Four On-site Workshops on Next-Generation Sequencing Data Analysis Tools

20 April 2016 - 10:10am by Rolando Garcia-Milian

The End-user Bioinformatics Program at the Yale Cushing/Medical Library is hosting these four workshops on tools for the analysis of NGS data. Besides the two trainings on tools for functional analysis of NGS data already supported by the Medical Library (Ingenuity Pathway Analysis and MetaCore), we will have a presentation on Partek Flow, and another one on CLC Bio (QIAGEN). The medical library will ask for feedback on these tools for future support and licensing. If you are interested in attending any of these presentations, please register to reserve your seat. Please contact Rolando Milian for questions or comments.

Title:    Introductory Workshop to MetaCore and Key Pathway Advisor – Pathway Analysis of “Omics” Data
This hands-on training workshop will highlight basic functionalities as well as cover use cases to:

  • Predict upstream regulators of gene expression using causal reasoning
  • Use synergic enrichment analysis of upstream regulators and observed gene expression changes to identify key pathways associated with your data
  • Compare between experiments to uncover phenotypic differences using enrichment analyzes
  • Search and explore genes, proteins, diseases and compounds

Registration required
Date & Time:    9:00am - 11:00am, Thursday, April 28, 2016
Location:    Beaumont room (2nd floor), SHM, 333 Cedar St, New Haven CT 06510
Presenter:    Deborah Riley, PhD, Senior Solution Scientist – Thomson Reuters Life Sciences

Title:    Start-to-finish Analysis Software for NGS & Microarray Data.
(miRNA-Seq Analysis with Partek: Serum miRNA Study in Alcohol Use Disorder Subjects Suggests Alterations of CNS Structure and Function)     
During this seminar, we will feature a successful miRNA-Seq based study of extracellular miRNAs in 20 individuals diagnosed with alcohol use disorder (AUD).  We will demonstrate how to go from raw NGS data to biological interpretation using Partek software.  Analysis of the sequencing data using Partek Flow will include:

  • checking the quality of reads
  • generating aligned reads
  • quantifying miRNA levels
  • determining differentially expressed miRNAs

By integrating miRNA-Seq results in Partek Genomics Suite, we will demonstrate how differentially expressed miRNAs impact CNS structure and function using Partek Pathway.  Lastly, miRNA expression microarray data will be analyzed in Partek Genomics Suite to validate findings from the next generation sequencing data.
Registration required
Date & Time:    9:00am - 11:00am, Tuesday, May 3, 2016
Location:    C-103 - SHM 333 Cedar St, New Haven CT 06520
Presenter:    Dr. Eric Seiser, Field Application Scientist, Partek Incorporated


Title:    Ingenuity Pathway Analysis Hands On Training
If you have gene (including RNAseq), protein and metabolic expression data, you should be using IPA to guide you with the biological interpretation of your data.  Using IPA you will learn how to rapidly understand:

  • Pathway involvement and change
  • Effected biological processes
  • Causal regulators and their directional effect on genes, functions and diseases across multiple time points or doses. You will also learn to explore IPA’s knowledge and discovery tools that allow you to relate the most recent literature findings to your research.  

Requirement:  Laptop and active IPA account (Request your account here)
Registration required
Presenter: Devendra Mistry, PhD, Field Application Scientist, Ingenuity Products, QIAGEN
Date & Time:    9:00am - 11:30am, Tuesday, May 10, 2016
Location:    C-103 - SHM 333 Cedar St, New Haven CT 06510


Title: CLC Genomics Workbench
Overview of Application, Importing NGS read data, QC & Pre-processing

  • De novo assembly – Genomes & Transcriptomes. Characterizing Contigs, Joining & Finishing
  • Mapping/Alignment to Reference, Variant Calling, Annotation & Filtering
  • RNA Seq Analysis Workflow & Tools
  • Overview of Microbial Modules (Finishing & Microbial Genomics)
  • CLC Biomedical Workbench & Ingenuity Variant Analysis
  • Prebuilt intuitive pipeline for your human DNA-seq data that allows you to quickly go from reads or called variants to identifying and prioritizing the casual variants.

