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Access to Partek Flow for the analysis of NGS data available to Yale biomedical researchers

July 8, 2016 - 2:11pm by Rolando Garcia-Milian

The Yale Medical Library is providing access to Partek Flow, a Graphical User Interface and user-friendly software for the analysis of RNA, SmallRNA, and DNA sequencing experiments. A webinar showing how to use this software will take place in SHM C-103 on August 4, 2016 (see details below). Webinar: NGS Data Analysis in Partek Software Description: Why have over 5,000 scientific articles cited Partek software for turning their data into discovery? Because it empowers scientists to perform sophisticated statistical analyses with intuitive point-and-click actions, no command-line knowledge needed.  Join us for a complimentary webinar to see how Partek Flow software can be used to analyze your RNA, SmallRNA, and DNA sequencing experiments. Using an RNA-Seq data set, we’ll demonstrate how to check read quality, align reads against a reference genome, quantify RNA transcript levels, and identify differentially expressed genes. We’ll show you how to save your analysis steps and parameters in your own start-to-finish, repeatable and shareable pipeline. The webinar will conclude with a live Q&A session. Flow that aligns RNA-Seq reads to a reference genome using the STAR aligner followed by quantification of reads to a transcriptome (from https://documentation.partek.com/display/FLOWDOC/Pipelines) Date & Time:      9:30am - 11:00am, Thursday, August 4, 2016 Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520 Campus:              Medical School Presenter:          Eric Seiser, PhD, Field Application Scientist, Partek Inc.

YaleNews article on the Library's 75th anniversary

June 24, 2016 - 9:11am by Andy Hickner

We enjoyed the YaleNews' story on the Library this week in commemoration of our 75th anniversary.  In addition to outlining the history of the Library's founding, author Mike Cummings interviewed faculty members and Library Director John Gallagher to highlight some of our current priorities and activities: “We see ourselves as partners in research,” Gallagher said, adding that the library not only assists researchers in accessing information and data but also in advising them on how to manage both — which is important because funding organizations increasingly require making the findings of sponsored research available for use by others. (Dr Paul) Barash, who uses the library several times a week, praised the library’s willingness and ability to adapt and tailor its service to meet the needs of researchers and clinicians. “They’ve kept up,” he said.  “You can’t necessarily say that about every institution at Yale, but the library has done a great job of adapting its resources and services.” Check out the full article here.

2016 Journal Citation Reports released

June 23, 2016 - 4:20pm by Andy Hickner

The 2016 update of the Journal Citation Reports (JCR) is now available. The JCR provide annual metrics for peer-reviewed journals, including Journal Impact Factors (JIF) and other data that can be used to evaluate a journal's impact on its field. You can learn more about the JCR and other journal-level metrics of research impact by watching our video tutorial on the topic. 

Winners of the "Happy birthday, Harvey" Instagram contest

June 20, 2016 - 9:54am by Andy Hickner

(by Melissa Grafe and Charlotte Abney Solomon)   In celebration of Harvey Cushing's birthday on April 8th and the Medical Library’s 75th Anniversary, the Medical Historical Library invited all Instagram users visiting the Harvey Cushing/John Hay Whitney Medical Library at Yale to share their best photos taken within our space. Contestants used the hashtag #HappyBirthdayHarvey and tagged our account, @yalemedhistlib. On display are the winners of the Instagram Challenge.   Brainiest Instagram: Best photo taken in the Cushing Center @rolfoid- Jon Rolfe Jon commented on his photograph that “The Cushing Center is a fun place for brainy Yale students.” Most Studious Instagram: Best photo taken while studying in the library- Honorable mention @annapziganshina- Anna Ziganshina Anna tells us that "it is never too early to learn." Judges’ Favorite Instagram: Best photo overall @archibrarian- Diane DiFazio What inspired Diane to take this particular photo:  “A few things: I expected a beautiful reading space at YMHL, but I'm often drawn to the details, and the metalwork in the Library caught my attention, so I took this photo because it represented medicine (hello, rod of Asclepius!), as well as the distinctive bookcases, other Tudor-style interior details, natural lighting, and bi-level space. My background's in architecture and I'm a librarian, so it was thrilling to be in a space that was both well-designed and inspiring; the Library continues the architectural traditions of great libraries. (And, I love how Harvey Cushing's ideas were realized by his friend and former classmate, architect Grosvenor Atterbury.) I thought the balustrades around the mezzanine (in the rotunda, too) were interesting, but I didn't realize how cool Atterbury's design really was until later! I thought, "Neat, I wonder if that's wrought iron," but later read that the railings are aluminum ... with decorative steel cutouts (!), and that it was all designed to mask lighting fixtures, which is such a fantastic modern way of the architect to handle things! So good.”   Happiest Birthday Instagram: Best selfie or other photo including an image of Harvey Cushing or the words “Happy Birthday Harvey” @kevin.a.nguyen- Kevin Nguyen With this selfie, Kevin noted, "Biology gives you a brain, but life transforms it into a mind."     Most Collectible Instagram: Best photo taken of an image, book, or other item in any CWML current or historical collections @sona.ghorashi- Sona Ghorashi Sona accompanied her photograph with this comment: "A path to the light through the shadows, at the Medical library."    Most Studious Instagram: Best photo taken while studying in the library @magic_meg- Megan Ritchey Megan captioned this lovely image of the Medical Historical Library with "The whole place to myself.”  

