Training Sessions for the Winter Semester at the Cushing/Whitney Medical Library

29 January 2016 - 3:41pm by Andy Hickner

The Cushing/Whitney Medical Library has prepared the following menu of training sessions for the winter semester. It includes training on how to do literature search, patent search, use of Cytoscape, genome browsers, EndNote, systematic reviews, functional analysis, variant annotation, and more. Since seating is limited, please register to reserve yours by following the links next to each session.

Please contact Vermetha Polite for questions or comments on these sessions.

PubMed: Improve your Skills

Description:        PubMed is one of the most comprehensive resources for searching the biomedical literature.  Most researchers have used it at one time or another, but it may be time to brush up on your search skills to ensure that you 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 timesaving features such as saving searches and how to link out to full-text.

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

Date & Time:      5:00pm - 5:50pm, Thursday, February 4, 2016

Registration Required:


Date & Time:      5:00pm - 5:50pm, Thursday, February 18, 2016

Registration Required:


Date & Time:      12:00pm - 12:50pm, Friday, February 26, 2016

Registration Required:


Date & Time:      5:00pm - 6:00pm, Wednesday, March 2, 2016

Registration Required:


Date & Time:      5:00pm - 5:50pm, Tuesday, March 22, 2016

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Date & Time:      5:00pm - 5:50pm, Wednesday, April 13, 2016

Registration Required:


RefWorks Basics

Description:        Learn basic features and use of this web-based citation management system, such as setting up a Yale account (no purchase required), exporting citations from external databases and importing them into your account, and using RefWorks with MS Word to create citations in context and bibliographies for your manuscripts. This class is one hour.

Date & Time:      12:00pm - 1:00pm, Wednesday, January 27, 2016

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

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.

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

Date & Time:      3:00pm - 4:00pm, Thursday, January 21, 2016

Registration Required:


Date & Time:      5:00pm - 6:00pm, Wednesday, January 27, 2016

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Date & Time:      2:00pm - 3:00pm, Friday, February 5, 2016

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Date & Time:      5:00pm - 6:00pm, Wednesday, February 10, 2016

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Date & Time:      5:00pm - 6:00pm, Wednesday, February 24, 2016

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Date & Time:      5:00pm - 6:00pm, Tuesday, March 8, 2016

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Date & Time:      2:00pm - 3:00pm, Wednesday, March 16, 2016

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Date & Time:      1:00pm - 2:00pm, Friday, March 25, 2016

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Date & Time:      5:00pm - 6:00pm, Thursday, April 7, 2016

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Date & Time:      5:00pm - 6:00pm, Wednesday, April 27, 2016

Registration Required:


Enhance your Library Skills

Description:      Are you new to the Medical Campus? Need a refresher on how to use the Medical Library?  Information experts will assist you in finding everything from books in the online catalog to locating peer-reviewed full-text articles including when and how to request materials through our Interlibrary Loan service. You will be surprised about the resources and services available to you.

Use the library catalog to find materials including books, prints, maps, and more

Decipher confusing citations

Find full-text articles

Identify article databases in your subject area

Distinguish when and how to request material through Interlibrary Loan

Identify your librarian

Date & Time:      2:00pm - 2:50pm, Thursday, January 28, 2016

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

Registration Required:


Tools for gene enrichment analysis

Description:                        Bioinformatics enrichment tools play an important role in identifying, annotating, and functionally analyzing large list of genes generated by high-throughput technologies (e.g. microarrary, RNA-seq, ChIP-chip). This workshop will provide an overview of the principle, type of enrichments, and the infrastructure of enrichment tools. By using concrete examples, it will also introduce some of the most popular tools for gene enrichment analysis such as DAVID, GSEA, and WebGestalt, as well as the proprietary softeare MetaCore.

Date & Time:      12:00pm - 1:30pm, Thursday, February 4, 2016

Location:              SHM L Simbonis Room 101A Yale Medical Library, 333 Cedar St. New Haven CT 06520

Registration Required:


Systematic Reviews: Conducting comprehensive searches

Description:        One critical step in the SR process is to comprehensively search the literature. This workshop will introduce procedures to ensure that your search is comprehensive, methodical, transparent and reproducible.

Date & Time:      1:30pm - 3:00pm, Wednesday, February 10, 2016

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

Registration Required:


The VERY Basics of the Unix Command Line

Description:        A lot of biomedical software programs do not come with a graphical user interface (GUI), and a Unix command-line terminal environment is required to run such programs. In this 2-hour session, you will learn the basics of a Unix command-line terminal, such as how to navigate the file system, the permission and security structure, and how to run programs from the command line. No previous Unix or command-line experience is required to attend this session.

