21 August 2015 - 3:52pm by Rolando Garcia-Milian

The National Center for Biotechnology Information is developing a new type of BLAST called SmartBLAST. It process the user query in such a way that presents the three best matches from the non-redundant protein sequence database along with the two best protein matches from well-studied reference species. In addition, it provides results that match the query from the Conserved Domain Database (CDD)
SmartBLAST accepts only one query at a time- either as FASTA sequence or protein accession number/GI- and uses a combination of BLAST and a multiple sequence alignment to produce its results. It first uses the query to search the non-redundant (nr) protein database. Then, it searches the reference database with BLASTP, followed by a multiple sequence alignment on the six sequences (the query and five subject sequences) using the COBALT multiple sequence alignment program.

Screen capture showing the results of a SmartBLAST for TP53 (GI:187830777). Panel A shows the five matching sequences are represented as a phylogenetic tree and a graphical overview. The matches are color-coded: matches from the reference species are green, matches from the non-redundant protein database are blue, and your query is yellow. Panel B represents the results from the multiple alignments.

If you would like to see how SmartBLAST work, please register here for this 15-minute webinar: “Introducing SmartBLAST a Rapid Protein Identification Tool” -September 2, 2015 from 12:00- 12:15 PM at the Medical Library. 

Join the End-User Bioinformatics Network (EBNET) and become a member of a grass root community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research at Yale.

New discount for Yale authors on article-processing charges

20 August 2015 - 9:55am by Andy Hickner

Yale is now a “Supporter Member” of the open access publisher BioMed Central. Yale’s membership provides Yale authors with a 15% discount on article-processing charges of all articles accepted for publication in BioMed Central, Chemistry Central or SpringerOpen journals. Yale’s membership in BioMed Central was made possible through funding from Arcadia.

BioMed Central publishes more than 100 online journals in biology and medicine. The articles in the journals are open access (no subscription or 'pay-per-view' charges), are indexed in PubMed, and are archived in PubMed Central.

Yale’s institutional page on BioMed Central lists Yale authors’ articles and links to more information for authors.

Please feel free to contact Nathan Rupp with questions. For more information on Yale Library’s support of open access, please see Open Access Support.

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

14 August 2015 - 12:59pm 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.

Fall 2015 classes and training at the Medical Library

13 August 2015 - 12:11pm by Andy Hickner

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.
Date & Time:      12:00pm-1:00pm, Wednesday, September 2, 2015
Location:    Medical Library, Room 103 TCC, 333 Cedar St, New Haven, CT 06520
Presenter:     Holly Nardini
Registration Required  

Date & Time:    12:00pm-1:00pm, Thursday, October 8, 2015
Location:    Medical Library, Room 103 TCC, 333 Cedar St, New Haven, CT 06520
Presenter:    Holly Nardini
Registration Required   

Date & Time:    12:00pm - 1:00pm, Thursday, November 5, 2015
Location:    Medical Library, Room 103 TCC, 333 Cedar St, New Haven, CT 06520
Presenter:    Holly Nardini
Registration Required  

Date & Time: 12:00pm - 1:00pm, Friday, December 11, 2015  
Location: Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
Presenter: Holly Nardini
Registration Required 

Interpretation of variants from human next-generation sequencing studies using Ingenuity Variant Analysis
Description: Ingenuity Variant Analysis addresses the challenge of human variant identification and interpretation. It combines analytical tools and integrated content to rapidly analyze variants by drilling down to a small, targeted subset of variants based both upon published biological evidence and your own knowledge of biology. You can easily and quickly interrogate found variants from multiple biological perspectives, explore different hypotheses, and identify the most promising variants for follow-up.
This tool leverages the Ingenuity Knowledge Base, a repository of expertly curated biological interactions and functional annotations created from millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. These include rich details, links to the original article, and are reviewed for accuracy by Ph.D. scientists. The curated content is structured into an ontology that allows for contextual information, computation by the applications, and synonym resolutions.
This interactive introductory seminar will demonstrate capabilities of Variant Analysis and Ingenuity Knowledge Base, and will review preset filtering cascades and added flexibility to customize or create your own interactive cascades in minutes for various kinds of analyses.
The seminar includes demo part and questions and answers session. You are welcome to provide specific agenda suggestions and sign up for a personalized demo and/or consultation