"Exploration, Encounter, and Exchange with Harvey Cushing”: Theresa Barden's National History Day project

June 17, 2016 - 4:43pm by Andy Hickner

By Terry Dagradi, Cushing Center Coordinator Theresa Barden, a 9th grade student at Coventry High School, Rhode Island, visited the Cushing Center last year with her sister Mary Barden, a 4th year Yale medical student, and in her words "was amazed." Theresa decided to participate in this year’s National History Day, with the theme "Exploration, Encounter, and Exchange,” and did her project on Dr. Harvey Cushing.  As the coordinator of the Cushing Center, I was happy to accept her request for an interview to answer questions regarding Harvey Cushing and the Cushing Tumor Registry.  The results of her work are in!  See below, the photo of her impressive National History Day project. "Thank you so much for your interview! I ended up placing in 1st for my division. (Senior individual exhibit). In the beginning of June, I'm going to Washington DC to compete in nationals. Thanks again!”   Theresa Barden  - April 13, 2016 The Cushing Center is open for research!

2016-2017 Gyorgyey Fellows

June 15, 2016 - 2:18pm by Andy Hickner

The Medical Historical Library, Cushing/Whitney Medical Library, is pleased to announce the following recipients of the Ferenc Gyorgyey Research Travel Award for 2016-2017: Whitney Wood, Postdoctoral Research Fellow, Department of History, Classics and Archaeology, Birbeck, University of London A New Way to Birth?  Herbert Thoms and the International Natural Childbirth Movement Whitney Wood’s research explores the natural childbirth movement in Canada.  As part of this research, Wood will be examining the Herbert Thoms papers (https://hdl.handle.net/10079/fa/mssa.ru.0656), as Thoms was an international leader in the movement and produced quite a bit of material on the topic of natural childbirth. Whitney Wood is planning to come to the Medical Historical Library in Spring 2017. Erin Travers, Doctoral Candidate, History of Art and Architecture, University of California, Santa Barbara Boundaries of the Body: The Art of the Anatomy in the Seventeenth-Century Netherlands Erin Travers will be examining Dutch anatomies, particularly Jacob van der Gracht’s drawing book, Anatomie der wtterlicke deelen van het menschelick lichaem.  These anatomies form the basis of her dissertation.  She will at the Medical Historical Library July 18th-23rd, 2016. Many thanks to the selection committee: John Warner and John Gallagher.

"Harvey Cushing and John Fulton: Two Founders Bonded By Science, Medicine, And Books": Full video of June 3 event now online

June 9, 2016 - 9:14am by Andy Hickner

On June 3, 2016 the Cushing/Whitney Medical Library hosted a talk titled "Harvey Cushing and John Fulton: Two Founders Bonded By Science, Medicine, And Books."  The focus of this event was a conversation between Drs. Dennis D. Spencer and Gordon M. Shepherd, moderated by Cynthia Tsay, YSM ’18. The panel spoke about the personal and professional relationship of these men, and touched upon the founding of the Yale Medical Library and how they worked together to make it a reality.   At the post-lecture reception, we also took a few photos of attendees with Harvey Cushing himself: Dr. Cushing's great-grandson, Harvey Cushing Dr. Frank Lobo and Sharon McManus Dr. Dennis Spencer and Harvey Cushing Library Curator of Prints and Drawings Susan Wheeler L to R: John Gallagher, Cushing's great-great-grandson Kevin Cushing, Dr. Gordon Shepherd, Cushing's granddaughter Kate Whitney, Dr. Dennis Spencer, Cynthia Tsay

