Home


Off-Campus Access

Blogs

(2 X 2) 2 High-throughput Data Analysis Workshops X 2 on NCBI Public Databases.

19 September 2016 - 10:09am -- Rolando Garcia-Milian

Cushing/Whitney Medical Library has organized these four workshops, two of them on high-throughput data analysis tools and two on NCBI public databases. Although these are free and open to any Yale affiliate, registration is required due to limited seating.  

Title:      NGS Data Analysis in Partek® Software: Onsite Workshop

Registration: http://schedule.yale.edu/event/2819565

Description:   

Morning Session (Overview, Hands On: Analysis on RNA-Seq Data): 9:00AM – 12:00PM

Free access to Partek Flow is provided by the Yale Medical Library. Register for an account here

This session will start with an overview of Partek Software solutions followed with a hands on RNA-Seq Data Analysis in Partek Flow. Topics will include how to use statistical tests to identify differentially expressed transcripts and alternative spliced genes among sample groups, how to generate a list of genes of interest and identify high level biological trends using Gene Ontology.

  • Import data (fastq, bam, text format)
  •  Perform QA/AC (Pre-alignment QA/AC, Post-alignment QA/QC)
  • Trim bases
  • Alignment
  • Gene/transcript abundance estimate (E/M)
  •  Differential expression detection (GSA, ANOVA)
  • Filter gene list
  • GO Enrichment Analysis
  • Visualization
    • Quality score distribution
    • Base composition
    • PCA scatterplot
    • Dotplot
    • Volcano plot
    • Hierarchical clustering
    • Chromosome view

Afternoon Session (Open Lab; Q&A): 1:30PM – 4:00PM

We hope to see you there!

 
Date & Time:     9:00am - 12:00pm, Thursday, September 29, 2016

Location:           C-103, SHM, 333 Cedar St

Campus:           Medical School

Presenter:          Eric Seiser, PhD, Field Application Scientist, Partek Inc.

 

Title: Broadcast. Navigating NCBI Molecular Data Using the Integrated Entrez System and BLAST

Registration: http://schedule.yale.edu/event/2832345

Description: This workshop will be broadcasted from the Taubman Health Sciences Library, Univ Michigan, and provides an introduction to the NCBI molecular databases and how to access the data using the Entrez text-based search system and BLAST sequence similarity search tool. You will learn the varied types of available molecular data, and how to find and display sequence, variation, genome information using organism sources (Taxonomy), data sources (Bioproject) and emphasizing the central role of the gene as an organizing concept to navigate across the integrated databases (Gene, Nucleotide, Protein, dbSNP and other resources).

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

Presenter: Peter Cooper, Ph.D. of the National Center for Biotechnology Information

Date/time: 9:00am - 12:00pm, Tuesday, October 4, 2016

 

Title: Broadcast. A Practical Guide to NCBI BLAST

Registration: http://schedule.yale.edu/event/2832347

Description: This workshop will be broadcasted from the Taubman Health Sciences Library, Univ Michigan and highlights important features and demonstrates the practical aspects of using the NCBI BLAST service, the most popular sequence similarity service in the world. You will learn about useful but under-used features of the service. These include access from the Entrez sequence databases; the new genome BLAST service quick finder; the integration and expansion of Align-2- Sequences; organism limits and other filters; re-organized databases; formatting options and downloading options; and TreeView displays. You will also learn how to use other important sequence analysis services associated with BLAST including Primer BLAST, an oligonucleotide primer designer and specificity checker; the multiple protein sequence alignment tool, COBALT; and MOLE-BLAST, a new tool for clustering and providing taxonomic context for targeted loci sequences (16S, ITS, 28S). These aspects of BLAST provide easier access and results that are more comprehensive and easier to interpret.

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

Presenter: Peter Cooper, Ph.D. of the National Center for Biotechnology Information

Date/time: 9:00am - 12:00pm, Wednesday, October 5, 2016

 

Title:      Make new discoveries with your OMICs data: Hypothesis testing and assumption-free exploration

Registration: http://schedule.yale.edu/event/2832289

Description:       

10AM- Noon:

  • Exemplary workflows for different experiment designs
  • Hypothesis testing and Assumption-free data exploration
  • Working with annotations, dynamic and interactive plots

Input data: any matrix multivariate data (RNAseq, Microarrays, Proteomics, miRNA, Metabolomics, Lipidomics, methDNA, Mulitplex and FACS, Clinical data, Biomarkers, etc.), as well as publicly available GEO data, gene sets files, gene ontology. Complete list is available here.