Date & Time:    11:00 AM - 12:30PM, Tuesday, September 15, 2015
Location:    C-103, SHM 333 Cedar St, New Haven CT 06520
Presenter:    Shawn Prince, Bioinformatics Consultant, Sr. Field Application Scientist.
Registration Required

Advanced Searching Techniques
Description:    Take your searching skills to the next level. Covers command language to perform searches, field searching and more. Come with your questions!
Date & Time:    12:00pm-1:00pm, Monday, September 21, 2015
Location:    Medical Library, Room 103 TCC, 333 Cedar St, New Haven, CT 06520
Presenter: Holly Nardini
Registration Required   

Novel Online Tools for Mining the Biomedical Literature
Description: 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 & Time:    12:00pm - 1:30pm, Tuesday, September 22, 2015
Location:    Medical Library, Large Conference Room 101A, 333 Cedar St, New Haven CT 06520
Presenter:    Rolando Milian
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 - 1:00pm, Thursday, October 1, 2015
Location:    Medical Library, Large Conference Room 101A, 333 Cedar St, New Haven CT 06520
Presenter: Rolando Milian
Registration Required 

Tools for 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, MetaCore, and WebGestalt.

Date & Time:    12:00pm - 1:30pm, Thursday, October 15, 2015
Location:    SHM L Room 101A Yale Medical Library, 333 Cedar St. New Haven CT 06520
Presenter:    Rolando Milian
Registration Required   

Give Your PubMed Skills a Tune Up
Description:     PubMed is one of the most comprehensive resources for searching the biomedical literature.  Most researchers have used it 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.
Date & Time:     12:00pm - 1:00pm, Monday, October 26, 2015
Location:    Medical Library, Room 103 TCC, 333 Cedar St, New Haven, CT 06520
Presenter:    Holly Nardini
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, November 5, 2015
Location:    Medical Library, Large Conference Room 101A, 333 Cedar St, New Haven CT 06520
Presenter:    Rolando Milian
Registration Required    

Systematic Review: 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:    12:00pm - 1:00pm, Friday, November 13, 2015
Location:    Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
Presenter:    Holly Nardini
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

Date & Time:    12:00pm - 1:00pm, Wednesday, November 18, 2015
Location:    Medical Library, Large Conference Room 101A, 333 Cedar St, New Haven CT 06520
Presenter:    Rolando Milian
Registration Required     

Citation Analysis: Tools of the Trade
Description:     This one-hour class examines the features of Scopus, Web of Knowledge, Essential Science Indicators and Google Scholar. Tips and techniques for utilizing these products will be discussed.
Date & Time:    12:00pm - 1:00pm, Wednesday, December 2, 2015
Location:    Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
Presenter:    Holly Nardini
Registration Required   

Making Sense of Genomic Variation
Description: In this session we will review the most popular databases and tools used to annotate, analyze and visualize genomic variations. [More details on this session soon]
Date & Time:    12:00pm - 1:30pm, Thursday, December 3, 2015
Location:    Medical Library, Large Conference Room 101A, 333 Cedar St, New Haven CT 06520
Presenter:    Rolando Milian
Registration Required    

Scheduled Service interruption for Elsevier products on August 1

29 July 2015 - 12:06pm by Andy Hickner

There will be an interruption of service for Elsevier platforms and solutions due to scheduled maintenance.

On Saturday, August 1, access to Elsevier platforms will be unavailable due to a scheduled maintenance for approximately 4.5 hours starting at 06:00 PM EST. 

