Free NCBI Training Workshops

February 23, 2016 at 12:55 pm | Posted in Continuing Education, Professional Development | Leave a comment




Cytoscape sessions open for NAHSL members

January 27, 2016 at 9:34 am | Posted in Continuing Education, Uncategorized | Leave a comment

Rolando Garcia-Milian was one of our Jay Daly Technology Award winners.

His project was to bring in Marci Brandeburg from the University of Michigan, Taubman Health Sciences Library to present 2 workshops on Cytoscape.  Both workshops are being held on March 3, 2016 at the Yale School of Medicine in New Haven, CT.   Both workshops are free and open to NAHSL members.  Seating is limited so registration is required.

Thank you, Rolando.

Workshop information and registration:

Cytoscape: Going from Raw Data to a Publishable Image

These hands-on workshops will demonstrate the use of Cytoscape, an open source molecular interactions visualization tool. Cytoscape allows for the exploration of molecular interactions and biological pathways and integrates these networks with annotations, gene expression profiles, and other data.  One session, “Cytoscape:  Going from Raw Data to a Publishable Image,” will cover core functions, such as learning how to import network and attribute data, change visual properties to easily distinguish biologically significant relationships, create a legend for the image, manually add nodes/edges, etc.

Registration free, but limited seating :

Date:   Thursday, March 3, 2016

Time: 9:00am – 12:00pm

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

Campus:        Medical School

Presenter:      Marci Brandeburg, University of Michigan, Taubman Health Sciences Library

Cytoscape apps with a Focus on MetScape

Calendar: Medical Library Workshops

This hands-on workshop will provide an introduction to Cytoscape apps, which add functionality to the core software.  It will focus on a specific app example, MetScape, which is used to visualize and interpret metabolomics and gene expression data in the context of human metabolic networks.  A brief introduction to other apps, such as MCODE (cluster finding tool), SocialNetwork (builds co-publication networks), and MetDisease (annotates metabolic networks with MeSH disease terms) will be included.

Registration free, but limited seating:

Date:   Thursday, March 3, 2016

Time: 1:30pm – 4:00pm

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

Campus:        Medical School

Presenter:      Marci Brandeburg, University of Michigan, Taubman Health Sciences Library



NAHSL Innovation: Engaging Students During Bibliographic Instruction

October 15, 2013 at 3:12 pm | Posted in NAHSL Innovations | 3 Comments

NAHSL Innovations are a way for our members to share their successful innovations or best practices with their colleagues. If you are aware of an innovation that you would like to suggest, please visit the NAHSL Innovations webpage.

Thank you to Jessica Kilham of the Lyman Maynard Stowe Library at the UCONN Health Center for sharing the latest NAHSL Innovation. Jessica has come up with a unique interactive way to teach bibliographic instruction.

“As an instruction librarian, I am always looking for new ideas to engage students during bibliographic instructions.  My latest approach is to have them build a search using cards that I pass out.  Printed on the cards are keywords, MeSH terms, MeSH terms with subheadings, Boolean operators, quotation marks and parentheses.  Working in small groups, students are given a very vague topic and told to create a search strategy using the cards that have been given.  Almost instantly the students are actively discussing strategy and seeking clarification on concepts that they do not understand.

Engaging students in the learning process increases their attention during the class and promotes meaningful learning.   More importantly, it makes the class fun and exciting!”

Jessica Kilham

Information & Education Services Librarian Lyman Maynard Stowe Library UCONN Health Center Farmington, Connecticut 06034

Jessica Kilham's NAHSL Innovation Jessica Kilham’s NAHSL Innovation

Jessica Kilham's NAHSL Innovation

Jessica Kilham’s NAHSL Innovation

MLA Annual Meeting: CE Recap

May 13, 2013 at 2:43 pm | Posted in Continuing Education, Professional Development | Leave a comment

702: Evidence-Based Practice: Introduction to Study Design and Critical Appraisal

Instructor: Connie Schardt, MLS, AHIP, FMLA, Duke University Medical Center.
Thanks to a NAHSL Professional Development Award, I was able to attend a CE class at the recent MLA Annual Meeting.The course was broken up into 4 one-hour sections, and I will briefly describe each of these.

1. Introduction and Study Design
This section of the course introduced participants to the “EBM Cycle”, which includes:

• Assessing the situation
• Asking a clinical question, PICOTT (PICO, with the additions of Type of Question and Type of Study)
• Acquire (literature search)
• Appraise (assess validity)
• Apply

Types of questions include therapy, harm, diagnosis, prognosis and prevention. In order by methodology beginning with those with the least strength to those with the strongest, most studies fit in the following categories: case reports (and case studies), case control studies, cohort studies, randomized controlled trials (RCTs), systematic reviews, and meta-analysis. There are also a number of qualitative studies in the literature (particularly in the field of nursing), which seek to explain behavior through observation. Participants also learned the strengths and weaknesses of each kind of study and how to search for them using PubMed (filters). Small group exercises challenged the class to identify article types after reading their abstracts.

2. Therapy: Critical Appraisal
Sources of potential bias were covered during this section. Important concepts include “Concealed Allocation Selection Bias” and “Blinding Assessment Bias”. Other topics to measure validity include similarity at baseline or similar prognosis. Equal treatment of both populations is also important, as the experimental intervention should be the only thing that differs between the control and experimental populations. The acronym, “FRISBE” was introduced. This acronym stands for Follow-up, Randomization and Concealed Allocation, Intention to Treat, Similar Baseline Characteristics, Blinding and Equal Treatment.

