Blogs

BIOBASE TRAINING WORKSHOP

16 April 2015 - 2:18pm by Rolando Garcia-Milian

Sponsored by the Cushing/Whitney Medical Library

Date & Time:    9:00am - 12:30pm, Friday, June 5, 2015
Location:    The Anlyan Center Auditorium (N 107), 300 Cedar Street New Haven, CT 06520
Campus:    Medical School
Presenter:    Dr. Alex Kaplun, Field Applications Scientist, BIOBASE
Registration:    Free and open to Yale affiliates – limited seating- REGISTER HERE

 
PROTEOME™’s powerful ontology search query system, with specialized tools for gene set analysis and pathway visualization, allows scientists to quickly find answers to questions relevant to their research. It works seamlessly with TRANSFAC®, an internationally unique knowledgebase containing data on eukaryotic transcription factors and miRNAs, their experimentally-proven binding sites, and regulated genes, which supports research into gene regulation. Based on TRANSFAC®'s broad compilation of binding sites, positional weight matrices are derived which can be used with the included Match tool to search DNA sequences for predicted transcription factor binding sites. TRANSFAC enables you to identify transcription factors affecting gene expression in your microarray and RNA-Seq experiments, as well as predict how they, in combination, can induce observed gene expression patterns.

In the PROTEOME™ section, the attendees will learn to:
1.    Search for individual gene, disease, and drug reports by name.
2.    Browse for sets of genes, diseases, and drugs which share a desired set of characteristics.
3.    Upload a list of genes and identify those characteristics which are statistically over-represented (NEW)
4.    Export annotated characteristics for a gene list.
5.    Visualize protein-protein networks, overlaid with disease and drug assignments
6.    Annotate custom sequences.

Network visualization using the BKL Pathfinder tool.

In the TRANSFAC section, the attendees will learn to:
1.    Search for individual transcription factors and miRNAs, their experimentally-characterized binding sites and regulated genes, and ChIP experiments.
2.    Create positional weight matrices of transcription factor binding sites using set of aligned experiment-derived sites.
3.    Predict transcription factor binding sites (single sites or combinations) within a promoter or DNA sequence.
4.    Analyze high-throughput data sets for models of transcription factor binding (NEW).
5.    Perform statistical analysis of your differential expression data to determine which transcription factors are responsible for the observed effect (NEW).
6.    Perform step-by-step comprehensive microarray and ChIP-seq data analysis in easy-to-use, guided workflows (NEW).

67th Annual Associates Lecture

25 March 2015 - 10:14am by Katie Hart

Please join us for the 67th annual lecture of the Cushing/Whitney Medical Library Associates on April 8, 2015 at 4pm in the Historical Medical Library. This year's speaker is Dr. Unni Karunakara, Senior Fellow, Jackson Institute for Global Affairs and Resident Fellow, Morse College, Yale University and past international president of Médecins Sans Frontières. Dr. Karunakara's lecture is entitled "Humanitarian Duties and Action."

 

National Center for Biotechnology Information workshops broadcasted from the University of Michigan Medical Center

20 March 2015 - 10:53am by Rolando Garcia-Milian

The Yale Medical Library will be hosting a National Center for Biotechnology Information workshop series (broadcasted from the University of Michigan Medical Center). Please register (next to each workshop title) since seating is limited

Navigating NCBI Molecular Data through the Integrated Entrez System and BLAST (May 5, 9:00am - 11:30am EDT) REGISTER HERE

Gene Expression Resources at the NCBI (May 5, 1:00pm - 3:30pm EDT) REGISTER HERE

Human Genes, Variation, and Medical Genetics Resources (May 6, 9:00am - 11:30am EDT) REGISTER HERE

NCBI Genomes, Assemblies and Annotation Products: Microbiome to Human (May 6, 1:00pm - 3:30pm EDT) REGISTER HERE

Each workshop consists of four 2.5-hour hands-on sessions emphasizing a different set of NCBI resources. Each session uses specific examples to highlight important features of the resources and tools under study and to demonstrate how to accomplish common tasks. Attendees will learn among others:

  • The content of the sequence databases and uses these as exemplar Entrez molecular databases.
  • The importance of derivative data such as NCBI Reference Sequences (RefSeqs) and sequence-related Entrez information hubs such as Taxonomy, HomoloGene and Gene.
  • Aspects of the Entrez interface to collect and download a specific set of records, to narrow the search, and to use the pre-computed relationships available in the Entrez system to find related sequences, genomic regions, genomic maps, homologous genes and proteins, pathways and expression information.
  • The practical aspects of working with NCBI BLAST, the most popular sequence similarity service in the world.
  • How to use the features of the updated service including direct access from the Entrez sequence databases.
  • The integrated databases to find phenotypes, literature, sequences (genome, mRNA and protein), and variations.
  • How to map variations onto genes, transcripts, proteins, and genomic regions.
  • Gain experience using additional tools and viewers associated with Entrez. These include the Graphical Sequence Viewer, the Variation Viewer, Gene View in dbSNP, and the 1000 Genomes Browser.