The platforms and solutions involved are:

  • Elsevier Research Platforms: ScienceDirect, Scopus (including Author Feedback Wizard), Engineering Village, Mendeley
  • Research Intelligence: SciVal Funding
  • R&D Solutions: Reaxys, Embase, Geofacets

To stay up to date with any developments, follow the individual Twitter accounts for the products.

Day of Data 2015 Call for Posters

27 July 2015 - 12:04pm by Rolando Garcia-Milian

Yale University undergraduates, graduate students, post-doctoral researchers, faculty, and staff are invited to submit posters for the 2015 Yale Day of Data, which will be held on September 18, 2015.  Any researcher who uses data for research can submit a poster!

The Day of Data is a university-wide event that will feature speakers from a number of disciplines discussing how they use data in their work. The presentations and posters from the 2013 & 2014 Day of Data events are available on the conference site:

We are looking for posters that describe how you collect, store, manage and use data in the course of a research project, but will also accept posters that more generally describe research that depends on data. Data may be of any kind and on any scale -- from small datasets collected during field work, to qualitative data, to big data projects using data from telescopes and other methods.

Please upload an abstract of the poster or the finished poster in digital format and a short description to the conference platform at: by August 28, 2015.

Successful submissions will be informed by September 4, 2015 and will be responsible for printing their own posters (see the poster guidelines from ITS: and uploading the PDF version of their poster to the conference website. If you have any questions, please contact Carla Heister at

Join the End-User Bioinformatics Network (EBNET) and become a member of a community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research at Yale.

Follow the Medical Historical Library on Instagram, Twitter, and Pinterest

24 July 2015 - 3:18pm by Andy Hickner

The Medical Historical Library is now on Instagram!  Charlotte Abney, one of our student workers and a graduate student in the Program in the History of Medicine, is the force behind the account.  We’re also on Twitter (@YaleMedHisLib) and experimenting with Pinterest.   

On display until July 30th! Children’s Medical Literature, 1950s-1990s

24 July 2015 - 2:00pm by Andy Hickner

Children's book image
Image from Nada Iveljić, We go to the doctor. Zagreb, 1974.

This exhibit, on display for a final week in the Medical Historical Library, features books and other publications written for children about medical topics. Story books, pamphlets, coloring books, and comic books are published by various groups as a way to teach children about illness, medical care, and health topics at an age-appropriate level.  The exhibit was organized by Charlotte Abney, graduate student in the Program in the History of Science and Medicine.

For young children, picture books introduce the ideas of doctors, dentists, and appointments by telling gentle stories of normal or routine treatment by medical professionals. This collection includes picture books from a number of different countries. Each of these books tells a reassuring story of a young child or cartoon protagonist who needs to visit a doctor, hospital, or dentist and is well cared for by medical professionals.

Children's book image
Image from Helen Oxenbury, La visite chez le docteur. Paris, 1983. 

Books and comics for older children, often published by health care companies and government agencies, teach lessons in staying healthy, personal hygiene, and the use of medical devices. This display includes a coloring book about pharmacies published by a pharmaceutical company; books about drug abuse by a doctor and the United States Drug Enforcement Agency, respectively; and two comic books, one in which Dennis the Menace learns about household poisons and one in which superheroes save the planet while teaching kids how to avoid asthma attacks.

The materials on display here are part of a collection of printed material in the history of medicine recently donated by William Helfand.

Children's book image
Children’s books from a recent donation by William Helfand

Helfand has been a collector of prints since the 1950s, and medical ephemera since 1969. In 1983, Helfand exhibited materials related to the “American Medical Show” in the rotunda of the Cushing/Whitney Medical Library. He has given multiple gifts of posters, prints, books, and patent medicine advertising in the past fifteen years, and he continues to support the library through scholarship, helping to identify medical bookplates in the collection.

Over the past fifteen years, Yale libraries have received over a thousand titles and numerous other items in donations from from Helfand, his daughter, Jessica Helfand ’82, ’89 MFA, Senior Critic in Graphic Design at the Yale School of Art, and her late husband William Drenttel, Senior Faculty Fellow and Social Enterprise Fellow at the Yale School of Management.

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