Spotlight on Humanities in Medicine Collection

June 8, 2016 - 4:39pm by Alyssa Grimshaw

Spotlight on the Humanities in Medicine Collection Check out the newest book in the Humanities in Medicine Collection, The Gene: An Intimate History. Excerpt from the book cover: From the Pulitzer Prize-winning, bestselling author of The Emperor of All Maladies—a magnificent history of the gene and a response to the defining question of the future: What becomes of being human when we learn to “read” and “write” our own genetic information? Siddhartha Mukherjee has a written a biography of the gene as deft, brilliant, and illuminating as his extraordinarily successful biography of cancer. Weaving science, social history, and personal narrative to tell us the story of one of the most important conceptual breakthroughs of modern times, Mukherjee animates the quest to understand human heredity and its surprising influence on our lives, personalities, identities, fates, and choices. Throughout the narrative, the story of Mukherjee’s own family—with its tragic and bewildering history of mental illness—cuts like a bright, red line, reminding us of the many questions that hang over our ability to translate the science of genetics from the laboratory to the real world. In superb prose and with an instinct for the dramatic scene, he describes the centuries of research and experimentation—from Aristotle and Pythagoras to Mendel and Darwin, from Boveri and Morgan to Crick, Watson and Franklin, all the way through the revolutionary twenty-first century innovators who mapped the human genome. As The New Yorker said of The Emperor of All Maladies, “It’s hard to think of many books for a general audience that have rendered any area of modern science and technology with such intelligence, accessibility, and compassion…An extraordinary achievement.” Riveting, revelatory, and magisterial history of a scientific idea coming to life, and an essential preparation for the moral complexity introduced by our ability to create or “write” the human genome, The Gene is a must-read for everyone concerned about the definition and future of humanity. This is the most crucial science of our time, intimately explained by a master. Humanities in Medicine Collection is located across from the Circulation Desk.

SCOPA Lunch & Learn, June 8 at 1pm

June 2, 2016 - 4:46pm by Andy Hickner

(by Katie Hart) Librarians attending the Medical Library Association Annual meeting in May.  Left to right:  Andy Hickner, Denise Hersey, Nathan Rupp, Holly Grossetta Nardini, Rolando Garcia Milian, Mark Gentry.  You’re invited to a SCOPA sponsored Lunch & Learn at the Cushing/Whitney Medical Library on June 8th at 1pm. Join us to hear recent presentations given at the Medical Library Association annual conference. Please feel free to bring a lunch or perhaps make a stop at the famous medical school carts. The four presentations we will be reprising for you are: Design, Implementation, and Evaluation of a Medical Library Program to Support Biomedical Research in the 'Omics Era – Rolando Garcia-Milian (presenting), Janis Glover, and John Gallagher. This presentation discusses the strategies used to design and implement our end-user bioinformatics support program. It also provides results on training, resources, tools, and services available to Yale biomedical researchers.  Putting the Pieces Together: Finding a Point-of-Care Solution for an Academic Medical Center – Denise Hersey (presenting), Mark Gentry, Janene Batten, Nathan Rupp, and Holly Grossetta Nardini. The Cushing/Whitney Medical Library assembled a task force composed of librarians, physicians, nurses, and hospital IT staff to compare and evaluate DynaMed Plus and UpToDate – two resources used at the beside to provide clinical care – and then recommend which product best meets the needs of our associated hospitals, informing the subscription renewal process for 2016-2017. The Yale Medical Subject Headings (MeSH) Analyzer: A New Tool for Search Refinement – Holly Grossetta Nardini and Lei Wang. The presentation describes our MeSH analysis methodology, a technique that helps craft more comprehensive searches, and the use of a new tool that saves time by doing this analysis automatically. The Yale MeSH Analyzer helps refine searches, particularly those where indexing is challenging, by creating a quick, scannable grid of MeSH terms for easy review. Using Omeka for Online Exhibits – Andy Hickner (presenting), Melissa Grafe, Kerri Sancomb, and Francesca Livermore (5 minute lightning talk). Omeka is a web publishing platform for online exhibitions. Andy will describe how Yale University Libraries conducted a pilot of Omeka for the Libraries’ online exhibition needs and share lessons from our experience. See you there!

Future Medical Librarians at STEM Career Fair

May 24, 2016 - 11:18am by Holly Grossetta Nardini

by Kate Nyhan These future medical librarians are students at Wilbur Cross High School in New Haven attending a career fair to learn about STEM careers. Research and education librarian Holly Grossetta Nardini, reference librarian Melissa Funaro, and public health librarian Kate Nyhan (pictured) talked with students from New Haven's public schools about what medical librarians do, how informationists fit into the health care team, and how these young people can prepare for STEM careers like ours. We were impressed with the confident kids at this STEM career fair. Many of them already have career goals, and lots of them discussed quite sophisticated strategies for seeking and evaluating information online. A good number of these students have visited the Cushing Center and learned about the history of science and medicine there. The best part of this career fair was interactive: live searches in PubMed on health care topics relevant to these students. Speaking of which -- are you the track coach whose runners found an article suggesting that a short warm-up is as effective as a long one? I promise we talked to these young athletes about the importance of searching comprehensively. If they cherry-picked this evidence to get out of doing the long warm-up, remind them that evidence-based medicine is based on a thorough literature review! Many thanks to Many Mentors, the Yale League of Black Scientists, and Wilbur Cross High School. We were glad to be part of the STEM career fair team, and we look forward to next year. And in the long term, we hope we can look forward to welcoming some of these talented students to the always rewarding profession of medical librarianship!  
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