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Archive for the ‘Data’ Category

2016 NLM Georgia Biomedical Informatics Course

Friday, October 9th, 2015

Applications are now being accepted for the 2016 National Library of Medicine Georgia Biomedical Informatics Course. One section will be held April 3-9 and another September 11-17 in Young Harris, Georgia. Applications will be accepted until December 7. All applicants will be notified by the end of January or early February of their application status. Travel, hotel, and meals of all successful applicants will be paid for by Georgia Regents University (soon to be Augusta University).

To Prepare Your Application:

  • Describe your short term goals (3-5 years) related to your reasons for wanting to take this course (approx. 300 words.)
  • Summarize your research experience with this course subject (approx. 300 words)
  • State your expectations. Describe what you hope to gain by taking this course (approx. 300 words.)
  • Submit your CV with your application.
For more information and to apply, visit For questions, contact Adrienne Hayes at

Jason Bengtson Named as Informationist and Co-Principal Investigator for NIH Grant

Wednesday, September 30th, 2015

Jason Bengtson headshot

SCC/MLA member Jason Bengtson, MLIS, MA, was recently named as the Informationist and Co-Principal Investigator on a successful application for an Informationist Supplement to grant 3-R01-DC000354-27A1 under the direction of Principal Investigator Dr. Brenda Farrell from Baylor College of Medicine. This supplement will fund the curation and management of electrophysiological data obtained from outer hair cells isolated from the inner ear of Cavia Porcellus. This data has significant implications for inner ear research. Jason is the Innovation Architect for The Texas Medical Center Library.

To learn more about NLM Administrative Supplements for Informationist Services in NIH-funded Research Projects visit

Data Science Hackathon September 21-23 in Baltimore

Monday, August 24th, 2015

The following is an announcement from the NIH Big Data 2 Knowledge email list. If you are in the South Central Region and are interested in attending, please consider applying for a Professional Development Award to cover related expenses.

The NIH Big Data to Knowledge (BD2K) program and the NIH Library are pleased to join the Johns Hopkins (JHU) Bloomberg School of Public HealthDepartment of Biostatistics in announcing the first JHU DaSH – Data Science Hackathon – on September 21-23, 2015 in Baltimore.

The organizers– Drs. Brian Caffo, Leah Jager, Jeff Leek and Roger Peng – include JHU professors who teach the popular Coursera Data Science Specialization. This Data Science Hackathon will provide an opportunity for hands-on training that reinforces and builds on data management and analysis skills such as those covered in the MOOC specialization (completion of the specialization is not a prerequisite).

“This event will be an opportunity for data scientists and data scientists-in-training to get together and hack on real-world problems collaboratively and to learn from each other. The DaSH will feature data scientists from government, academia, and industry presenting problems and describing challenges in their respective areas. There will also be a number of networking opportunities where attendees can get to know each other.”
— Simply Statistics blog post

JHU DaSH will provide a local opportunity for NIH scientists and trainees to participate in a data science Hackathon. For more information, see NIH staff or trainees who would like to attend should complete the application at (no later than Aug 14th) rather than the one on the website. For questions, contact Lisa Federer ( in the NIH Library. Non-affiliates of NIH should apply directly through

Send in Your Application to Participate in “A Librarian’s Guide to NCBI” Bioinformatics Course

Friday, August 21st, 2015

Librarians specializing in health and related sciences are invited to participate in the next offering of the bioinformatics training course, “A Librarian’s Guide to NCBI,” sponsored by the National Library of Medicine (NLM), the National Center for Biotechnology Information (NCBI), and the National Network of Libraries of Medicine, NLM Training Center (NTC). Enrollment is limited to 25 participants.

The course provides knowledge and skills for librarians interested in ‘helping patrons use online molecular databases and tools from the NCBI. Prior knowledge of molecular biology and genetics is not required. Participating in the Librarian’s Guide course will improve your ability to initiate or extend bioinformatics services at your institution.

