as twittering, and a particular micro-blog is referred to as a feed. Eccles



Facebook logo

Facebook logo.

Library has a Twitter feed called EHSLibrary, which is updated as often asthe EHSLibrary blog.

Eccles Library also has a presence on Facebook, themost popular social-networking site on the Web.Part of the power of Web 2.0 applications isdemonstrated in how these tools work togethercreating networks of information. For example,using two free Web 2.0 applications, HootSuite and

Ping.fm, when a post is added to the Eccles Library blog (EHSLibrary) it isautomatically posted on the library's Facebook page, and to the library'sTwitter feed (EHSLibrary). So no matter which social media our patronsprefer Eccles Library has a presence in it.

For more information on social networking software contact ToddVandenbark; 801-581-5263.

Ceiling Project Flickr Slideshow by Todd Vandenbark

TV-Dec 3, 2009



MLA Health InformationLiteracy Logo


MLA Releases Web-based Health Information Literacy Tutorial

The Medical Library Association (MLA) is happy toannounce the availability of a new free, web-basedhealth information literacy tutorial, Prescription forInformation: Addressing Health InformationLiteracy. The Prescription for Information tutorial isfor health care professionals and emphasizes theimportance of health literacy and the challengespatients face with understanding medicalterminology. The tutorial also helps participantsrecognize the impact that low health literacy has onpatient care and learn about quality healthinformation resources and strategies available to

them and their patients. It also describes health literacy services providedby medical librarians.

The Prescription for Information tutorial, developed by Gail Kouame,consumer health coordinator, National Network of Libraries of Medicine,Pacific Northwest Region, University of Washington-Seattle, is based onPutting Information into Health Literacy: The Health Information LiteracyCurriculum, developed by Sabrina Kurtz-Rossi on behalf of MLA. Both thetutorial and health information literacy curriculum were produced as part ofMLA's Health Information Literacy Research Project, funded under NationalLibrary of Medicine (NLM) contract HHSN276200663511/NO1-LM-6-3511,with co-principal investigators Jean P. Shipman, AHIP, FMLA, and Carla J.Funk, CAE. The curriculum was developed with input from more than 1,100health professionals in the United States and Canada, who found the contentof the session useful to their practices.

The free tutorial and two versions of the mediated curriculum are availableon MLA's Health Information Literacy site.

The Medical Library Association, a professional nonprofit educationalorganization, comprises health sciences information professionals with morethan 4,000 members worldwide. Through its programs and services, MLAprovides lifelong educational opportunities, supports a knowledgebase ofhealth information research, and works with a global network of partners topromote the importance of quality information for improved health to thehealth care community and the public.



JPS- August 7, 2009



Todd Vandenbark, Web Services Librarian


Introducing . . . Todd Vandenbark

Todd Vandenbark began serving as theSpencer S. Eccles Health Sciences LibraryWeb Services Librarian on July 22, 2009. Hisrole will be to lead the library's effort todevelop a state-of-the-art web presence thatresponds effectively to the needs of itspatrons and communities. He will also assistwith the library's educational programs bydeveloping classes on new Web technologiesand teaching curriculum-integrated courses,as well as providing reference services tolibrary patrons.

Todd began his association with libraries byserving as a student volunteer at his junior

high and high school libraries. He went on to work in a variety ofemployment settings after college: lifeguard, daycare teacher, researchassistant, school bus driver, data entry, martial arts instructor, telecomcustomer service rep, webmaster and Keebler elf. Most recently, Toddworked as a part-time temporary Special Projects Developer at Ball StateUniversity Libraries in Muncie, Indiana.

Todd received his B.A. in Psychology from Luther College in Decorah, Iowa,followed by extensive coursework in Early Childhood Education at theUniversity of Minnesota, Minneapolis campus. He received his Masters ofLibrary Science and Technology Management at the School of Library andInformation Science, Indiana University, Indianapolis campus, in May 2009,where he also worked as a Graduate Assistant on the Shaping OutcomesProject managing their website and providing technical support toinstructors and participants.

Besides spending time with his wife, Marie, and two daughters (Alissa, age9, and Sonia, age 18), Todd enjoys reading, swimming, biking, hiking,camping, playing folk and children's music and storytelling.

