Requesting Medical Historical rare books and materials online

24 July 2015 - 11:48am by Andy Hickner

(By Melissa Grafe)

You can now request locked Medical Historical Library books through Orbis, instead of emailing staff at the Historical Library.  Please do this when you want access to our locked stacks materials, for use in our Historical Library Office/reading room, or any events, sessions, or classes that you may be holding.  For classes or other events, please email Melissa Grafe at to discuss scheduling and support.

From Orbis, in the Holdings area:

Orbis screenshot

The first time you “Request for Use in the Medical Historical Library,”  you will be prompted to register, unless you’ve already registered as a patron at Beinecke or Manuscripts and Archives.  After that, the information will automatically populate in the form. Just put in what date you are planning to come to the Medical Historical Office to view the materials, and Submit the request!  

We may have to take your photograph and check your Yale ID, even if we know you, as part of joining this system with Beinecke/Manuscripts and Archives and updated security protocols.

Within the next few months we will expand the ability to request materials from the Medical Historical Library’s finding aids, which you can discover in the Yale Finding Aid database. The finding aids are lists, usually down to the folder level, from our archival collections, including the papers of doctors, our medically themed sheet music collection, and the William Van Duyn tobacco advertising collection.

If there are materials that are not in Orbis, you can still fill out a request manually, filling in as many details as you know concerning the object you want.  Many of the materials featured in our digitized collections fall in this category.

New point of care tool: DynaMed Plus

9 July 2015 - 10:38am by Andy Hickner

Yale University and Yale-New Haven Hospital now have access to DynaMed Plus, which allows you to get answers to your clinical questions fast.  This clinical information resource is written by physicians, and features a rigorous evidence-based editorial process which provides synthesized information and objective analysis to answer your clinical questions quickly and easily.

DynaMed Plus features: 

  • Overviews and recommendations
  • Thousands of graphics and images
  • Precise search results
  • Expert reviewers
  • Specialty content
  • Mobile access
  • Micromedex Clinical Knowledge Suite drug content 

For questions about this new product, please contact your librarian or visit our documentation about DynaMed Plus on mobile devices

Training Sessions - Summer 2015 at the Cushing/Whitney Medical Library

8 July 2015 - 2:40pm by Rolando Garcia-Milian

Introduction to Ingenuity Pathway Analysis

Description:     What is IPA and what questions can it address?

  • Overview of key features in IPA
  • Ingenuity Knowledge Base
  • Search & Pathway Building - Gene/ Chemical, Functions, Drug Targets
  • Advanced Search: Limiting results to a molecule type, family or disease-association.
  • Building pathways: Creating a pathway, pathway navigating, Using Build and Overlay tools
  • Bioprofiler
  • Dataset Analysis: Interpretation of Gene, Transcript, Protein and Metabolite Data
  • Data Upload and Analysis:  Uploading and formatting a dataset, setting analysis parameters and running an analysis
  • Pathway Analysis and Canonical Pathways
  • Downstream Effects Analysis and identifying downstream functions and processes that are likely affected
  • Upstream regulators Analysis
  • Causal Network Analysis and identifying likely root regulators
  • Regulator Effects Analysis to link upstream regulators with downstream functions and processes that are affected
  • Comparison analysis and comparing multiple observations

Date & Time:  9:00am - 12:00pm, Wednesday, July 15, 2015

Location:         C-103 333 Cedar St, New Haven CT 06520

Campus:          Medical School

Presenter:       Dr. Kate Wendelsdorf, Applied Advanced Genomics, QIAGEN Informatics

Registration required


Advance Ingenuity Pathway Training: Integrated Analysis and Interpretation of Variant and Gene Expression Data from Breast Cancer Subtypes

            Methods that jointly interpret genomes and transcriptome data from disease case samples may be able to identify disease-specific factors and pathogenicity mechanisms that may not be observable on a single data type. These insights can then be used create more effective screenings or treatments.

Here we show how jointly analyzing tumor-specific genotypes and gene expression can indicate medically important differences among tumor subtypes. Pairing two tools from Ingenuity® Systems – Variant Analysis  (for interpreting human genome data) and IPA® (for transcriptome data) – we trace differences between breast tumors that spread quickly (Claudin-low) versus slowly (luminal) to sequence variation that likely governs Epithelial-to-Mesenchymal Transition (EMT).

Variant Analysis was used to filter genomic variants in RNA seq data to a shortlist of those plausibly involved in driving tumor spread. IPA is then used to leverage gene expression patterns from the same dataset to identify molecular pathways involved in the metastatic phenotype of Claudin-low breast cancers. The seminar will demonstrate how using a combination of IPA features and QIAGEN tools can provide insight in to phenotype-causing pathways for experimental follow-up and hypothesis testing.

Date & Time:  1:00pm - 4:00pm, Wednesday, July 15, 2015

Location:         C-103 333 Cedar St, New Haven CT 06520

Campus:          Medical School

Presenter:       Dr. Wendelsdorf- QUIAGEN

Category:        Bioinformatics

Registration required  


Managing your References with EndNote

Description:     EndNote is a citation-management software application that makes saving citations and then citing them within documents easy. EndNote's pre-formatted style templates, specific to journal instructions, make it easy to insert references into your papers as you write them. In this class you will learn how to easily add citations into your EndNote library, attach PDFs, and insert references into your research papers.