NCBI's Entrez as a discovery system. Image courtesy of Dr. Peter Cooper, NCBI.

MLA awards 2015 Louise Darling Medal to Yale partner HINARI

17 March 2015 - 8:37pm by Andy Hickner

Library staff with Louise Darling awardLibrary staff and HINARI collaborators Nathan Rupp, Khadija El-Hazimy, and John Gallagher with the Louise Darling award.

The Medical Library Association (MLA) has announced that it has awarded its Louise Darling Medal for Distinguished Achievement in Collection Development in the Health Sciences to the HINARI Access to Research in Health Programme for 2015. HINARI partners with publishers around the world to deliver scholarly health information and content (articles, books, and databases) to developing countries around the world who otherwise could not afford these resources. Under the guidance of Nathan Rupp, the library’s Head of Collection Development and Management, the Cushing/Whitney Medical Library plays and essential role in supporting HINARI by helping update publisher content in the HINARI database. HINARI is headquartered at the World Health Organization in Geneva and is part of the Research4Life (R4L) series of programmes which also includes AGORA (agriculture), ARDI (applied technology), and OARE (environment). Yale University Library is a Founding Partner in Research4Life, starting with the launch of HINARI in 2002. 

Free CME courses now available through Henry Stewart Talks

12 March 2015 - 12:26pm by Andy Hickner

Yale Affiliates can now earn CME credits for listening to the Biomedical and Life Sciences Collection of the Henry Stewart Talks. Yale University and YNHH, as well as individual faculty and staff, spend hundreds of thousands of dollars to fulfill these requirements.

On the home page (linked above) you should see that you now have CME available. (If you don't, you may need to log in to the Yale VPN.) Anyone at Yale wanting to fulfill their CME credits as required by the American Medical Association, or other professional organization, can click to register.  

Access to Electronic Books and Journals via ClinicalKey

5 March 2015 - 9:29am by Nathan Rupp

Cushing/Whitney Medical Library provides access to ClinicalKey, a clinical search engine that provides easy access to over 1,100 electronic books and over 600 electronic journals across over thirty medical specialties. It includes titles like Boron’s Medical Physiology; Bolognia’s Dermatology; and Goldman’s Cecil Medicine, along with the Clinics of North America series, all of which can be accessed via Orbis, the Yale University Library catalog (http://orbis.library.yale.edu/) and the Medical Library’s e-book and e-journal lists (http://elibrary.med.yale.edu/).

Clinicians may find ClinicalKey's evidence-based point-of-care tool First Consult particularly useful. 

If you have any questions about ClinicalKey, please contact your personal librarian or departmental library liaison.

New guide to Open Access initiatives supported by Yale Library

27 February 2015 - 12:28pm by Andy Hickner

There is a new guide to Open Access initiatives supported by Yale Library.

The page lists OA programs in two categories:

  • those that provide Yale authors discounts on open access publication fees
  • OA initiatives supported through library memberships

The guide will be updated as YUL joins additional OA programs.

For further reading on Open Access, we recommend the SPARC OA page, Wikipedia entry, or one of several books the library holds on the subject.   

Library website update: New dropdown menus to launch February 20

11 February 2015 - 1:51pm by Andy Hickner

More changes are coming to the Medical Library website on February 20, when we plan to update our main navigation menu.

"But," I hear you ask, "what IS this menu you refer to?"  This menu is what you see in the block box in the image below - or, if you look above this post, the links in the orange bar.

During the process of redesigning the library's homepage, we began to identify additional opportunities to improve this menu, thereby making it easier for users to navigate the entire library website.  We tested a revised menu with a small series of users earlier this month, and used their feedback to further refine the new menu.

You can preview the new menu here (visible on the Yale network only). 

Key proposed changes include:

  • New labeling:  The "Find" section is now labeled "Databases, Articles, & Books" in order to better convey exactly what content users will find in this section.  Likewise, "Computing & Technology Support" has been re-labeled "Library Technology."
  • New sections: "Tutorials & Guides," "Research Help, & "Library Technology" are intended to help users more quickly locate popular pages on the library website.
  • New links:   We used Google Analytics data about what pages are most used to add popular links to nearly every section.  For example, you'll find a new link to the "Citation management" LibGuide under "Tutorials & Guides" to make it easier to access tools like Refworks and Endnote Web.   
  • Re-organized content:  Some of the content previously found under "Portals" has been moved to other sections; for example, the Evidence-Based Practice guide is now linked under Tutorials & Guides, and most of the old (lengthy) Services list has been re-allocated under "Research Help" or "Library Technology."

The new navigation menu will launch the evening of Friday, February 20 in order to minimize inconvenience to users.  I will post additional reminders late next week.

Please contact me directly with any questions, suggestions or concerns, or if you just can't find something in the new menu.    

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