TV - August 7, 2009



Kathleen Amos, NLM Fellow


Welcome Kathleen Amos!

Welcome to Kathleen Amos, who started with theSpencer S. Eccles Health Sciences Library at the end ofAugust 2009 as a second year National Library ofMedicine (NLM) Associate Fellow. Ms. Amos spent ayear as a fellow at NLM in Bethesda, MD, and with asecond year award, she will have the opportunity towork with the Eccles Library staff to learn more abouthow our health sciences library operates and how wepartner with our campus and communityconstituencies. Ms. Amos is one of three NLM first yearfellows to have this second year opportunity.

Ms. Amos brings a lot of experience to her fellowship. She "received herMLIS in May 2008 from Dalhousie University in Halifax, Nova Scotia and alsoholds a BA in Sociology and Social Anthropology from Dalhousie. She hasexperience in cataloging and database management as a student assistantin an academic library, as well as varied practicum experience in the HealthSciences Library and the Family Resource Library of the Izaak Walton KillamHealth Centre. She has been involved as a volunteer with a patient recorddatabase at the Maritime Medical Genetics Service and served as theSecretary for the Dalhousie University Student Chapter of the CanadianLibrary Association" [from NLM website].

Please join us in welcoming Ms. Amos to the University of Utah!

JPS-August 7, 2009

4/19/2015 Vandenbark


Gliffy Logo


Cool Tools - Gliffy

While many people are familiar with the mostpopular Web 2.0 applications such as Wikipediaand Facebook, there are a number of free anduseful tools available for creating professional-looking projects. Gliffy is an onlinediagramming software package that allows

users to quickly and easily "create professional-looking flowcharts,diagrams, floor plans, technical drawings, and more." It is also a great wayto quickly create website maps, diagram entity relationships, and developprototype user interfaces. Users can share, print, or export any diagramcreated for use elsewhere. If you can click-and-drag using your computermouse, and type a few letters, you can use Gliffy.

To get started, sign up at the Gliffy home page. Gliffy offers two types ofaccounts - free and premium. When you first sign up for an account you geta free 30-day trial at the premium level. This reverts to a free basic accountlevel unless you pay a quarterly subscription fee. As Gliffy is web-based,there is no software to install, and it is compatible with both Windows andMac platforms, as well as all major Web browsers.

Drag-and-drop shapes from Gliffy's extensive library to create a diagram.Click and drag to connect shapes with lines that shift and adjust as youmove the shapes around. Add text inside shapes, labels outside shapes, anduse color to distinguish and clarify different portions of the drawing. You caneven upload images (up to 2 MB) to use in the diagrams. Gliffy allows usersto collaboratively edit drawings by emailing a link to colleagues. Oncefinished, drawings can be published on the Web or exported in variousgraphic formats (JPEG, SVG, or PNG). Gliffy does add its logo and anadvertising tag line to the bottom of each exported image, but these areeasily removed using image-editing software such as Adobe Photoshop,Fireworks, Gimp, Image Well, OpenOffice Draw and others.

Gliffy feature summary:

Basic account: free with a limit of 20 MB image uploadsPremium account: $5/month, paid quarterly; multi-user and

institutional subscriptions available; ad-freeUnlimited number of drawings allowed at both levelsForum and online help featuresRevision control

4/19/2015 Vandenbark


Export diagrams as imagesPublish diagrams to blogs and websites

Giffy screen shot.

Cool Tools Disclaimer: The user assumes full responsibility for use ofapplications or technology.

TV-August 16, 2009



NCBI logo.


Tools for Data Mining

According to the May 2009 issue of the AAMCReporter, March 9, 2009 marked the day PresidentObama overturned the federal ban on embryonic stemcell research. With this announcement it is anticipatedthere will be an increase in this area of research.

Academic institutions will be playing an enormous role as research centersacross the U.S. prepare to request federal funds.

The Spencer S. Eccles Health Sciences Library views this as an opportunityto promote the many online databases, tools and utilities from the NationalCenter for Biotechnology Information (NCBI) that exist to supportresearchers who need data to better understand the molecular processesaffecting human health and disease.