Registration required
Date & Time:    1:00pm - 3:00pm, Tuesday, May 10, 2016
Location:    C-103 - SHM 333 Cedar St, New Haven CT 06510
Presenter:    Devendra Mistry, PhD, Field Application Scientist, Ingenuity Products, QIAGEN  

The Yale Medical Library is Providing Access to the Human Gene Mutation Database (HGMD®)

17 April 2016 - 9:45pm by Rolando Garcia-Milian

As part of its End-user Bioinformatics Program, the Cushing Whitney Medical Library is providing access to the the Human Gene Mutation Database (HGMD®) to all Yale affiliates. This database organizes all known genotypes responsible for causing human inherited disease along with disease-associated polymorphisms published in the peer-reviewed literature— HGMD mutation data are manually curated from the scientific literature.

HGMD is available in two versions: one public, one obtainable by subscription. The public version is maintained is only updated twice per annum and is permanently 3 years out of date. The professional version is available to both commercial and academic/non-profit users via subscription from BIOBASE (QIAGEN). Access to HGMD should be done by following this link ( and clicking on HGMD (access to BIOBASE Proteome or TRANSFAC continue to be provided by the medical library). VPN is required if connecting off-campus.

HGMD does not cover either somatic or mitochondrial mutations. For these, please visit COSMIC and MitoMap For pharmacological variants, PharmGKB The Medical Library offers regular training sessions on how to use these and other resources for variant annotation e.g. Database of Genomic Variants, DECIPHER and Copy Number Variation in Disease.

Please check the class calendar or contact Rolando Milian if you are interested in learning how to use these resources.

Geographic Information Systems Open House

15 April 2016 - 2:48pm by Mark Gentry

Miriam Olivares, GIS Librarian, now consults with Medical Library patrons on Wednesday afternoons.  We are kicking off this service with Open Houses on April 27 and May 4.  Drop in between 3pm and 5pm with your questions about geospatial applications in medicine and public health – or just come to hear more about this service.  Join us in our Gordon Conference Room (L101) at the front of the library, or get more information here.

Supply drive for mothers this week, sponsored by YSM students

12 April 2016 - 9:39am by Andy Hickner

Maybe you've noticed a donation box in the library lobby.  YSM students involved with AMWA (American Medical Women's Association) & ACOG (American College of Obstetrician's & Gynecologists) District I are gathering supplies for 2 organizations that provide supplies for survivors of domestic violence and other underserved women: The Women's Health Resource Center (NH) and The Women's Center of Rhode Island.  

The Women's Resource Center would like diapers & wipes, which are essential supplies for mothers' health

The Women's Center of RI would like:

  • Toiletries (shampoo, toothpaste, deodorant, etc)
  • Women's and infant's clothing & supplies (socks, winter boots, baby lotion)
  • Cleaning supplies (dish soap, sponges, laundry detergent)
  • Used cell phones to refurbish and give to survivors of domestic violence and sexual assault. 

The supply drive runs this week, Monday through Friday. 

Study space restrictions, week of April 4

4 April 2016 - 12:56pm by Andy Hickner

(by Katie Hart)

The Medical Library spaces are heavily booked this week. The Historical Library will be closed at some point almost every day, and the Morse Reading Room will be closed on Wednesday and Thursday afternoons. Study space in other parts of the library will be at a premium. Also, a brief reminder that Wednesday is the Annual Associates Lecture.

Here are a list of the closing times for our spaces:

Monday, 4/4: 

Historical Library,  3-7pm, “The Emperor’s New Genes: Science, Race, Justice, and the Allure of Objectivity” Lecture sponsored by HSHM and the office of the Provost 

Tuesday 4/5: 

Historical Library, 4:30-5:30pm, Class

Wednesday 4/6: 

Historical Library, 2-7pm,  Associates Lecture

Morse Reading Room, 3-8pm, Associates Reception

Thursday 4/7:

Historical Library, 9-11:30, Second Look groups

Morse Reading Room, 12:30-3:30pm, Second Look speed meetings with faculty

Friday 4/8: 

