Blogs

Resource Spotlight: Ingenuity Variant Analysis

13 August 2018 - 12:19pm by Caitlin Meyer

 

Welcome to Resource Spotlight! The Cushing/Whitney Medical Library provides access to an incredible array of databases, e-book collections, software and more. In this series of posts, we’ll be showcasing highlights from our collection.

In this edition of Resource Spotlight, we’ll be looking at Ingenuity Variant Analysis (IVA). IVA is a web-based tool that combines analytical tools and content from the Ingenuity Knowledge Base to help identify disease variants in human sequencing data. 

The product allows you to select multiple samples to analyze together. From there, you can design the forthcoming analysis and add any relevant biological terms to help narrow down the list of variants likely contributing to the disease or phenotype at hand. IVA supports a range of upload formats, including Variant Call Format (VCF), Genome Variation Format (GVF) and Complete Genomics files (Var, MasterVar, High confidence junction, etc.). 

After you have set up your data, IVA lets you interact with the data with a series of customizable filters. Some of the filter types include: biological context, genetic analysis, predicted deleterious, cancer driver, pharmacogenetics, and more. 

Keep an eye on the library’s class calendar for trainings on IVA and all bioinformatics-related software. In the meantime, Qiagen, the company that produces IVA, has produced webinars, tutorials, and guides to help you get started. 

Finally, please note that the library’s license to IVA is for academic and research use only.  Results may not be incorporated into a diagnostic product or service. 

Request an IVA account.

For questions on how to best use IVA, feel free to contact Rolando Garcia-Milian.

Reno-relocation

9 August 2018 - 3:00pm by Kelly Perry

If you haven't stopped by the library recently you may notice that things are a bit...  different.  We have optimized the spaces that will not be part of the renovation project for your comfort and convenience. 

What does that mean for you?  Can you still access the all-important things the library offers, such as study materials, computers...  the bathrooms?  Of course you can! 

Map of the library during renovations

Here we have a map of the layout of the library during the renovations (click this link to view the map as a .PDF).  We'll soon have additional signage and other guides to help you find your way during these first few months of the construction.  Of course, please feel free to ask any staff member to help you at any time.

We are grateful for your patience during this time, and look forward to the exciting collaborations this renovation will bring!

Meet our first Simbonis Intern!

6 August 2018 - 11:13am by Kelly Perry

We are delighted to share a report on the work of our first Simbonis intern, Emma Brennan-Wydra, who joined the staff in the Medical Historical Library at the end of May 2018.  Emma offered the following glimpses into her life and experiences as our intern:

I graduated from Yale College in 2015 with a double major in Chemistry and Women's, Gender, and Sexuality Studies, focusing on the multiple intersections of science, education, gender, bodies, and power. During my time at Yale, I also played flanker for the Yale Women's Rugby Football Club, designed lighting for theater and dance productions, organized a truly astounding number of LGBTQ-related events, and served as the producer of the Fifth Humour, Yale's oldest (and best) sketch comedy troupe. After college, I moved to the Boston area, where I worked as a ballroom dance instructor, played bass in an alternative rock band, and volunteered with the Massachusetts Transgender Political Coalition.

Emma Brennan-WydraI'm now a master's student at the University of Michigan School of Information, where I've mostly been taking classes relating to libraries, archives, and the preservation of information, but I've also dabbled in data science, programming, and survey research methodology. In addition to my coursework, I work as a research assistant at the University of Michigan College of Engineering, where I'm part of a multidisciplinary group studying engineering education, and in the fall, I'll be a teaching assistant for a master's level introductory course in statistics and data analysis. (I also try to find the time to go out salsa or swing dancing, when I can!) After I finish graduate school next spring, I'm hoping to get a position in an academic library.

I had visited the Medical Historical Library and the Cushing Center a few times for class as an undergrad at Yale, but to be honest, I didn't know very much about medical libraries before I started my summer internship. One of my personal learning goals for the summer was to learn more about different facets of academic and medical librarianship, both through direct experience and by talking to other librarians, in hopes of developing more specific career plans for myself. In my six weeks at the Medical Historical Library, I've had the opportunity to get to know librarians from every department of the Cushing/Whitney Medical Library and hear more about the work they do, and I've also gotten to work on a number of different projects in and around the Medical Historical Library for myself. Unfortunately, I'm not really any closer to identifying a “dream job” because everything has been so interesting!

My first project for the summer was processing a recently acquired collection of medical illustrations drawn by Mildred Codding for our library's benefactor and namesake, neurosurgeon Harvey Cushing, along with photographic reprints, notes, correspondence, and other materials that Cushing used in the preparation of his books and articles. Archival processing, I quickly learned, is all about decision-making. As I was planning out how I might want to organize the collection, I found it helpful to imagine what kinds of questions future researchers might be asking. Would the researcher need to find all of the materials from one specific publication, for example, or might they be interested in Cushing's editorial process more broadly? If the materials are organized one way, it might make it easy to answer one type of research question, but other kinds of information or functionality may be lost in exchange. Most of the time with archival processing, there isn't one “right” answer. After I physically organized the materials into new folders and boxes, I began entering information about the collection into ArchivesSpace, an archives-specific information management application that is used across the Yale Library system. This facilitated the creation of a finding aid, which is a document describing an archival collection, designed to help researchers find materials of interest. You can view the finding aid I made here.