1-2PM:

Getting started session – take advantage of a trial access for Yale! Have a look the info uploaded to the Yale Library folder, including presentation, case studies, tutorials, etc.

Qlucore tools allow researchers to perform advanced visualization, exploration and statistical analysis of omics data with the help of an intuitive GUI. Targets of interest can be further explored in terms of biological insight using GO and GSEA.  Unmatched speed, immediate visual feedback, continuous visualization, and synchronized views significantly shorten both data-to-result and query-to-discovery times.

By combining right annotations with statistical methods, data selection tools, and the eliminated factors function, a very broad range of different experiment designs can be analyzed with exceptional productivity. This solution draws upon both innovative and classical approaches, fueled by best-in-class industrial and academic research.

Qlucore Omics Explorer helps you advance your research by:

  • boosting the speed of your analysis at least by 50%
  • generating new ideas, hypotheses, and giving you a new prospective on your data, and questions you ask of it
  • helping recognize significant insight that is specific to biological process, disease, or function, as well as assumption-free exploration
  • keeping your projects on track with simple QC checks on every step
  • providing publication ready graphics, and intermediate results for collaboration.

Qlucore Omics Explorer is used by big commercial companies as well as major research organizations and Universities across Europe and US. (e.g., Boehringer Ingelheim, Roche Diagnostics,  AstraZeneca, DFCI, BWH, Harvard, MD Anderson, MSKCC, MedImmune, Novo Nordisk, etc.).

Date & Time:     10:00am - 12:00pm, Thursday, October 27, 2016

Location:           C-103 - SHM 333 Cedar St

Campus:            Medical School

Presenter:          Yana Khalina-Stackpole, PhD, Business and Support manager, Qlucore

’The AIDS Suite,’ HIV-Positive Women in Prison and Other Works by Artist/Activist Sue Coe

12 September 2016 - 12:16pm -- Andy Hickner

A drawing from "The AIDS Suite"
A drawing from "'The AIDS Suite,' HIV-Positive Women in Prison and Other Works by Artist/Activist Sue Coe"

YaleNews recently profiled the Library's upcoming exhibition of “’The AIDS Suite,’ HIV-Positive Women in Prison and Other Works by Artist/Activist Sue Coe." As YaleNews' Mike Cummings reports, "The exhibit... features 27 drawings and prints by Coe, whose work has been published in The New York Times, The New Yorker, and Rolling Stone":

Coe’s artwork is represented in the collections of major museums, including (the) Metropolitan Museum of Art, Museum of Modern Art, and Whitney Museum of American Art.

Five of the large-format drawings on display are from “The AIDS Suite,” a series of drawings she made from 1993 to 1994 based on her experiences observing patients of Dr. Eric Avery, an artist, activist, and psychiatrist, on the AIDS ward of the University of Texas Medical Branch in Galveston, Texas. 

Join us this Thursday, September 15 for a conversation with Coe and Dr Avery at 5pm in the Medical Historical Library.

Fall Training Sessions on Bioinformatics at the Medical Library

6 September 2016 - 10:40pm -- Rolando Garcia-Milian

The Yale Medical Library is offering a number of bioinformatics training session this Fall. These sessions are free and open to any Yale affiliate but registration is required due to limited seating.

Please contact Rolando.milian@yale.edu  for questions or comments.

 

Title: The VERY Basics of the Unix Command Line

Registration required: http://schedule.yale.edu/event/2800083

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.

Date: Thursday, October 6, 2016

Time: 10:00am - 12:00pm

Location: Cushing/Whitney Medical Library, Room 103 TCC, 333 Cedar St

Campus: Medical School

 

Title: Introduction to Enrichment Analysis Tools

Registration required: http://schedule.yale.edu/event/1154118

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 free tools for enrichment analysis as well as those licensed by the Medical Library

Date: Thursday, September 8, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St. Campus: Medical School

 

Title: Making Sense of Genomic Variation: Part 1 SNP Annotation

Registration required: http://schedule.yale.edu/event/2794996

The specific combination of genetic variation in an individual defines not only the external appearance but also susceptibility to diseases, cancer, genetic disorders, drug response, etc. This explains the great interest in discovering and cataloging these variations and using them for disease association and functional studies, among others. In this session we will review the most popular databases and tools to annotate, analyze and visualize genetic variations. Some of the databases and tools that will be discussed are:

  • dbSNP
  • Online Mendelian Inheritance in Man a comprehensive, authoritative compendium of human genes and genetic phenotypes.
  • GWAS Catalog/PheGenI
  • EBI-Ensembl Variant Effect Predictor to annotate and determine the effect of variants on genes, transcripts, and protein sequence, as well as regulatory regions.
  • And more…

Date: Thursday, September 22, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St.