Online Pre-Course and In-Person Course Components
The two parts to “A Librarian’s Guide to NCBI” are listed below. Applicants must complete both parts. Participants must complete the pre-course with full CE credit (Part 1) in order to advance to attend the 5-day in-person course (Part 2).

Part 1: “Fundamentals in Bioinformatics and Searching,” an online (asynchronous) course, October 26-December 11, 2015.
An additional offering of this class will be in January-February 2016.

Part 2: A 5-day in-person course offered on-site at the National Library of Medicine in Bethesda, Maryland, March 7-11, 2016.

Application deadline: September 14, 2015

For more information and a link to the application, visit the NLM Technical Bulletin article: K. Majewski. NLM Tech Bull. 2015 Jul-Aug;(405):e4.

MLA Webcast on Data Management

Monday, March 2nd, 2015

MLA is offering a webcast on data management. The program, “The Diversity of Data Management: Practical Approaches for Health Sciences Librarianship,” will have Lisa Federer, AHIP, Kevin Read and Jacqueline Wirz present strategies and success stories for data management.

Wednesday, April 22, 2015, 1:00-2:30pm CST

This webcast is designed to provide health sciences librarians with an introduction to data management, including how data is used within the research landscape, and the current climate around data management in biomedical research. Three librarians working with data management at their institutions will present case studies and examples of products and services they have implemented, and provide strategies and success stories about what has worked to get data management services up and running at their libraries.

More information on the program and speakers can be found on MLANET.

SRA Toolkit Webinar

Tuesday, February 24th, 2015

The Next Generation of Access to Sequencing Data: Using NCBI’s SRA Toolkit to Access Data from dbGaP and SRA

Next Wednesday, February 25, NCBI staff will present a webinar on the SRA Toolkit (Sequence Read Archive), a system for accessing the approximately 3.4 Petabases of next-generation genomic and expressed sequence data housed in the NCBI Sequence Read Archive (SRA). As data sets become larger, mining information and performing comparisons directly from structured databases becomes increasingly necessary. The SRA Toolkit is not only capable of dumping the data out as a fastq or sam file, but also provides direct analysis and comparison from specific genomics regions across hundreds or thousands of samples.

In the webinar, we will show examples of configuration and use of the Toolkit for both public SRA and controlled access data associated with studies in the Database of Genotypes and Phenotypes (dbGaP).

To register for this webinar, please go here:

Data Management Curriculum Now Available

Monday, November 18th, 2013

Ones and zeros

The Lamar Soutter Library at the University of Massachusetts Medical School has recently released the New England Collaborative Data Management Curriculum which offers openly available materials that librarians can use to teach research data management best practices to students in the sciences, health sciences and engineering fields, at the undergraduate and graduate levels. The materials in the curriculum are openly available, with lecture notes and slide presentations that librarians teaching RDM can customize for their particular audiences. The curriculum also has a database of real life research cases that can be integrated into the curriculum to address discipline specific data management topics.

Each of the curriculum’s six online instructional modules aligns with the National Science Foundation’s data management plan recommendations and addresses universal data management challenges. Included in the curriculum is a collection of actual research cases that provides a discipline specific context to the content of the instructional modules. These cases come from a range of research settings such as clinical research, biomedical labs, an engineering project, and a qualitative behavioral health study. Additional research cases will be added to the collection on an ongoing basis. Each of the modules can be taught as a stand-alone class or as part of a series of classes. Instructors are welcome to customize the content of the instructional modules to meet the learning needs of their students and the policies and resources at their institutions.



Updated Evaluation Booklets from OERC Now Available

Monday, September 30th, 2013

Guest Author: Susan Barnes, Assistant Director, NN/LM Outreach Evaluation Resource Center (OERC), Health Sciences Libraries and Information Center, University of Washington

OERC Booklet Covers

The 2nd Edition of the Planning and Evaluating Health Information Outreach Projects series of 3 booklets is now available online from the NN/LM Outreach Evaluation Resource Center (OERC).