After I finished the finding aid, I began planning a small exhibition to display some of the beautiful surgical illustrations by Mildred Codding that are part of the new archival collection. The scope of the exhibition quickly broadened to include not only Mildred Codding but also two of the other women who worked with Harvey Cushing: secretary Madeline Stanton and pathologist Louise Eisenhardt. Cushing, like many doctors of the time, employed a large team of female assistants whose work was often uncredited and whose names have been largely forgotten. But these three women—Codding, Stanton, and Eisenhardt—went on to have distinguished careers of their own that extended decades past Cushing's death in 1939. As I began cobbling together a plan for my exhibition, I drew on a variety of sources, including biographies of Harvey Cushing, obituaries and tribute articles, birth and death records, reports from the Peter Bent Brigham Hospital, photographs from the Harvard Medical School Archives, and collections of correspondence and diaries held here at Yale. I also had conversations with others who had some curatorial experience so I could learn more about how to create a strong, cohesive exhibit, and I tried to select items, images, and stories that capture some of what made Codding, Stanton, and Eisenhardt so special. My exhibit, titled More Than a 'Harem': The Lives and Legacies of Dr. Harvey Cushing's Female Associates, is currently on display in the Cushing Center and also available online. It has been such an honor and a delight to have the opportunity to learn about these exceptional women, and I'm so excited to share what I learned with the public.

One of the things that excites me most about my future career as an academic librarian is the day-to-day variety of the work, so having the opportunity to experience a taste of that in my internship has definitely been a plus! In addition to processing an archival collection and curating an exhibition, I've also updated and migrated an online exhibition about the Yale School of Nursing to the new Omeka platform, cataloged glass plate photographic negatives of Harvey Cushing's patients, written and edited labels for an exhibit about tobacco advertising, and more. I've learned so many new skills and technologies through this internship, but I've also gotten to do work that employs my preexisting interests and strengths. Although I previously thought I might want to work as a librarian in a subject specialist role for chemistry or another science field, I've thoroughly enjoyed both the medical and historical aspects of my work here.

Furniture Moving

2 August 2018 - 11:29am by Kelly Perry

We will be moving furniture on Friday the 3rd, Monday the 6th, and Tuesday the 7th from 7:30am to 3pm.  The movers will be transferring furniture from all parts of the library as we wrap up our preparations for renovation.

Expect disruptions, possible room closures, and lots of activity during these times.

We apologize for any inconvenience.

Movers relocate furniture in the Morse Reading Room.Movers relocate furniture in the Morse Reading Room.

 

 

 

 

 

 

 

 

 

 

 

 

Renovation prep begins Monday, July 30th

26 July 2018 - 10:36am by Kelly Perry

Beginning Monday, July 30, you will notice an increase in noise and disruption at the Cushing/Whitney Medical library as work begins to prepare the space for the renovation project.

On Monday, the Information Desk and staff will be relocated to the Circulation Desk area at the front of the library.

Also on Monday, movers will be on site to relocate and remove furniture in advance of construction.  They will be moving tables and other furniture throughout all floors of the library.  These moves will occur over the course of the day and there will be noise associated with this work, especially between the Information Room and Morse Reading Room.  This work will require the temporary removal and/or relocation of computer workstations.

If you require quiet study space, please consider another location during this time.

To stay informed of renovation news, please sign up for the HHH email list.  You’ll be the first to know of the latest news related to the renovation project and its effect on library services.

Questions and comments can be sent to https://library.medicine.yale.edu/renovation/contact.

Free Trial to MedOne Plastic Surgery!

23 July 2018 - 9:23am by Lindsay Barnett

The Cushing/Whitney Medical Library is hosting a free trial to MedOne Plastic Surgery!  The trial will run through August 31, 2018.  An App is available for iOS and Android operating systems; search for MedOne App in the respective app stores.

Access the trial here

This trial includes comprehensive access to Thieme’s complete portfolio in aesthetic and reconstructive plastic surgery:

  • Thieme’s entire E-Book library of 150 books including CORE TEXTS for residency programs
  • Essentials of Plastic Surgery by J. Janis and Essentials of Aesthetic Surgery by. J. Janis
  • Surgical procedures providing step-by-step instruction on core techniques and approaches
  • Learn from the Master series of videos providing training on cutting-edge techniques
  • More than 50,000 images for download and use in other applications
  • Training Center, interactive Q&A bank for board exam prep
  • MedOne App available for Android and iOS devices

Let us know what you think!  Contact Lindsay Barnett with feedback.