An annotated list of the NCBI online databases, tools and utilities follows.These NCBI resources are freely available to anyone with access to theInternet. The NCBI Tools for Data Mining website presents six categories ofinterest:

1. Nucleotide Sequence Analysis2. Protein Sequence Analysis and Proteomics3. Structures4. Genome Analysis5. Gene Expression6. Tools for Programmers

If you have any questions about these databases, please contact Jeanne LeBer (801-585-6744), Education and Research Librarian at the Eccles Libraryfor more information.

1. Nucleotide Sequence AnalysisThe Basic Local Alignment Search Tool (BLAST) for comparing gene

and protein sequences against others in public databases now comesin several types including PSI-BLAST, PHI-BLAST, and BLAST 2sequences. Specialized BLASTs are also available for human,microbial, malaria, and other genomes, as well as for vectorcontamination, immunoglobulins, and tentative human consensussequences.

Electronic PCR - allows you to search your DNA sequence forsequence tagged sites (STSs) that have been used as landmarks invarious types of genomic maps. It compares the query sequence



against data in NCBI's UniSTS, a unified, non-redundant view of STSsfrom a wide range of sources.

Entrez Gene - each Entrez Gene record encapsulates a wide range ofinformation for a given gene and organism. When possible, theinformation includes results of analyses that have been done on thesequence data. The amount and type of information presented dependon what is available for a particular gene and organism and caninclude: (1) graphic summary of the genomic context, intron/exonstructure, and flanking genes, (2) link to a graphic view of the mRNAsequence, which in turn shows biological features such as CDS, SNPs,etc., (3) links to gene ontology and phenotypic information, (4) linksto corresponding protein sequence data and conserved domains, (5)links to related resources, such as mutation databases. Entrez Gene isa successor to LocusLink.

Model Maker - allows you to view the evidence (mRNAs, ESTs, andgene predictions) that was aligned to assembled genomic sequence tobuild a gene model and to edit the model by selecting or removingputative exons. You can then view the mRNA sequence and potentialORFs for the edited model and save the mRNA sequence data for usein other programs. Model Maker is accessible from sequence mapsthat were analyzed at NCBI and displayed in Map Viewer.

ORF Finder - identifies all possible ORFs in a DNA sequence bylocating the standard and alternative stop and start codons. Thededuced amino acid sequences can then be used to BLAST againstGenBank. ORF finder is also packaged in the sequence submissionsoftware Sequin.

Organism Specific Resources - Bee, Cat, Chicken, Cow, etc.SAGEmap - provides a tool for performing statistical tests designed

specifically for differential-type analyses of SAGE (Serial Analysis ofGene Expression) data. The data include SAGE libraries generated byindividual labs as well as those generated by the Cancer GenomeAnatomy Project (CGAP), which have been submitted to GeneExpression Omnibus (GEO). Gene expression profiles that comparethe expression in different SAGE libraries are also available on theEntrez GEO Profiles pages. It is possible to enter a query sequence inthe SAGEmap resource to determine what SAGE tags are in thesequence, then map to associated SAGEtag records and view theexpression of those tags in different CGAP SAGE libraries.

Spidey - aligns one or more mRNA sequences to a single genomicsequence. Spidey will try to determine the exon/intron structure,returning one or more models of the genomic structure, including thegenomic/mRNA alignments for each exon.

Splign - is a utility for computing cDNA-to-Genomic alignmentsbased on a variation of the Needleman-Wunsch algorithm combinedwith Blast for compartment detection and greater performance.

VecScreen - a tool for identifying segments of a nucleic acidsequence that may be of vector, linker, or adapter origin prior tosequence analysis or submission. VecScreen was developed to combatthe problem of vector contamination in public sequence databases.

Viral Genotyping Tool - a web-based program that identifies thegenotype (or subtype) of recombinant or non-recombinant viralnucleotide sequences. It works by using BLAST to compare a querysequence to a set of reference sequences for known genotypes.Predefined reference genotypes exist for three major viral pathogens:



human immunodeficiency virus 1 (HIV-1), hepatitis C virus (HCV) andhepatitis B virus (HBV), as well as for poliovirus. User-definedreference sequences can be used at the same time. The querysequence is broken into segments for comparison to the reference sothat the mosaic organization of recombinant sequences is revealed.The results are displayed graphically using color-coded genotypes.Therefore, the genotype(s) of any portion of the query can quickly bedetermined.