Campus: Medical School

 

Title: Making Sense of Genomic Variation: Part 2 Structural Variants

Registration required: http://schedule.yale.edu/event/2795002

Structural variation encompasses diverse types of genomic variants including deletions, duplications, inversions, transpositions, translocations, among others. In many cases, determining whether a particular genetic variant is pathogenic or benign and its correlation with respect to a patient's disease phenotype is challenging.

In this session we use online resources and tools to find, retrieve, annotate, and visualize structural variants

  • NCBI’s database of genomic structural variants dbVar
  • Database ofDatabasE of Chromosomal Imbalance and Phenotype in Humans
  • Genomic Variants DGVa
  • UCSC and Ensembl genome browsers

Date: Thursday, October 6, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St.

Campus: Medical School

 

Title: Introduction to Genome Browsers. Part 1 Ensembl

Registration required: http://schedule.yale.edu/event/2795004

Ensembl provides access to genomic information with a number of visualization tools. By using Ensembl researchers can download data directly (e.g., genomic sequences), visualize many types of data (e.g., structural, variation, regulatory) directly on a genome assembly. In this session will review the basic functionalities and navigation of Ensembl by using specific examples. We will also use BioMart interface to answer questions and retrieve data and information from databases without the need of having any programming expertise.

Date: Thursday, October 20, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St.

Campus: Medical School

 

Title: Understanding Research Impact

Registration required: http://schedule.yale.edu/event/2803327

Nowadays, it is not uncommon for employers, academic institutions, and funding agencies to ask for evidence of research impact before making important decisions, such as tenure promotions, academic honors, or grant awards. Therefore, it is important for researchers to understand what research impact is and what they can do to document, enhance, measure and present their research impact to those decision makers. This session introduces the core concepts of research impact, its deep roots and long tradition, the various quantitative metrics of impact, and an emerging practical framework for telling impact stories. This session also introduces how to publish and disseminate research work in ways that improve discoverability and therefore enhance impact.

Date: Thursday, November 10, 2016

Time: 10:30am - 11:30am

Location: Cushing/Whitney Medical Library, Room 103 TCC, 333 Cedar St

Campus: Medical School

 

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

Registration required: http://schedule.yale.edu/event/2795006

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 introduces 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: Thursday, December 1, 2016

Time: 11:00am - 12:30pm

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

Campus: Medical School

 

Title: The VERY Basics of the Unix Command Line

Registration required: http://schedule.yale.edu/event/2803929

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.

Date: Thursday, December 8, 2016

Time: 10:00am - 12:00pm

Location: Cushing/Whitney Medical Library, Room 103 TCC, 333 Cedar St.

Campus: Medical School

 

For a full list of training sessions including PubMed, EndNote, etc. , please visit the medical library calendar: http://library.medicine.yale.edu/classes

Mark your calendars: Our 75th Anniversary Celebration, October 5

30 August 2016 - 11:30am -- Andy Hickner

The Cushing/Whitney Medical Library is celebrating our 75th anniversary with a special event on Wednesday, October 5, 2016, from 3-5pm in the Medical Historical Library. Stop by "The Medical Library at 75" exhibit, view videos and stories about the library collected this year, and take a selfie with Harvey Cushing. We hope you can join us! 

Starting Wednesday, September 7, we are also launching our weekly "Find Harvey" challenge, with special prizes. Stay tuned for further details by liking our Facebook page, where we are posting a series of facts about the history of the library. 

Find Harvey in the library and return him to the Circulation Desk to win a travel mug prize pack.  Finders will be entered into a Grand Prize Drawing to be held on October 5

Our therapy dog Finn's hours for fall 2016 (UPDATED September 6)

25 August 2016 - 9:52am -- Andy Hickner

Our therapy dog Finn returns on Friday, September 2. Finn will be here most Fridays from 10am-noon noon-2pm, including: 9/2, 9/9, 9/23, 9/30, 10/14, 10/28, 11/4, 11/11, 11/18, 12/2, 12/9.  Finn is taking a couple of Fridays off, including 10/21 (October break) and 11/25 (Thanksgiving break). 