Getting Started with Community-Based Outreach (Booklet 1)
What’s new? More emphasis and background on the value of health information outreach, including its relationship to the Healthy People 2020 Health Communication and Health Information Technology topic areas

Planning Outcomes-Based Outreach Projects (Booklet 2)
What’s new? Focus on uses of the logic model planning tool beyond project planning, such as providing approaches to writing proposals and reports.

Collecting and Analyzing Evaluation Data (Booklet 3)
What’s new? Step-by-step guide to collecting, analyzing, and assessing the validity (or trustworthiness) of quantitative and qualitative data, using questionnaires and interviews as examples.

These are all available free to network members. To request printed copies, send an email to  PDF versions of all three booklets are available here: .

The Planning and Evaluating Health Information Outreach Projects series, by Cynthia Olney and Susan Barnes, supplements and summarizes material in Cathy Burroughs’ groundbreaking work from 2000, Measuring the Difference: Guide to Planning and Evaluating Health Information Outreach. Printed copies of Burroughs’ book are also available free—just send an email request to

A Tool to Help Visualize Your Data: the Periodic Table of Visualization Methods

Wednesday, September 25th, 2013

Is a table worth a thousand words?  Sometimes you need an understandable and memorable diagram that will illustrate what you are trying to say.  This Periodic Table of Visualization Methods (a resource from provides examples of 100 visualization methods.

Periodic Table of Visualization MethodsThis table is not just a cool looking list of visualization methods, but it also uses the format that we are familiar with from the Periodic Table of Elements to organize the visualization techniques into different types and purposes.

For example, the chart is color coded from yellow to purple. The colors represent different kinds of visualization types: Data Visualization; Information Visualization; Concept Visualization; Strategy Visualization; Metaphor Visualization; and Compound Visualization (examples below).  Scrolling over each box in the Table will bring a pop-up window with an example in it.

In addition, several other pieces of information about the methods are contained in this table.  There are icons that show if the visualization method is process visualization (depicting a temporal sequence) or structure visualization (depicting conceptual relationships), and whether the different methods show macro patterns (overview) or micro patterns (detail), and finally whether the methods demonstrate divergent or convergent thinking. These can help you determine whether this visualization technique might be right for you.

Here are some examples from each of the main categories of visualization methods:

Data Visualization: example Area Chart

Data Visualization: Area Chart

Information Visualization: example Radar Chart

Information Visualization: Radar Chart Cobweb

Concept Visualization: example Argument Slide

Concept Visualization: Argument Slide

Strategy Visualization: example Fishbone Diagram

Strategy Visualization: Fishbone Diagram

Metaphor Visualization: example Tree

Metaphor Visualization: Tree

Compound Visualization: example Knowledge Map

Compound Visualization: Knowledge Map

Using NN/LM’s Outreach Evaluation Resource Center Tools And Resources Guide

Friday, September 6th, 2013

images of people in a pie chart

One of the Centers in The National Network of Libraries of Medicine is the Outreach and Evaluation Resource Center (OERC).  This center is located at the University of Washington in Seattle, WA   The OERC has created a Guide to evaluation tools and other resources that you and your library can use to evaluate your programs:   Here are some of the tools and resources described in the Guide:

Community Oriented Outreach

  • Building Partnerships: tips on successful collaborations, tools for improving collaboration with community networks
  • Participatory Evaluation: toolkits for practical participatory evaluation, processes for conducting outcome-based evaluations

Evaluation Planning

  • OERC Guides to incorporating evaluation planning into your outreach projects
  • Evaluation planning resources from other organizations, including logic models
  • List of outreach projects funded by NLM

Data Collection and Analysis

  •  Needs Assessments and Data Collection: access to data indicators, tips for questionnaire development, guides for using Appreciative Inquiry for evaluation
  • Data Analysis: Resources for statistical methods and guides for analyzing qualitative and quantitative data

An image of a series of data visualizations, known as a data dashboard

Reporting and Visualizing:

  • Data Dashboards: guides for creating popular data dashboards
  • Data Visualization: teachings of Edward Tufte and lists of visualization methods
  • Reporting: tools for presentation design and TEDtalks about presentation structure