2. Protein Sequence Analysis and ProteomicsThe Basic Local Alignment Search Tool (BLAST) for comparing gene

and protein sequences against others in public databases, now comesin several types including PSI-BLAST, PHI-BLAST, and BLAST 2sequences. Specialized BLASTs are also available for human,microbial, malaria, and other genomes, as well as for vectorcontamination, immunoglobulins, and tentative human consensussequences.

BLink - ("BLAST Link") displays the results of BLAST searches thathave been done for every protein sequence in the Entrez Proteins datadomain.

CD Search - search the Conserved Domain Database with ReversePosition Specific BLAST.

CDART - when given a protein query sequence, CDART displays thefunctional domains that make up the protein and lists proteins withsimilar domain architectures.

Open Mass Spectrometry Search Algorithm (OMSSA) - The OMSSAsearch service allows proteomics researchers to submit the massspectra of peptides and proteins for identification. OMSSA thencompares these mass spectra to theoretical ions generated from datalibraries of known protein sequences and ranks the results using ascore derived from classical hypothesis testing.

TaxPlot - a tool for 3-way comparisons of genomes on the basis ofthe protein sequences they encode. To use TaxPlot, one selects areference genome to which two other genomes are compared. Pre-computed BLAST results are then used to plot a point for eachpredicted protein in the reference genome, based on the bestalignment with proteins in each of the two genomes being compared.

3. StructuresCn3D - Cn3D is a helper application for your web browser that

allows you to view 3-dimensional structures from NCBI's Entrezretrieval service. Cn3D runs on Windows, Macintosh, and Unix.

VAST Search - VAST Search is NCBI's structure-structure similaritysearch service. It compares 3D coordinates of a newly determinedprotein structure to those in the MMDB/PDB database.

CD Search - search the Conserved Domain Database with ReversePosition Specific BLAST.

4. Genome AnalysisEntrez Genomes - whole genomes of over 1000 organisms. The

genomes represent both completely sequenced organisms and thosefor which sequencing is in progress. All three main domains of life -bacteria, archaea, and eukaryota - are represented, as well as manyviruses, phages, viroids, plasmids, and organelles.. Entrez Genomesprovides graphical overviews of complete genomes/chromosomes and



the ability to explore regions of interest in progressively greater detail.COGs - Clusters of Orthologous Groups - a natural system of gene

families from complete genomes. Clusters of Orthologous Groups(COGs) were delineated by comparing protein sequences encoded in43 complete genomes, representing 30 major phylogenetic lineages.Each COG consists of individual proteins or groups of paralogs from atleast 3 lineages and thus corresponds to an ancient conserveddomain.

Map Viewer - shows integrated views of chromosome maps formany organisms, including human and numerous other vertebrates,invertebrates, fungi, protozoa, and plants. Map Viewer is used to viewassembled genomes (either draft or complete) and is a valuable toolfor the identification and localization of genes and other biologicalfeatures. Multiple map displays are aligned based on shared markerand gene names when available, and sequence map displays arebased on a common sequence coordinate system. Sequence data forchromosome regions of interest can be downloaded, biologicalannotations can be viewed in graphical format and/or downloaded intabular format, and gene models can be manipulated in the associatedModelMaker tool.

SKY/M-FISH & CGH Database - The NCI and NCBI SKY/M-FISH andCGH Database is a repository of publicly submitted data from SpectralKaryotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH), and Comparative Genomic Hybridization (CGH), which arecomplementary fluorescent molecular cytogenetic techniques. SKY/M-FISH permits the simultaneous visualization of each human or mousechromosome in a different color, facilitating the identification ofchromosomal aberrations; CGH can be used to generate a map ofDNA copy number changes in tumor genomes. Collaborative projectwith the National Cancer Institute. ( data submission instructions...)

5. Tools - Gene ExpressionGEO Gene Expression Omnibus - The Gene Expression Omnibus

(GEO) provides several tools to assist with the visualization andexploration of GEO data. Datasets may be viewed as hierarchicalcluster heat maps, providing insight into the relationships betweensamples and co-regulated genes. Individual gene expression profilesshowing significant differences between experimental subsets may belocated using average subset rank value comparisons. Related geneexpression profiles may be identified on the basis of sequencesimilarity, profile similarity, or homology. Indicators of datasetnormalization quality are provided as distribution graphs, and byflagging outliers. Links to other NCBI sequence, mapping andpublication database resources are provided where possible.

