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Reader's Advisory: "Darkness Visible," Depression Screening Month, and the Styron-Yale connection

17 October 2016 - 10:21am by Andy Hickner

Darkness Visible by William Styron"In depression this faith in deliverance, of ultimate restoration, is absent. The pain is unrelenting, and what makes the condition intolerable is the foreknowledge that no remedy will come—not in a day, an hour, a month, or a minute. It is hopelessness even more than pain that crushes the soul." 

-- William Styron

If you're a Yale Health patient, you probably received an email announcing "October is Depression Screening Month."

Many, if not most, of the readers of this post will have either struggled with depression at one point or have helped a loved one battle the disease. When a close family member suffered an episode of major depression a few years ago, I did a lot of reading on the topic.  One of the most vivid and eloquent first-hand accounts of depression is Darkness Visible:  A memoir of madness by the great novelist William Styron. 

Styron and his family lived in Connecticut, and it was to Yale-New Haven Hospital (YNHH) where Styron was admitted, suicidal, at the nadir of his depression in 1985.  In part thanks to the care he received at YNHH, Styron was able to recover and went on to document his experience.  While the story of depression told in Darkness Visible is terrifying, Styron argues that there is hope for the suffering patient:

"To most of those who have experienced it, the horror of depression is so overwhelming as to be quite beyond expression, hence the frustrated sense of inadequacy found in the work of even the greatest artists... If our lives had no other configuration but this, we should want, and perhaps deserve, to perish; if depression had no termination, then suicide would, indeed, be the only remedy. But one need not sound the false or inspirational note to stress the truth that depression is not the soul’s annihilation; men and women who have recovered from the disease—and they are countless—bear witness to what is probably its only saving grace: it is conquerable."

You can borrow a copy of the book from Yale University Libraries using Quicksearch.  

New at Yale: Covidence, a tool for systematic reviewers

3 October 2016 - 4:10pm by Andy Hickner

(by Holly Grossetta Nardini)

Covidence interface

The Library recently licensed a web-based tool to streamline the tedious task of producing systematic reviews. Covidence has an intuitive, easy-to-use interface that makes screening articles faster, while still following the recommended protocols for producing systematic reviews. It even works on mobile devices, allowing you to chip away at screening during small windows of time. To use Covidence, contact your medical librarian to open an account. At least one member of the research team must be based at Yale, but Covidence allows for seamless collaboration across institutions. Including a librarian on the research team will improve the quality of the literature search, which is the foundation for a systematic review. Consult our Systematic Review Service page for details. 

 

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

19 September 2016 - 10:09am by 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 by 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 by 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 by 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 by 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 by 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 by 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.

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