Free and open to any Yale University student, faculty and staff. 

Registration required since the number of seats is limited.

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

Date & Time:      2:00pm - 4:00pm, Thursday, February 11, 2016

Registration Required:


Date & Time:      10:00am - 12:00pm, Thursday, April 14, 2016

Registration Required:


Introduction to patents and patent searching

Description:        Patents are challenging but important sources for product development and discovery of technical information. This workshop will provide a basic introduction to the patent literature and the United States patent process. We will look at tools and strategies for locating patents and intellectual property.

Date & Time:      2:00pm - 3:00pm, Friday, February 19, 2016

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

Registration Required:


Introduction to Genome Browsers

Description:        In this workshop we will learn how to navigate the genome browsers from NCBI's Genome Workbench, UCSC Genome Browser, and Ensembl. These browsers are valuable tools when identifying, localizing genes, and looking at their information in the genomic context. By using concrete examples, it will be shown how to locate a human gene, download a gene sequence and its upstream sequence, locate Single Nucleotide Polymorphisms (SNPs) and conserved regions, and use the browsers to download results in a batch

Date & Time:      12:00pm - 1:30pm, Thursday, February 25, 2016

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

Registration Required:


Cytoscape: Going from Raw Data to a Publishable Image

Description:        These hands-on workshops will demonstrate the use of Cytoscape, an open source molecular interactions visualization tool. Cytoscape allows for the exploration of molecular interactions and biological pathways and integrates these networks with annotations, gene expression profiles, and other data.  One session, “Cytoscape:  Going from Raw Data to a Publishable Image,” will cover core functions, such as learning how to import network and attribute data, change visual properties to easily distinguish biologically significant relationships, create a legend for the image, manually add nodes/edges, etc.

Date & Time:      9:00am - 12:00pm, Thursday, March 3, 2016

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

Presenter:          Marci Brandeburg, University of Michigan.

Registration Required:


Cytoscape apps with a Focus on MetScape

Description:        This hands-on workshop will provide an introduction to Cytoscape apps, which add functionality to the core software.  It will focus on a specific app example, MetScape, which is used to visualize and interpret metabolomics and gene expression data in the context of human metabolic networks.  A brief introduction to other apps, such as MCODE (cluster finding tool), SocialNetwork (builds co-publication networks), and MetDisease (annotates metabolic networks with MeSH disease terms) will be included.

Date & Time:      1:30pm - 4:00pm, Thursday, March 3, 2016

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

Presenter:          Marci Brandeburg, University of Michigan

Registration Required:


BioMart: A Research Data Management Tool for the Biomedical Sciences

Description:        Some complex biomedical questions cannot be answered by reading the published literature. These may require aggregation of data from several data sets. In this regard, BioMart ( is a freely available open source system that allows complex queries across more than 40 different biological data sets through a single web interface. Originally developed for the Ensembl genome browser, BioMart has been integrated into widely used software such as Galaxy, BioConductor, and Cytoskape. The BioMart interface is also used by data portals such as Ensembl, Wormbase, Gramene, and Reactome.


In this workshop we will use simple examples to demonstrate how to navigate, build queries, and save and export the results on BioMart such as:

- how to retrieve the Ensembl mouse genes and genomic locations in the first 10 Mbp of chromosome 1 region;

- retrieving 1 kb of upstream sequences from a cluster of human genes identified by an expression profile experiment;

- obtain a list of the SNPs that have been associated with RB1. For the SNPs, obtain several attributes such as source, rs ID, chromosome location, and pathogenicity


Date & Time:      12:00pm - 1:30pm, Thursday, March 10, 2016

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

Presenter:          Rolando Milian

Registration Required:


Novel Online Tools for Mining the Biomedical Literature


The rapid growth of experimental and computational biomedical data is being accompanied by an increase in the number of biomedical publications discussing these results. This makes retrieving relevant scientific information and identifying connections between findings, a challenging task. New literature-mining tools that make use of Natural Language Processing Algorithms and data visualization (e.g. CoreMine, NextBio, Semantic MEDLINE, etc) may be of help when sorting through this abundance of literature as discovery and hypothesis generating tools. This workshop provides an introduction on how to use some of these literature-mining tools when answering research questions and generating/narrowing hypothesis.