Tips for new students: Personal librarians, booking study rooms, and more

10 August 2016 - 4:14pm -- Andy Hickner

This week the library welcomes incoming students.  We felt it was a good time to highlight a few links you might find handy as you start your studies at Yale.

First, there's our personal librarian program.  Did you know every YSM, YSN, and YSPH student has a personal librarian?  Here's a video about the program that we love, made by YSM students back in 2009:

Here are a few more links you might find useful:

Welcome!  And stay tuned for more helpful tips.

Back to School Supply Drive, August 8-August 22, 2016

9 August 2016 - 12:36pm -- Andy Hickner
Yale’s diversity affinity groups are partnering to collect donations of school supplies for elementary students in New Haven’s Brennan-Rogers Magnet School.  Please consider donating new supplies, such as:
  • Binders
  • No. 2 pencils
  • Pens
  • Notebook paper
  • Erasers
  • Rulers
  • Scotch tape
  • Markers
  • Pocket folders
The Library is hosting a drop box in the lobby.  For questions, please contact the Office of Diversity & Inclusion at (203) 432-9667.

Beneath the Surface: Watermarks and Flayed Figures in Cushing’s Manuscript of Jacob van der Gracht

26 July 2016 - 10:31am -- Andy Hickner

(by Erin Travers*)

An image from Gracht Anatomie

Drawing after Jacob van der Gracht's Third Figure, Cushing Manuscript, Yale University. Early-18th century. Red and Black Chalk

On the back of a letter from the antiquarian and bookseller Menno Hertzberger, dated 29 March 1927, Harvey Cushing recorded his observations concerning a manuscript of Jacob van der Gracht’s printed drawing book, the Anatomy of the outer parts of the human body (The Hague, 1634; Rotterdam, 1660), which had been sent to Boston from Amsterdam. This text, prepared by the seventeenth-century Dutch painter and engraver for the use of “Painters, Sculptors, Engravers, and also Surgeons,” brought Van der Gracht renown during his life, and continues to be his most well known work today. The manuscript version contains twenty-two pages of text and illustration, including a handwritten version of Van der Gracht’s preface, a section on the bones taken from André du Laurens, fragmented comments on the muscles, and explanatory registers for the accompanying illustrations of skeletal and écorché figures that mimic those published in Andreas Vesalius’s De Humani Corporis Fabrica (Basel, 1543). Hopeful that the drawings may have been preparatory works for the engraved plates, on inspection, Cushing found that the use of red and black chalk to demarcate the flesh and bones of the figures, while visually pleasing, was not conducive to the medium of print. Moreover, he writes that the larger scale of the figures and the presence of the registers on the back of the illustrations, made it unlikely that these were the final cartoons from which Van der Gracht worked, though they may have been an earlier experiment by the seventeenth-century Dutch artist. Contemplating whether a previous owner may have added the text to the illustrations at a later date, Cushing noted, “The paper, however, in the original seven leaves of text bears the same watermarks as that on which the drawings are made. It would be interesting to know the date and place of this paper.”

During my time at the Harvey Cushing/John Hay Whitney Medical Library at Yale University as a Ferenc Gyorgyey Travel Research Grant recipient, I have pursued Cushing’s curiosity and investigated the watermarks hidden in the paper of the Van der Gracht manuscript to determine the date and location of its production.  Using online databases, including the Memory of Paper, (http://www.memoryofpaper.eu/BernsteinPortal/appl_start.disp) compiled by the Bernstein Consortium, my research makes use of resources that were not available to Cushing in the early twentieth century. Moreover, it is only with the relatively recent publications on Dutch watermarks, such as Theo and Frans Laurentius’s study of the Zeeland archives, or Nancy Ash, Shelley Fletcher, and Erik Hinterding’s works on Rembrandt’s prints, that this type of research is possible. Yet, despite the advances made in this field since the early twentieth century, this method for dating a work on paper should be approached with caution, as the medium is both geographically and temporally transient, and therefore should be considered as a general guide for attribution.

