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2016 Yale Day of Data: Save the Date and call for presentations

24 May 2016 - 5:27pm -- Andy Hickner

(by Kate Nyhan)

Since openness and reproducibility are watchwords for some disciplines (and, it sometimes feels, lightning rods in others!), we’re glad to announce that the 2016 Yale Day of Data will take as its theme open data, open software, reproducibility initiatives, and replication. Save the date now for our featured speakers on December 2: our own Harlan Krumholz, neuroscientist Erin McKiernan, and psychologist Brian Nosek. You can propose a presentation, too: Yale affiliates will give applied talks (twenty minutes), lightning talks (five minutes), and posters. If your work fosters discussions about standards for open data and reproducibility, or about best practices in transparent data management, look over the call for presentations and submit a description of your talk at http://bit.ly/dayofdata before September 15. Get more info, and sign up for the Yale Day of Data listserv, at http://elischolar.library.yale.edu/dayofdata/2016/

E-Journals and E-Books tool is temporarily down

24 May 2016 - 3:11pm -- Andy Hickner

UPDATE: As of 11:00am May 25, service has been restored.

The Library's E-Journals and E-Books tool is temporarily unavailable.  We are working to resolve this issue.  To access E-Journals in the meantime, please use Yale University Library's lookup tool.  For e-books, use Books+ and use the "Refine" option to the left of your search results to limit to Online format.

Future Medical Librarians at STEM Career Fair

24 May 2016 - 11:18am -- Holly Grossetta Nardini

by Kate Nyhan

Librarian Kate Nyhan discusses a career in health sciences librarianship with four high school students.These future medical librarians are students at Wilbur Cross High School in New Haven attending a career fair to learn about STEM careers. Research and education librarian Holly Grossetta Nardini, reference librarian Melissa Funaro, and public health librarian Kate Nyhan (pictured) talked with students from New Haven's public schools about what medical librarians do, how informationists fit into the health care team, and how these young people can prepare for STEM careers like ours.

We were impressed with the confident kids at this STEM career fair. Many of them already have career goals, and lots of them discussed quite sophisticated strategies for seeking and evaluating information online. A good number of these students have visited the Cushing Center and learned about the history of science and medicine there.

The best part of this career fair was interactive: live searches in PubMed on health care topics relevant to these students. Speaking of which -- are you the track coach whose runners found an article suggesting that a short warm-up is as effective as a long one? I promise we talked to these young athletes about the importance of searching comprehensively. If they cherry-picked this evidence to get out of doing the long warm-up, remind them that evidence-based medicine is based on a thorough literature review!

Many thanks to Many Mentors, the Yale League of Black Scientists, and Wilbur Cross High School. We were glad to be part of the STEM career fair team, and we look forward to next year. And in the long term, we hope we can look forward to welcoming some of these talented students to the always rewarding profession of medical librarianship!

 

Cushing/Whitney Medical Library welcomes our new director, John Gallagher

10 May 2016 - 1:23pm -- Andy Hickner

John Gallagher

The Cushing/Whitney Medical Library is delighted to announce the appointment of our new director, John Gallagher.

John joined the staff of the Yale Library in 1999 as a library services assistant in the Library Shelving Facility. He moved to the Medical Library in 2000 where he took the position of evening & weekend circulation supervisor, and was quickly promoted to the head of the circulation department. After completion of his Masters of Library Science in 2004, John was promoted again to the head of Access and Delivery Services. He was instrumental in pioneering and establishing the Scan on Demand service at the Cushing/Whitney Medical Library, which evolved into the Scan and Deliver service for the wider Yale Library system. He served as the library liaison to the Department of Orthopedics and Rehabilitation and co-chaired the library’s joint Department Committee for Best Practices, a university-wide initiative to foster and promote better management/labor relations and collaboration through interest-based problem solving. During this time, John also chaired a management/labor Access Services Assessment Task Force that reduced check-in errors at all libraries.

As deputy director for Public Services and later associate director, John oversaw the completion of a number of major medical library renovations, including a complete renovation of the Medical Historical Library’s rare book stacks and staff areas, the construction of a Secure Reading Room, and the construction of the Cushing Center.

In 2012, John was selected to participate in the National Library of Medicine/Association of Academic Health Sciences Libraries’ Leadership Fellowship Program. John's participation in this prestigious and highly competitive program gives testimony to the quality of his leadership abilities.

Susan Gibbons, University Librarian and Deputy Provost for Libraries & Scholarly Communication commented, "John’s appointment is fantastic. Not only do we add a talented colleague to the library’s senior leadership team, but John’s career demonstrates the opportunities for career advancement at Yale University Library."

Even with all his responsibilities, John has an open door policy and welcomes staff to share their thoughts, ideas and feelings with him. John is a mentor, teacher, friend and leader.  We welcome John as our new director!

Library profiled in spring 2016 issue of Nota Bene

10 May 2016 - 10:42am -- Andy Hickner

Nota Bene

The spring 2016 issue of Nota Bene: News from the Yale Library is now available online. This issue has a particular focus on the work of the Harvey Cushing/John Hay Whitney Medical Library as it marks its 75th anniversary this year.  In addition to telling the story of the Medical Library, the issue profiles some of the current projects, resources, collections, and exhibits that are making an impact at Yale and in the medical community worldwide.

2016 Class Gift: The anatomy donor tree

3 May 2016 - 11:48am -- Andy Hickner

(Guest post by the YSM, YSN, and PA Classes of 2016)

If you've visited the library recently, this unusual sculpture may have caught your eye as you entered.  The 2016 Class Gift is a collective effort between the Yale School of Medicine, School of Nursing, and Physician Associate Program.  The gift is a tree sculpture made from molds of the limbs of first-year students in the 3 programs, and serves as a reminder of the collaborative process between the bodies of students and donors in the anatomy course.  We invite everyone to write notes thanking the donors or describing what the service, donations, or anatomy course meant to them on ribbons and to pin them on the tree. 

Day of Data 2016 Spring Discussion Series: Outcome Defined Organization of Patient Profiles

25 April 2016 - 11:48am -- Rolando Garcia-Milian

The Day of Data 2016 Spring Discussion Series will feature Dr. Alexander Cloninger. Dr. Cloninger has active applied collaborations with medical researchers at the Center for Outcomes Research and Evaluation at Yale and the National Institutes of Health. His current research deals with defining and analyzing patient similarity for the purposes of clustering and outcome prediction.

  • Thursday, May 5, 2016
  • 1:30 – 3:00 pm
  • Sterling Memorial Library Lecture Hall

Alex Cloninger is a Gibbs Assistant Professor in the Applied Mathematics Program at Yale, where he as been since 2014. He completed his Ph.D. at University of Maryland as a member of the Norbert Wiener Center for Harmonic Analysis, and his undergrad at Washington University in St. Louis. His research interests lie in the areas of machine learning and diffusion geometry, ranging from theory to implementation and data processing, with a focus on developing novel algorithms to work with medical data.

SPONSORED BY
Yale Center for Research Computing
Yale Institution for Social and Policy Studies
Yale University Library
For more information, click here 

 

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

20 April 2016 - 10:10am -- 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  
 

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