Historical Library, 9:30-11:30am, Dean’s office 

Historical Library, 12-3pm, Wellness Project Seminar “Cultivating Resilience in the Face of Burnout” 

#HappyBirthdayHarvey Instagram Challenge from @YaleMedHistLib

28 March 2016 - 2:35pm by Andy Hickner

(by Charlotte Abney Solomon, Medical Historical Library)

#HappyBirthdayHarvey Instagram Challenge

In celebration of Harvey Cushing's birthday and our 75th Anniversary Year, the Medical Historical Library invites all Instagram users visiting the Harvey Cushing/John Hay Whitney Medical Library at Yale to share their best photos taken here! Enter the contest by posting photos that are publicly visible on Instagram and tag them with our hashtag #HappyBirthdayHarvey and our account, @yalemedhistlib. One winner in each contest category will receive a prize package (listed below) and have their photo included in our new exhibit, Life of the Library, opening next week in the Foyer of the Medical Library.

Photos must be taken, tagged #HappyBirthdayHarvey and @yalemedhistlib, and posted between midnight on April 1, 2016 and noon on April 8, 2016. A team of judges from the Medical Historical Library staff will select the winners. Winners will be notified and the winning photos announced and reposted through our account on Friday afternoon. Winners will be invited to directly submit the highest-resolution copy of the image they have available for inclusion in the exhibit.

Prize Categories

Judges’ Favorite Instagram: Best photo overall
Prize package: An extended private tour of the Cushing Center with photographer and Cushing Center Coordinator Terry Dagradi, for up to six people, arranged by appointment; photo included, and featured as the overall winner, in the Life of the Library exhibit; and Library travel mug gift pack.

Brainiest Instagram: Best photo taken in the Cushing Center
Prize package: A private showing of a selection of important rare books of science and medicine in the Medical Historical Library collections with Historical Librarian Melissa Grafe, Ph.D., for up to four people, on a theme of your choice and arranged by appointment; photo included in the Life of the Library exhibit; and Library travel mug gift pack.

Happiest Birthday Instagram: Best selfie or other photo including an image of Harvey Cushing or the words “Happy Birthday Harvey”
Prize package: A copy of Harvey Cushing: A Biography; photo included in the Life of the Library exhibit; and Library travel mug gift pack.

Most Collectible Instagram: Best photo taken of an image, book, or other item in any CWML current or historical collections
Prize package: A custom-made poster of any image of your choice from the CWML collections; photo included in the Life of the Library exhibit; and Library travel mug gift pack.

Most Studious Instagram: Best photo taken while studying in the library
Prize package: A copy of Medicine at Yale: The First 200 Years; photo included in the Life of the Library exhibit; and Library travel mug gift pack.

Most Helpful Instagram: Best photo with library staff
Prize package: A custom-made poster of any image of your choice from the CWML collections; photo included in the Life of the Library exhibit; and Library travel mug gift pack.

Best Staff & Family Member Instagram: Best photo taken by CWML staff or staff family member.
(CWML staff and family members are not eligible for any other categories.)
Prize: Baked treats for the winner's office on a date of your choosing.

Rules for submission

  • The contest is open to anyone visiting the Cushing/Whitney Medical Library between April 1- April 8, 2016. CWML staff members and their families are only eligible to enter the Staff & Family Member category.
  • Photos must be original and have been taken and posted by the entrant between midnight on April 1, 2016 and noon on April 8, 2016. Photos must be posted, tagged, and publicly visible within this time period to be eligible.
  • Post photos on Instagram and use the hashtag #HappyBirthdayHarvey and the account @yalemedhistlib.
  • By submitting to this contest, you consent to the following:  I grant to Yale University (“Yale”) and the Harvey Cushing/John Hay Whitney Medical Library the right to copy, reproduce, distribute, transmit, broadcast, exhibit, display, edit, or otherwise use my photograph, my name, and biographical information for educational, promotional, or other purposes that support Yale’s mission. I understand that these rights are granted to Yale and may be used in whole or in part without compensation. I affirm that the subjects in my photo have agreed that their likenesses may be used with the terms and conditions of this contest as listed above.
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