Date:     Thursday, March 24, 2016

Time:     12:00pm - 1:30pm

Location:              Cushing/Whitney Medical Library at Yale University, Simbonis Conference Room 101A, 333 Cedar St, New

Presenter:          Rolando Milian

Registration Required:


My Bibliography and SciENcv: grant reporting, compliance and biosketch through MyNCBI

Description:        Although not required at this point, the NIH suggest the use of the Science Experts Network Curriculum Vitae (SciENcv), -a MyNCBI online tool- that serves as an interagency system designed to create biosketches for multiple federal agencies. This, along with the use of My Bibliography for grant activity reporting and NIH Public Access Policy compliance, increases the importance using MyNCBI as a tool for managing NIH-sponsored research. This workshop introduce researchers, research assistants and administrators on the effective use of these online tools and will cover the following among other topics:

How to create MyNCBI account and how to link it to the eRA Commons account

How to delegate your account

 How to populate and manage My Bibliography

How to use My Bibliography for grant reporting/compliance

How to use SciENcv to create different biosketches (from scratch, from external source, etc)

How to create and ORCID ID* and how to link SciENcv to that ORCID ID


*ORCID stands for Open Research and Contribution ID. Some publishers and journals (Springer, Wiley, Journal of Neuroscience, The Journal of Immunology, etc.) are asking authors to submit their ORCD ID along with their manuscripts for publication.


Date & Time:      12:00pm - 1:00pm, Thursday, April 21, 2016

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

Presenter:          Rolando Milian

Registration Required:




Cushing/Whitney Medical Library 75th Anniversary Kickoff

25 January 2016 - 4:23pm by Andy Hickner

(by Janene Batten)

Over the course of 2016, the Cushing/Whitney Medical Library will be celebrating 75 years since its founding.   The Medical Library’s anniversary kick-off event on Friday was a great success. Harvey Cushing himself made a special appearance. He was available for photographs with everyone, including these 3 students.

students with Cushing cutout

Interim director John Gallagher cuts the cake

Everyone enjoyed the cake, which featured the Library’s 75th logo.  The Library has also begun to collect audio snippets of people's recollections of the Library. We will soon begin to update the library's Facebook page with these stories.

Dr Duffy, Mark Gentry, and Janene Batten

You are welcome to attend any of the variety of 75th Anniversary Events which are open to our patrons and friends. If you have a special memory, please share your story . And as the year progresses, come back and read the impact that the Library has had on others.

Call for donations of Second Year Show videos/DVDs

25 January 2016 - 11:48am by Andy Hickner

The Medical Historical Library is looking for videos/DVDs for the Medical School’s Second Year Shows.  We tend to get requests for the shows on at least yearly, when the current Second Year Show is in production. While we have some of the shows, we don’t own the last few years (2011-2015) and very little before 2005.  If you own a Second Year show, please considering donating (or allowing us to make copies) of the show for our Archives.  

Winter 2016 exhibit: "Contra Cocaine and Other Works by Robbie Conal, Guerrilla Artist"

25 January 2016 - 11:30am by Andy Hickner

Robbie Conal contra cocaine poster

The powerful, gritty political posters of Robbie Conal are seen on city streets and the walls of major museums. This selection includes "Contra Cocaine," 1988, which addresses the introduction of crack cocaine into the U.S. via Los Angeles in the 1980s and "Freedom From Choice," 1992, on a woman's right to abortion information in publicly funded clinics. From Conal's series of political portraits, former Speaker of the U.S. House of Representatives John Boehner appears in "Wealth Care," 2011.

The exhibit is open to the public and runs Thursday, January 21, 2016 - Friday, April 1, 2016.

Contest Winners for "Discovering the Beauty of Science"

13 January 2016 - 4:08pm by Andy Hickner

(by Rolando Garcia Milian and Terry Dagradi)

Last summer we invited Yale biomedical researchers (undergrads, graduate students, postdocs, faculty, associate researchers, etc.) to share results from their work where they felt the images produced in search of science crossed over to art.  We thank all of you who submitted and appreciate your willingness to share with the community. 

The images were reviewed by a committee including New Haven sculptor Gar Waterman, Sarah Fritchey (Curator / Gallery Director at Artspace New Haven), and Dr. Derek K. Toomre, Associate Professor of Cell Biology and Director of the YALE 'CINEMA’ Laboratory. Together, they selected many of the images currently on exhibit in the foyer of Cushing/Whitney Medical Library as well as the three 1st Honor awardees.

The 1st Honor Awardees are:

Marco Onorati, Department of Neurobiology

Neurons in a Dish, 2015

Juror comments: “Neuron: Good rendition, dreamy quality”  “The fantastic crystalline structure in the center of this composition is very powerful. The sense of pull and energy is so forceful that it almost suggests a big bang moment.”

Neurons in a Dish

(Click to view larger image)

Neurons differentiated in a dish from stem cells.  Microphotograph, fluorescence. 