Fleur-de-lys watermark
Fleur-de-lys watermark

"IV" countermark
"IV" countermark

Together, watermark analysis and study of the formal properties of the drawings offers complementary evidence through which we can determine the relation of the manuscript to the published drawing book. The Cushing manuscript offers a clean and consistent watermark of a Strasbourg Bend, a shield with two diagonal bands that is mounted by a fleur-de-lis, and a countermark of the letters “IV."  Indicting the initials of the paper maker Jean Villedary (1668-1758), the countermark, design of the watermark, their size and relation to the vertical chain lines of the paper are consistent with samples dating from Amsterdam and London between 1718 and 1722, making it likely that the manuscript was produced in the first quarter of the eighteenth century (Churchill, no. 437 and Heaward, nos. 73 and 78). Given this date, the possibility that the drawings could have been executed prior to the publication of the printed text is unlikely, and visual analysis of the figures confirms this hypothesis. The process of engraving in the early modern period entailed the incision of a design into a copper plate, which was coated with ink and then pressed onto a piece of paper, transferring the image and resulting in the reversal of the initial example. Essentially, the preparatory work and final print should appear as mirror images of one another. However, in the case of the Cushing manuscript, the figures share the orientation found in the final prints. 

Carefully adhering to the model provided by the prints, the drawn figures that occupy the Cushing manuscript are copies made at a later date, and as such offer information concerning the continued engagement with and changing expectations of these types of illustrations by artists and anatomists. Questions concerning this shift are addressed in my on-going dissertation research, which examines the exchange and adaptation of pictorial knowledge between artists and anatomists in the seventeenth-century Netherlands. I am grateful to the Cushing/Whitney Medical Library for its support of my project, and greatly appreciate the opportunity to investigate an inquiry first raised by Cushing nearly one hundred years ago.

Erin Travers

*Erin Travers is a PhD candidate, history of art and architecture, University of California, Santa Barbara, and a 2016 Ferenc Gyorgyey Fellow

The Library at 75: Remembering the first PC in the library

22 July 2016 - 4:22pm -- Andy Hickner

The First PC in the Library : Looking back as we celebrate the 75th Anniversary of the Cushing/Whitney Medical Library from Lei Wang on Vimeo.

As part of our 75th anniversary commemorations, we recently sat down with retired Library Director Kenny Marone and Assistant Director Jan Glover to talk about some of their memories of decades past and to learn how the Library has changed over the years.  In this excerpt from their conversation, Kenny and Jan reminisce about when the first PC came to the Library.  Watch more 75th anniversary video interviews, and share your own stories, at http://library.medicine.yale.edu/75.

Spotlight on the Humanities in Medicine Collection

14 July 2016 - 6:31pm -- Alyssa Grimshaw

Spotlight on the Humanities in Medicine Collection

 

Check out the newest book in the Humanities in Medicine Collection, Aliceheimer’s Alzheimer’s Through the Looking Glass.

Image of the cover of Aliceheimer's Alzheimer's Through the Looking Glass

Excerpt from the book cover:

“Alice was always beautiful—Armenian immigrant beautiful, with thick, curly black hair, olive skin, and big dark eyes,” writes Dana Walrath. Alice also has Alzheimer’s, and while she can remember all the songs from The Music Man, she can no longer attend to the basics of caring for herself. Alice moves to live with her daughter, Dana, in Vermont, and the story begins.

Aliceheimer’s is a series of illustrated vignettes, daily glimpses into their world with Alzheimer’s. Walrath’s time with her mother was marked by humor and clarity: “With a community of help that included pirates, good neighbors, a cast of characters from space-time travel, and my dead father hovering in the branches of the maple trees that surround our Vermont farmhouse,Aliceheimer’s let us write our own story daily—a story that, in turn, helps rewrite the dominant medical narrative of aging.”

In drawing Alice, Walrath literally enrobes her with cut-up pages from Alice’s Adventures in Wonderland. She weaves elements from Lewis Carroll’s classic throughout her text, using evocative phrases from the novel to introduce the vignettes, such as “Disappearing Alice,” “Missing Pieces,” “Falling Slowly,” “Curiouser and Curiouser,” and “A Mad Tea Party.”

Walrath writes that creating this book allowed her not only to process her grief over her mother’s dementia, but also “to remember the magic laughter of that time.” Graphic medicine, she writes, “lets us better understand those who are hurting, feel their stories, and redraw and renegotiate those social boundaries. Most of all, it gives us a way to heal and to fly over the world as Alice does.” In the end, Aliceheimer’s is indeed strangely and utterly uplifting.

Want to know more about this book? Here is the link to the New York Times blog post by Nancy Stearns Bercaw: http://well.blogs.nytimes.com/2016/06/21/alzheimers-disease-as-an-adventure-in-wonderland/?_r=0 

Humanities in Medicine Collection is located across from the Circulation Desk.

Pages

Subscribe to RSS - blogs