 

Noise Alert for Friday, July 13th and Saturday, July 14th

13 July 2018 - 12:11pm by Kelly Perry

Basement stacks, where drilling will take place.

Workers will be in the library this afternoon and tomorrow to install additional electrical service in preparation for the renovation project.  This work will take place near the four pillars on the E-level next to the book stacks.  This work may be noisy and library users may want to seek other space in the library during this time.

The work is slated to take place today (Friday, 7/13) from 4pm until approximately 10pm and tomorrow (Saturday, 7/14) from 7am to 3pm.  We apologize for this necessary inconvenience and appreciate your patience as we begin the renovation project.

Please contact Judy Spak (judy.spak@yale.edu) with any questions.

The Cushing/Whitney Medical Library would like to thank Hongyu Liu and Tao Wang for their donation of the glossary “English-Chinese Glossary of Basic Human Anatomy.”

6 July 2018 - 11:31am by Melissa Funaro

John Gallagher receiving a donation from Hongyu Liu

The Cushing/Whitney Medical Library benefits from the generosity of many donors. Our library’s founders, Doctors Harvey Cushing, Arnold C. Klebs and John F. Fulton, donated their collection of books to Yale on the premise that a new medical library is created.  Over the years, the library’s collections grew rapidly between gifts and purchases, often made from endowments that donors provided.

Today, the tradition continues, as donations help ensure a rich collection of books and other materials. Recently we received a donation of three copies of a glossary titled “English-Chinese Glossary of Basic Human Anatomy,” a gift from the authors, Hongyu Liu and Tao Wang.

If you are interested in donating materials or funds to the library, please take a look at this page! https://library.medicine.yale.edu/about/policies/gift

 

More Than a 'Harem' : The Lives and Legacies of Dr. Harvey Cushing's Female Associates

5 July 2018 - 2:39pm by Kelly Perry

More Than a 'Harem' : The Lives and Legacies of Dr. Harvey Cushing's Female Associates

Want to learn more about the smart and dedicated women who supported the work of our namesake, Harvey Cushing?  Explore our newest exhibition, curated by Emma Brennan-Wydra, Stanley Simbonis Intern for the Medical Library, and now on view in the Cushing Center!

Throughout his career, Dr. Harvey Cushing employed a team of women who assisted him as secretaries, typists, medical artists, operative photographers, laboratory technicians, and more.  Cushing's female associates referred to themselves jokingly as his “harem,” but they were far more than that.  These working women were indispensable to Cushing, and their contributions are evident throughout his published works, as well as his diaries and correspondence.  Three of Harvey Cushing's assistants, in particular—secretary Madeline Stanton, neuropathologist Louise Eisenhardt, and medical illustrator Mildred Codding—are remembered not only for their proximity to the famed neurosurgeon, but also as leading lights in their own respective fields, with careers extending decades beyond Cushing's death in 1939.

Madeline Stanton, who worked as Cushing's secretary, played a major role in the organization and development of the historical collections at the Yale Medical Library (now the Cushing/Whitney Medical Library).  As Librarian of the Historical Collections from 1949 until 1968, Stanton maintained an “atmosphere of generous and kindly learning” in the Historical Library.  “She always knew,” recalled Gloria Robinson, wife of Yale neurosurgeon Dr. Franklin Robinson.  “She had endless special knowledge.”  (Photograph by Richard U. Light, courtesy of the Harvard Medical School Archives at the Countway Library of Medicine.)

Louise Eisenhardt, whom Cushing originally hired as an editorial assistant, obtained a medical degree for herself in 1925 and worked as Cushing's pathologist.  A leading expert on tumor diagnosis, Eisenhardt was the first woman president of the American Association of Neurological Surgeons and the first managing editor of the Journal of Neurosurgery, a position she held for 22 years.  She was also the curator of the Brain Tumor Registry, Cushing's collection of pathological specimens and patient records, which is now housed in the Cushing Center.  (Photograph by Richard U. Light, courtesy of the Harvard Medical School Archives at the Countway Library of Medicine.)

Mildred Codding was a medical illustrator who worked with Cushing from 1928 until his retirement from the Peter Bent Brigham Hospital in 1932.  Her surgical drawings and anatomical diagrams grace the pages of many of Cushing's published works.  A student and disciple of famed medical illustrator Max Brödel, Codding made masterful use of the carbon dust technique, resulting in wonderfully vivid, detailed, and realistic illustrations of living tissue.  After Cushing's retirement, Codding stayed on as an illustrator at the Brigham.  Her later illustrations appear in a number of major works, including Zollinger's Atlas of Surgical Operations.  (Photograph by Russell B. Harding, courtesy of the Brigham and Women's Hospital Archives.)

Learn more about these exceptional women at our new exhibition in the Cushing Center, which features photographs, correspondence, books, slides, and original surgical illustrations by Mildred Codding.  An online companion to the physical exhibition, which includes additional photographs and information, is available here.

 
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