Mustafa Khokha, Department of Pediatrics

Frog Head, Year: 2015

Juror comments: “Great composition and detail.”  “Just a cool thing, whatever it is”

Frog head

(Click to view larger image)

Xenopus laevis tadpole (frog). Brain (green) and Actin (red) and nuclei (blue) View from the back of the head over the Imaged with Leica Sp8 Confocal by Helen Rankin Xenopus Cold Spring Harbor Course.


Kate Henderson, Department of Pathology

Stones Dreaming, 2013

Juror comment: “My favorite - love this one - fabulous color and pattern”

Stones dreaming

(Click to view larger image)

Abstract digital composition of microscopy endocrine images.

Image description: I create environments from natural elements to give people a sense of place, describing emotional essence and energy that connects us to each other and everything around us. My images both describe and celebrate the intrinsically aesthetic structure of the natural world and the ever-present duality in all things. I invite the viewer to see and feel the world both within us and around us, experiencing the macro vs microelements common to all.

Painting-with-cells is how I describe the cyto-Illusions series. I start by using microscope images of human cells and also images of abstraction “found” in nature. Through layering and manipulation techniques, I create an image that mirrors micro images on a macro level. On one level the images are a colorful abstraction that allow the viewer to freely explore and experience the image on their own. Many images are suggestive of a specific element such as water, but others are more environmentally placed. On another level the images are about the reality of nature; cells of disease, the growth structure of plants, and the patterns of light filtered through the leaves.


The Viewers’ Choice Award

This was determined by all those who voted (404 votes total) on an exhibition album created on the Medical Library Facebook page.

Laura Pappalardo – Department of Neurology

Astrocytes display robust intracellular calcium response in model of astrogliosis, 2013


(Click to view larger image)

Astrocytes, a non-neuronal type of cell in the brain and spinal cord, respond to central nervous system insult through the incompletely understood process of reactive astrogliosis, which is a hallmark in pathologies such as multiple sclerosis and spinal cord injury. While the ramifications of astrogliosis are debated, it is agreed that in its extreme forms, this process leads to the formation of a scar, which is long-lasting and can inhibit the regeneration of injured neurons. While the molecular drivers of astrogliosis are an area of active investigation, a clearer understanding is needed. Here, we show that after a scratch injury, there is a robust intracellular calcium response, which propagates through the syncytium of confluent astrocytes (red indicates high intracellular calcium). This calcium transient leads to downstream signaling that can regulate the astroglial response to injury. We are currently working to investigate the mechanisms behind this phenomenon, paying particular attention to voltage-gated sodium channels.

Color scale represents the ratio of fluorescent signals induced by 340 and 380 nm excitation in cells loaded with Fura-2 AM. Scale bar, 50 ╡m. In collaboration with Stephen Waxman, Joel Black, Mark Estacion, and Omar Samad.

The Cushing/Whitney Medical Library celebrates 75 years

13 January 2016 - 2:04pm by Andy Hickner

Medical Library Rotunda

Join us as the Cushing/Whitney Medical Library celebrates 75 years of being YOUR library. We are planning a year long program of exciting events. Mark your calendar for these highlights and watch for additional events, exhibits and information.

January 22, 2016, 3-5pm
75th Anniversary Kickoff Party

April 6, 2016, 4pm
Associates Lecture and Reception, Immune system in health and disease. Dr. Ruslan Medzhitov

June 3, 2016, 3pm
Special Presentation, Harvey Cushing and John Fulton: Two Icons of the Roaring Twenties Bonded by Medicine and Books.  Dr. Dennis D. Spencer and Dr. Gordon Shepherd

October 5, 2016, 3-5pm
75th Anniversary Gala

Beaumont Club Lecture on "Historical Illustrations of Skin Disease" Exhibit, Friday, January 15

12 January 2016 - 10:35am by Andy Hickner

Skin disease lecture

On Friday 1/15 at 5pm, the Beaumont Club is sponsoring a lecture about the Library's exhibit “Historical Illustrations of Skin Disease: Selections from the New Sydenham Society Atlas 1860-1884.”  The lecture will be given by Jean Bolognia, MD, and Irwin Braverman, MD, both of the Department of Dermatology, and Susan Wheeler, Curator of Prints and Drawings at the Medical Library. More details are available on the School of Medicine calendar.

What's a guide? And how can Yale library guides help me?

11 January 2016 - 3:12pm by Andy Hickner

Librarians at Yale have developed numerous online guides for Yale users.  Here at Yale, our guides can provide a number of things, including:

  • Research guidance for a particular Yale course;
  • Instructions on how to research a subject;
  • Documentation for a research tool or service; or
  • Instructions on accessing and using collections or resources.

You might find different guides of particular interest based on your role and field, for example:

Get started exploring our full list of guides in the field of medicine, or browse all Yale guides including on topics outside the health sciences. 

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