Archive for the ‘Data’ Category
Monday, October 19th, 2015
NIH Library Research Data Informationist Lisa Federer, MLIS, MA, AHIP, will give a presentation on data visualization skills and tools for librarians Wednesday, October 28, 2015, 12:00-1:30pm Mountain, 1:00-2:30pm, Central Time. See full webinar description at http://www.mlanet.org/p/bl/et/blogid=61&blogaid=643.
Because the National Library of Medicine sees this as a strategic growth area for health sciences libraries, the NN/LM SCR Administrative Office is funding several sites throughout the South Central Region including:
- Alburqurque, New Mexico – University of New Mexico Health Sciences Library & Informatics Center, contact Pat Bradley for site specific information.
- Dallas, Texas – University of Texas Southwestern Health Sciences Digital Library and Learning Center, Contact Jon Crossno for site specific information.
- Houston, Texas, University of Texas MD Anderson Cancer Center Research Medical Library. Contact Laurissa Gann for site specific information.
- Little Rock, Arkansas – University of Arkansas for Medical Sciences Library, contact Susan Steelman for site specific information.
- New Orleans, Louisiana – Rudolph Matas Library of the Health Sciences, contact Elaine Hicks for site specific information.
- Tulsa, Oklahoma – Oklahoma State University Center for Health Sciences, contact Melissa Kash-Holley for site specific information.
See a recent blog post from Lisa Federer’s blog titled, “See One, Do One, Teach One: Data Science Instruction Edition.”
Sunday, October 18th, 2015
National Library of Medicine Informatics Lecture Series
Title: Use of Clinical Big Data to Inform Precision Medicine
Speaker: Joshua Denny, MD
Date: Wednesday, November 4, 2015
Time: 1:00 pm – 2:00 pm Central Time
Location: Lister Hill Center Auditorium
Abstract: Precision medicine offers the promise of improved diagnosis and more effective, patient-specific therapies. Typically, clinical research studies have been pursued by enrolling a cohort of willing participants in a town or region, and obtaining information and tissue samples from them. At Vanderbilt, Dr. Denny and his team have linked phenotypic information from de-identified electronic health records (EHRs) to a DNA repository of nearly 200,000 samples, creating a ‘virtual’ cohort. This approach allows study of genomic basis of disease and drug response using real-world clinical data. Finding the right information in the EHR can be challenging, but the combination of billing data, laboratory data, medication exposures, and natural language processing has enabled efficient study of genomic and pharmacogenomic phenotypes. The Vanderbilt research team has put many of these discovered pharmacogenomic characteristics into practice through clinical decision support. The EHR also enables the inverse experiment – starting with a genotype and discovering all the phenotypes with which it is associated – a phenome-wide association study (PheWAS). PheWAS requires a densely-phenotyped population such as found in the EHR. Dr. Denny’s research team has used PheWAS to replicate more than 300 genotype-phenotype associations, characterize pleiotropy, and discover new associations. They have also used PheWAS to identify characteristics within disease subtypes.
Brief Bio: Joshua Denny, MD is an Associate Professor in the Departments of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. A primary interest of his lab has been development of the PheWAS method applied to EHRs to rapidly uncover genetic pleiotropy and highlight potential drivers of genetic associations with endophenotypes. He helps lead efforts for local and network pharmacogenetics implementation activities. He is part of the NIH-supported Electronic Medical Records and Genomics (eMERGE) network, Pharmacogenomics Research Network (PGRN), and Implementing Genomics in Practice (IGNITE) networks. He is past recipient of the American Medical Informatics Association New Investigator Award, Homer Warner Award, and Vanderbilt Chancellor’s Award for Research. Dr. Denny remains active in clinical care and in teaching students. He is also a member of the National Library of Medicine Biomedical Library and Informatics Review Committee.
This talk will be broadcast live and archived at http://videocast.nih.gov/
Sign Language Interpreters will be provided. Individuals with disabilities who need reasonable accommodation to participate in this lecture should contact Ebony Hughes 301-451-8038 Ebony.Hughes@nih.gov or the Federal Relay (1-800-877-8339).
Jane Ye, Ph.D
Division of Extramural Programs
National Library of Medicine, NIH
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.
Wednesday, September 30th, 2015
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 http://grants.nih.gov/grants/guide/pa-files/PA-15-249.html.
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, seehttps://regonline.com/jhudash. NIH staff or trainees who would like to attend should complete the application at https://www.surveymonkey.com/r/NIH-JHUDaSH (no later than Aug 14th) rather than the one on the https://regonline.com/jhudash website. For questions, contact Lisa Federer (firstname.lastname@example.org) in the NIH Library. Non-affiliates of NIH should apply directly through https://regonline.com/jhudash.
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.
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.
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: https://attendee.gotowebinar.com/register/2847950984085163009
Monday, November 18th, 2013
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.
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
The 2nd Edition of the Planning and Evaluating Health Information Outreach Projects series of 3 booklets http://nnlm.gov/evaluation/guides.html#A2 is now available online from the NN/LM Outreach Evaluation Resource Center (OERC).
Getting Started with Community-Based Outreach (Booklet 1) http://nnlm.gov/evaluation/booklets508/bookletOne508.html
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) http://nnlm.gov/evaluation/booklets508/bookletTwo508.html
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) http://nnlm.gov/evaluation/booklets508/bookletThree508.html
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 email@example.com. PDF versions of all three booklets are available here: http://nnlm.gov/evaluation/guides.html#A2 .
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 firstname.lastname@example.org.