Date & Time:  2:00pm - 3:00pm, Wednesday, July 29, 2015

Location:         Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Campus:          Medical School

Presenter:       Denise Hersey

Category:        Reference Management Systems

Registration required   


Give your PubMed Skills a Tune Up

Description:     PubMed is one of the most comprehensive resources for searching the biomedical literature.  Most researchers have used it one time or another, but it may be time to brush up on your search skills to ensure that you have a relevant set of results.  In this class, we will go over PubMed search techniques, including how to quickly limit a search and the role of Medical Subject Headings (MeSH) in creating more effective searches. Participants will also learn time-saving features such as saving searches and how to link out to full-text.

Date & Time:  6:00pm - 7:00pm, Wednesday, July 29, 2015

Location:         Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Campus:          Medical School

Presenter:       Melissa Funaro

Category:        Reference Management Systems

Registration required    


Webinar: Introduction to Cytoscape: network visualization software

Description:     Cytoscape, an open source molecular interactions visualization tool, allows the exploration of molecular interactions and biological pathways and integrates these networks with annotations, gene expression profiles, and other data.  This webinar will provide an introduction to some of the core functionality of Cytoscape, including the loading and manipulation of experimental data.  For example, you will learn how to change visual properties to easily distinguish biologically significant relationships.  Many additional features and advanced analyses are available through Cytoscape’s extensive list of apps. Examples of apps are MetScape (allows for visualizing and interpreting metabolomic data), Reactome FI (Reactome Functional Interaction and pathway enrichment tool), and BiNGO (Gene Ontology Tool).

Date & Time:  11:30am - 12:30pm, Tuesday, August 11, 2015

Location:         Medical Library, Large Conference Room 101A, 333 Cedar St, New Haven CT 06520

Campus:          Medical School

Presenter:       Marci Brandenburg, Bioinformationist, Taubman Health Sciences Library, University of Michigan

Category:        Bioinformatics

Registration required

Join the End-User Bioinformatics Network (EBNET) and become a member of a community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research at Yale.

New Acquisitions: Posters on Social Justice and Medicine by Rachael Romero

19 June 2015 - 11:09am by Susan Wheeler

Sterilization poster

The Medical Historical Library has recently acquired a collection of twenty-nine posters and digital works on themes of social justice and health care by artist/activist Rachael Romero.  Many works date from 1975 to 1982 and were created by Ms. Romero for the San Francisco Poster Brigade which she co-founded.   Originally displayed on city streets—often on the sides of buildings—the posters bear messages such as “Decent Housing is a Basic Right.” and “Preventive Medicine, Not Costly Operations.”

Documented in the collection is “The Fight for the International Hotel,” which became a local cause cèlébre in 1976-78 when the hotel which provided low cost accommodations and community was threatened by, and subsequently razed for, development. 

Two recent original digital works reflect Ms. Romero’s personal odyssey through diagnosis and treatment of a brain tumor.

Ovid Personal and proxy server accounts briefly unavailable tomorrow, June 22

16 June 2015 - 9:18am by Andy Hickner

The Ovid Personal Edition System and the Proxy server account pages will be down tomorrow morning (Tuesday, June 22)  at 7:15 and will be unavailable until 7:45.  During this time, users will be temporarily unable to request a proxy account or password reminder.  Access to Ovid Personal login will also be unavailable.  

QIAGEN Clinical Insight®: new tool for clinical labs interpreting and reporting on genomic variants

9 June 2015 - 1:30pm by Rolando Garcia-Milian

QUIAGEN has announced the launching of its new tool Clinical Insight® (QCI)  for interpreting and reporting on genomic variant resulting from next-generation sequencing.  According to this company, the new tool can classify variant, identify treatment options, and perform geographical clinical trial matching. QCI has been evaluated in collaboration with Emory University School of Medicine and Dartmouth-Hitchcock Medical Center, among 50 other groups.  Clinical Insight® for Somatic Cancer provides clinical decision support for routine somatic cancer testing laboratories. QUIAGEN’s knowledge base contains millions of expert-curated biomedical finding and mutations from the literature and public databases that is used to build up-to-date pathways and networks related to diseases and drugs. The Cushing/Whitney Medical library provides access to two concurrent seats of QUIAGEN’s Ingenuity Pathway Analysis.

For questions on accessing IPA or any other knowledge based product (MetaCore, BIOBASE, etc.) through the medical library, please contact Rolando Milian

Join the End-User Bioinformatics Network (EBNET) and become a member of a community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research.

Medical Historical Librarian profiled in Yale Medicine

5 June 2015 - 1:26pm by Andy Hickner

Medical Historical Librarian Melissa Grafe is featured in the latest issue of Yale Medicine

Now, Grafe pursues her interests in medical education and the history of medicine at work every day. As director of the Medical Historical Library, she helps students and scholars navigate its collections, housed within the Cushing/Whitney Medical Library. She curates exhibits that showcase materials from the library’s more than 140,000 volumes, as well as thousands of manuscripts, drawings, prints, incunabula, and other items spanning every era of medical history. Recent exhibits range from the 16th-century anatomical drawings of Vesalius, some of which incorporate an ingenious lift-the-flap design not unlike what we see in children’s books today, to 1970s-era Technicolor posters highlighting the dangers of excessive drinking.

Read more here

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