SAGEmap -provides a tool for performing statistical tests designedspecifically for differential-type analyses of SAGE (Serial Analysis ofGene Expression) data. The data include SAGE libraries generated byindividual labs as well as those generated by the Cancer GenomeAnatomy Project (CGAP), which have been submitted to GeneExpression Omnibus (GEO). Gene expression profiles that comparethe expression in different SAGE libraries are also available on theEntrez GEO Profiles pages. It is possible to enter a query sequence inthe SAGEmap resource to determine what SAGE tags are in thesequence, then map to associated SAGEtag records and view theexpression of those tags in different CGAP SAGE libraries.



The Cancer Genome Anatomy Project (CGAP) - aims to decipher themolecular anatomy of cancer cells. CGAP develops profiles of cancercells by comparing gene expression in normal, precancerous, andmalignant cells from a wide variety of tissues.

UniGene DDD - Digital Differential Display - an online tool tocompare computed gene expression profiles between selected cDNAlibraries. Using a statistical test, genes whose expression levels differsignificantly from one tissue to the next are identified and shown tothe user. Additional information about UniGene is above, including alist of organisms represented.

6. Tools for ProgrammersEntrez Programming Utilities - E-Utilities are a set of programs that

provide a stable interface into the Entrez retrieval system. The eUtilsuse a fixed URL syntax that translates a standard set of inputparameters into values necessary for various NCBI softwarecomponents to search for and retrieve data from 23 Entrez databases.

Information Engineering Branch - IEB is responsible for developingNCBI's resources and databases. Access is provided to documentation,access to NCBI software tools and libraries, and announcements.

JB-August 16, 2009




New Resources Available for Scholarly Research

The Libraries at the University of Utah have recently subscribed to a numberof new resources for scholarly research. The following resources will be ofparticular interest to the Health Sciences Center campus.

JAMA and Archives BackfilesThe University of Utah community now has online access to the AmericanMedical Association's journals including JAMA and the Archives journalsdating back to 1883. The JAMA&Archives Backfiles include the following:

JAMA 1883-presentArchives of Dermatology 1920-presentArchives of Family Medicine 1992-2000Archives of General Psychiatry 1959-presentArchives of Internal Medicine 1908-presentArchives of Neurology 1959-presentArchives of Neurology & Psychiatry 1919-presentArchives of Pediatrics & Adolescent Medicine 1911-present

(formerly American Journal of Diseases of Children)Archives of Ophthalmology 1929-presentArchives of Otolaryngology-Head & Neck Surgery 1925-presentArchives of Surgery 1920-present

ScopusCourtesy of the J. Willard Marriott Library, the University of Utah communitycan search Scopus, "the largest abstract and citation database of researchliterature and quality web sources" covering scientific, medical and technicalinformation. "Updated daily, Scopus covers 29 million abstracts of over15,000 peer-reviewed titles from more than 4,000 publishers, 265 millionreferences, [23 million patent records from 5 patent offices] and 265 millionquality web pages through Scirus' web search to cover the scientific web"from 1996 to the present.

In addition to finding scholarly literature, "use the Journal Analyzer tocompare up to 10 Scopus sources on a variety of parameters such as thetotal number of citations, articles published, percentage of articles not cited,and trend line." Use the Citation Tracker to find out "how often articleshave been cited."

To learn more about searching Scopus check out their online tutorials orcheck the Eccles Library Workshops @ the Library page for training sessions.



Note: Web of Science (Science Citation) will no longer be available afterDecember 2009.

For more information about these new resources, contact Reference; 801-581-5534

MMM-Aug 17, 2009




Wimba Virtual Consultation with a Health Sciences Librarian

Consult with a health sciences librarian from theease and comfort of your computer. Need assistancewith searching PubMed or developing effectivesearch strategies? Want to know more aboutScopus? The Spencer S. Eccles Health Sciences

Librarians are offering virtual consultation to the University of Utah campususing Wimba, a virtual meeting environment. Wimba allows online sharingof video, audio, desktop, websites, presentation slides, documents,whiteboard, and chat. Think of Wimba as an alternative consultation andinstruction space.