3. Therapy: Reviewing the Results
In this class segment, validity criteria for RCTs were explained. Participants were asked to do a bit of math to demonstrate the results of a study in absolute versus relative terms. Absolute provides the exact (numerical) difference while relative provides a proportional (percentage) difference. The class was introduced to a 2×2 table to explain absolute risk reduction and relative risk reduction. These are important distinctions, in particular when listening to news in the general media, press releases, etc., which often distort the significance of results. The concept of “number needed to treat” (the average number of interventions needed to produce a desired effect once) was introduced. Given this background, participants were asked to critically appraise a therapy article.

4. Systematic Review: Critical Appraisal
In this final section of the course, participants were introduced to meta-analysis, narrative analysis and systematic reviews and shown how they differ. The parts of a forest plot, which can be used to compare the quality of different studies, were reviewed. Participants also discussed the indicators of high-quality, thorough systematic reviews. Some of the quality indicators include clear objectives, and comprehensive and reproducible search strategies. These can also be expressed as “frame”, “find”, and “filter”. The process for building a quality systematic review was introduced, and these include specific processes for initiating, finding, synthesizing, reporting and hopefully, publication. The process could take up to a couple of years for completion. Knowledge was tested by having participants compare 3 systematic reviews for quality.

Rating: Highly recommended!

Suggested Resources (from Connie Schardt and others):

Introduction to Evidence-Based Practice(Duke University Medical Center Library and Health Sciences Library, UNC-Chapel Hill)
ACP Journal Club (Subscription)
AJN Series on Evidence-Based Practice in Nursing (Free from publisher)
Centre for Evidence-Based Medicine (University of Toronto)
Centre for Evidence-Based Medicine (University of Oxford)
Cochrane Handbook for Systematic Reviews of Interventions
Duke EBM Website – Evidence Based Practice (Libguide from Connie Schardt)
EBM Resources from Dartmouth
Evidence Based Medicine Course (SUNY Downstate)
National Guidelines Clearinghouse
TRIP (Turning Research Into Practice) Database


Guyatt, Gordon. Users’ Guide to the Medical Literature: Essentials of Evidence-Based Clinical Practice. American Medical Association. 2008.
Guyatt, Gordon. Users’ Guide to the Medical Literature: A Manual for Evidence-Based Clinical Practice. American Medical Association. 2008.
PDQ Evidence-based Principles and Practice. Anne McKibbon and Nancy Wilczynski, PMPH-USA, 2009.

I hope that you have enjoyed this overview and that you get the chance to take this excellent class!

Nathan Norris, MA, MLS, AHIP
Information Specialist
Beth Israel Deaconess Medical Center
Boston, MA 02215
p: 617-632-8311 | f: 617-632-8316

Mendeley Tips from NAHSL 2012

January 3, 2013 at 5:41 pm | Posted in Awards and Recognition, Continuing Education, NAHSL Annual Meeting 2012, Professional Development | 2 Comments

Thanks to a NAHSL Professional Development Award, I was able to attend our excellent fall conference and also co-taught a class with Alison Clapp on Mendeley, one of the “cool free tools” available to us on the Web. I thought I would take this opportunity to write about some of the main things that we learned in preparing for our class in the hopes that it will inspire you to explore Mendeley yourself!

Without further ado, here are the top 5 things I learned about Mendeley in 2012:

1. Mendeley can be used as a free citation/PDF manager:

The Mendeley software is comprised of two components: a cloud/web-based version and a desktop version (these are synced together). After you create an account and customize your profile on the web-based version of Mendeley, you are able to download the desktop component. References/PDF files and citations can be tagged, grouped and manipulated. Putting citations and PDF files into your Mendeley library is as easy as drag and drop. Watch your staff say “wow” as you demo this feature! Mendeley also includes Adobe editing tools so that you can highlight and takes notes on those PDF files. In addition to the price “advantage”, Mendeley can be accessed from any computer, anywhere.

2. Mendeley can be used with word processing software:

Using the Mendeley plug-in for Word, you can insert references and create bibliographies. Mendeley also provides a number of styles including those from the AMA and APA. With this capability, the software is useful for researchers, clinicians as well as librarians.

3. Similar to LinkedIn, you can use Mendeley as your professional Web “presence”:

Options include adding a picture and a detailed online C.V. You also can create groups for either public or private collaboration. You can follow groups which are already formed. Note: there is a private Mendeley for Librarians group which you might want to join.

4. Mendeley is a huge multi-disciplinary citation and document repository:

This is a searchable database of more than 330 million documents and more than 2 million registered users. Subjects include everything from arts and literature to medicine, and there is both a basic and an advanced search page.

5. Mendeley is a work in progress:

Mendeley has been described as the “intersection between Facebook, PubMed and EndNote”. Like most Web-based free products, there is constant change in the software which can mean that you should be prepared for a “glitch” or perhaps a delay in connectivity.

All things considered, however, it is definitely worth trying Mendeley either for personal use or for potential use by your staff.

Let me know what you think!

Nathan Norris, MLS, AHIP
Information Specialist
Beth Israel Deaconess Medical Center
Boston, MA

P.S., Thanks to Alison Clapp for assistance with this post!

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