Blogs

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 (www.biomart.org) 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: http://elischolar.library.yale.edu/dayofdata/

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: http://elischolar.library.yale.edu/dayofdata/2015/Posters/ 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: http://its.yale.edu/centers/photo-and-design/conference-posters) and uploading the PDF version of their poster to the conference website. If you have any questions, please contact Carla Heister at carla.heister@yale.edu

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.

Requesting Medical Historical rare books and materials online

24 July 2015 - 11:48am by Andy Hickner

(By Melissa Grafe)

You can now request locked Medical Historical Library books through Orbis, instead of emailing staff at the Historical Library.  Please do this when you want access to our locked stacks materials, for use in our Historical Library Office/reading room, or any events, sessions, or classes that you may be holding.  For classes or other events, please email Melissa Grafe at melissa.grafe@yale.edu to discuss scheduling and support.

From Orbis, in the Holdings area:

Orbis screenshot

The first time you “Request for Use in the Medical Historical Library,”  you will be prompted to register, unless you’ve already registered as a patron at Beinecke or Manuscripts and Archives.  After that, the information will automatically populate in the form. Just put in what date you are planning to come to the Medical Historical Office to view the materials, and Submit the request!  

We may have to take your photograph and check your Yale ID, even if we know you, as part of joining this system with Beinecke/Manuscripts and Archives and updated security protocols.

Within the next few months we will expand the ability to request materials from the Medical Historical Library’s finding aids, which you can discover in the Yale Finding Aid database. The finding aids are lists, usually down to the folder level, from our archival collections, including the papers of doctors, our medically themed sheet music collection, and the William Van Duyn tobacco advertising collection.

If there are materials that are not in Orbis, you can still fill out a request manually, filling in as many details as you know concerning the object you want.  Many of the materials featured in our digitized collections fall in this category.

New point of care tool: DynaMed Plus

9 July 2015 - 10:38am by Andy Hickner

Yale University and Yale-New Haven Hospital now have access to DynaMed Plus, which allows you to get answers to your clinical questions fast.  This clinical information resource is written by physicians, and features a rigorous evidence-based editorial process which provides synthesized information and objective analysis to answer your clinical questions quickly and easily.

DynaMed Plus features: 

  • Overviews and recommendations
  • Thousands of graphics and images
  • Precise search results
  • Expert reviewers
  • Specialty content
  • Mobile access
  • Micromedex Clinical Knowledge Suite drug content 

For questions about this new product, please contact your librarian or visit our documentation about DynaMed Plus on mobile devices

Training Sessions - Summer 2015 at the Cushing/Whitney Medical Library

8 July 2015 - 2:40pm by Rolando Garcia-Milian

Introduction to Ingenuity Pathway Analysis

Description:     What is IPA and what questions can it address?

  • Overview of key features in IPA
  • Ingenuity Knowledge Base
  • Search & Pathway Building - Gene/ Chemical, Functions, Drug Targets
  • Advanced Search: Limiting results to a molecule type, family or disease-association.
  • Building pathways: Creating a pathway, pathway navigating, Using Build and Overlay tools
  • Bioprofiler
  • Dataset Analysis: Interpretation of Gene, Transcript, Protein and Metabolite Data
  • Data Upload and Analysis:  Uploading and formatting a dataset, setting analysis parameters and running an analysis
  • Pathway Analysis and Canonical Pathways
  • Downstream Effects Analysis and identifying downstream functions and processes that are likely affected
  • Upstream regulators Analysis
  • Causal Network Analysis and identifying likely root regulators
  • Regulator Effects Analysis to link upstream regulators with downstream functions and processes that are affected
  • Comparison analysis and comparing multiple observations

Date & Time:  9:00am - 12:00pm, Wednesday, July 15, 2015

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

Campus:          Medical School

Presenter:       Dr. Kate Wendelsdorf, Applied Advanced Genomics, QIAGEN Informatics

Registration required

 

Advance Ingenuity Pathway Training: Integrated Analysis and Interpretation of Variant and Gene Expression Data from Breast Cancer Subtypes

            Methods that jointly interpret genomes and transcriptome data from disease case samples may be able to identify disease-specific factors and pathogenicity mechanisms that may not be observable on a single data type. These insights can then be used create more effective screenings or treatments.

Here we show how jointly analyzing tumor-specific genotypes and gene expression can indicate medically important differences among tumor subtypes. Pairing two tools from Ingenuity® Systems – Variant Analysis  (for interpreting human genome data) and IPA® (for transcriptome data) – we trace differences between breast tumors that spread quickly (Claudin-low) versus slowly (luminal) to sequence variation that likely governs Epithelial-to-Mesenchymal Transition (EMT).

Variant Analysis was used to filter genomic variants in RNA seq data to a shortlist of those plausibly involved in driving tumor spread. IPA is then used to leverage gene expression patterns from the same dataset to identify molecular pathways involved in the metastatic phenotype of Claudin-low breast cancers. The seminar will demonstrate how using a combination of IPA features and QIAGEN tools can provide insight in to phenotype-causing pathways for experimental follow-up and hypothesis testing.

Date & Time:  1:00pm - 4:00pm, Wednesday, July 15, 2015

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

Campus:          Medical School

Presenter:       Dr. Wendelsdorf- QUIAGEN

Category:        Bioinformatics

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.

Date & Time:  2:00pm - 3:00pm, Wednesday, July 29, 2015

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

Campus:          Medical School

Presenter:       Denise Hersey

Category:        Reference Management Systems

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 have 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 time-saving features such as saving searches and how to link out to full-text.

Date & Time:  6:00pm - 7:00pm, Wednesday, July 29, 2015

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

Campus:          Medical School

Presenter:       Melissa Funaro

Category:        Reference Management Systems

Registration required    

 

Webinar: Introduction to Cytoscape: network visualization software

Description:     Cytoscape, an open source molecular interactions visualization tool, allows the exploration of molecular interactions and biological pathways and integrates these networks with annotations, gene expression profiles, and other data.  This webinar will provide an introduction to some of the core functionality of Cytoscape, including the loading and manipulation of experimental data.  For example, you will learn how to change visual properties to easily distinguish biologically significant relationships.  Many additional features and advanced analyses are available through Cytoscape’s extensive list of apps. Examples of apps are MetScape (allows for visualizing and interpreting metabolomic data), Reactome FI (Reactome Functional Interaction and pathway enrichment tool), and BiNGO (Gene Ontology Tool).

Date & Time:  11:30am - 12:30pm, Tuesday, August 11, 2015

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

Campus:          Medical School

Presenter:       Marci Brandenburg, Bioinformationist, Taubman Health Sciences Library, University of Michigan

Category:        Bioinformatics

Registration required

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.

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