Visit our Ask A Librarian page to schedule a virtual Web consultation with ahealth sciences librarian.

University of Utah staff and faculty can activate their own Wimba room viathe Campus Information System. You do not need to activate your ownWimba Room to take advantage of the library's Virtual Consult service. Seethe Technology Assisted Curriculum Center's (TACC) website for moreinformation about Wimba.

MMM-Aug 17, 2009



Open Access logo.


Open Access Week: Expanding Research and Increasing Impact

Sponsored by the J. Willard Marriott Library at theUniversity of Utah, Open Access Week featuresnational leaders and local experts addressing themany issues related to disseminating, accessing andre-using the results of scholarly and creativeresearch. Open Access Week 2009 is scheduled forOctober 19-23.

The keynote address will be given by distinguishedprofessor and noted author Dr. John Willinsky. Dr.Willinsky will discuss Openness and the Value ofLearning: The Intellectual Property Argument.(Monday, October 19 at 11:00 a.m. in the MarriottLibrary Gould Auditorium)

Among other events, Utah poet laureate Katherine Coles participates on apanel that addresses open access to poetry, fine arts, music andhumanities. (Thursday, October 22).

During Open Access Week, authors and creators can learn how to increaseinnovation by offering the path of least resistance to their work and gain theattention of readers, viewers and listeners. Administrators can learn waysfor the University to raise its profile and impact both funding levels andcommunity engagement. And all scholars can discover means for fosteringnew growth, advancing their discipline, and attracting new learners to theirarea of expertise.

For a list of events, dates, and times, visit the Open Access Week website.All events are free and open to the public.

If you have questions, contact Allyson Mower, Scholarly Communicationsand Copyright Librarian; 801-585-5458.

AM-JML August 16, 2009




J. Willard Marriott Library Rededication Planned!

On August 3, 2009 the west entrance of the J. Willard Marriott Libraryreopened, marking the completion of a four-year building-wide renovationproject. On the evening of October 2, 2009 the library will host a specialcelebration for University of Utah students, complete with a D.J., dancing,movies, and a burrito extravaganza. On October 26, 2009 the library will beformally rededicated with a program that includes an address by formerFirst Lady Laura Bush.

New spaces in the Marriott Library include the Grand Reading Room andadjoining Garden Terrace, which foster quiet study and reflection. TheKnowledge Commons, an information rich and technology-intensive studentcenter, embodies the integrated 21st century library. Mom's Café on levelone provides seating for 70. Other features include the AdvancedTechnology Studio to support digital scholarship, the Automated RetrievalCenter (ARC) for efficient robotic collection management, 20 high-techclassrooms, and state-of-the-art preservation facilities.

Watch for a full story about the Marriott Library renovation in the fall issueof Continuum.

For more information contact Mary Ross; 801-581-7791.

J. Willard Marriot Library at night.

MR-August 17, 2009



Farmers Market Graphic


Farmers Market Comes to the Health Sciences Campus

A mini version of the University of Utah FarmersMarket is coming to the Health Sciences campus onThursdays beginning August 20 through October 8,2009. The market will be open from 9:00 a.m. to 2:00p.m. Look for the booth on the plaza west of theSpencer F. and Cleone P. Eccles Health SciencesEducation Building. The market will offer a variety oflocal produce from Tagge's farms.

The Farmers Market is sponsored by numerouscampus groups: WellU, University Health Care, LowellBennion Community Service Center, Office of

Sustainability, and the Student Health Advisory Committee. The mission ofthe University's Farmers Market is "To enable students, faculty, staff, andthe surrounding community to purchase fresh, healthy, local produce andunique arts and crafts where they live, work and study; and to promote aculture of health, wellness, sustainability, and local economic development."

We are delighted to be a part of this fun and worthy effort - so bring yourrecycled shopping bag and plan to shop.

Photo's by Joan M. Gregory



JMS/JMG-August 16, 2009

Documents

Table of Contents - Eccles Health Sciences LibraryMLA Releases Web-based Health Information Literacy Tutorial Introducing Todd Vandenbark Welcome Kathleen Amos Cool Tools -- Gliffy