Archive for the ‘Education & Training’ Category
TITLE: Reproducible Research: Many Dimensions and Shared Responsibilities
DATE: Monday, March 14, 2016 – 11:30a – 1:30p (PDT)
VIDEOCAST: This workshop will be videocast.
INSTRUCTOR: Lisa Meier McShane, Ph.D., Chief, Biostatistics Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute
REGISTRATION: Not required.
WORKSHOP DESCRIPTION: Biomedical researchers have an ethical responsibility to ensure the reproducibility and integrity of their work, so that precious research resources are not wasted and, most importantly, flawed or misleading results do not make their way to clinical studies where the faulty evidence could adversely affect study participants. Many factors have been suggested as contributors to irreproducible biomedical research, including poor study design, analytic instability of measurement methods, sloppy data handling, inappropriate and misleading statistical analysis methods, improper reporting or interpretation of results, and, on rare occasions, outright scientific misconduct. These problems can occur in any type of biomedical study, whether preclinical or clinical, large or small. Examples of the many potential pitfalls will be discussed along with suggested approaches to avoid them. The first half of the seminar will focus mainly on issues that arise commonly in preclinical and small clinical studies or studies performed retrospectively using stored biospecimens. The second half will elaborate on aspects that are particularly problematic in research involving the use of novel measurement technologies such as “omics assays” which generate large volumes of data and require specialized expertise and computational approaches for proper data analysis and interpretation. The discussions will emphasize the importance of including in a research team all individuals with the needed expertise as early as possible in a project in order to promote a sense of engagement and facilitate good communication across disciplines. Shared credit for scientific accomplishments should be understood as an acceptance of shared accountability for the integrity of the work.
This lecture is part of a full day of scheduled events and activities for the second annual NIH Pi Day, which celebrates the intersection between the quantitative and biomedical sciences. Pi Day is an annual international celebration of the irrational number Pi, 3.14…, on March 14. On Pi Day and every day, NIH recognizes the importance of building a diverse biomedical workforce with the quantitative skills required to tackle future challenges.
The ACRL Roadshow Workshop, Scholarly Communication: From Understanding to Engagement! will be offered on Thursday, March 24, 8:30 am – 4:30 pm, at the Toll Room, Alumni House, on the UC Berkeley campus. Registration is free and limited to 100 participants. The session is directed towards librarians and library staff who need a broad foundational knowledge of scholarly communication issues. Participants will learn about and discuss content access barriers, intellectual property, emerging opportunities, and engagement with faculty and students. Attendees will leave with practical ideas for developing outreach activities and models for supporting changes in scholarly communication. The two presenters for this workshop will be Katie Fortney, Copyright Policy & Education Officer, California Digital Library, and Jaron Porciello, Digital Scholarship Initiatives Coordinator, Digital Scholarship and Preservation Services, Cornell University.
The Alumni House is a short distance from the Downtown Berkeley BART station. Parking around campus is limited and taking public transportation is recommended. For inquiries regarding the workshop, please contact Jean McKenzie, UC Berkeley Acting Associate University Librarian for Collections.
Sign up now for the Spring session of Discovering Toxnet, a four-week online Moodle class conducted by the National Library of Medicine Training Center (NTC) March 7 through April 6. The course provides an introduction to TOXNET and other NLM environmental health databases through videos, guided tutorials, and discovery exercises. The purpose of this class is to enhance familiarity with reliable environmental health and toxicology information from the National Library of Medicine and other reliable sources. Skills and knowledge acquired from this course will enable attendees to access, utilize and refer others to online environmental and toxicology information.
On March 7 the NN/LM Pacific Northwest (PNR) and MidContinental (MCR) Regions are co-sponsoring a forum that will provide an overview of current and potential uses of patient data to improve patient safety, quality of care and evidence-based practice, Using Data to Improve Clinical Patient Outcomes. The event will be live streamed, linking presenters and participants in videoconference studios located at the University of Washington in Seattle and University of Utah in Salt Lake City. Librarian participants will have the opportunity to explore how they can contribute to the use of clinical data as evidence and what skills they can develop to support health care organizations in the use of data. Online or in-person attendance options are available. Registration is free, but required. The session will be archived, and a captioned recording will be made available within a few weeks of the event.
In preparation for this forum, both Regions are offering Data Curation / Management Journal Clubs, using both the MLA’s Discussion Group Program structure along with the new PubMed Commons Journal Clubs (PCJC) structure. Look forward to their analysis of recent data curation/management articles in the Plains to Peaks and Dragonfly newsletters!
Five ways to submit next-gen sequence data to NCBI’s Sequence Read Archive (SRA)
Wed, February 17, 2016, 10:00-11:00 am PT
In this webinar you will learn how to use five different ways to submit your next gen sequence data to NCBI’s Sequence Read Archive. These include external submission services through Illumina’s BaseSpace, MOTHUR (for microbial ecology data) and the iPlant Collaborative. In addition NCBI provides the new SRA submission portal and soon will offer the ability to upload data to SRA through FTP and the Aspera command line client in the new submission portal.
NCBI resources for cancer research
Wed, March 2, 2016, 10:00-11:00 am PT
This workshop provides an overview of NCBI molecular resources for cancer researchers. In the first part of the webinar you will learn to more effectively use the Entrez text-based search system and the BLAST sequence similarity search tool to find data relevant to cancer research including sequence, variation, gene and expression information. The second part of the presentation will focus on accessing large-scale genomics datasets. You will learn how to search for, access and download DNA-seq, RNA-seq, Epigenomics and Metagenomics datasets and how to access the tools and APIs at NCBI that can be used to extract relevant subsets of that data for cancer research.
The National Library of Medicine has announced the launch of MedPix®, a free online medical image database originally developed by the Departments of Radiology and Biomedical Informatics at the Uniformed Services University in Bethesda, MD. The MedPix collection categorizes and classifies the image and patient data for each of several subsets of image database applications (e.g. radiology, pathology, ophthalmology, etc.). The content material is both high-quality and high-yield and includes both common and rare conditions. Most cases have a proven diagnosis (pathology, clinical follow-up). The teaching file cases are peer-reviewed by an Editorial Panel. The primary target audience includes resident and practicing physicians, medical students, nurses and graduate nursing students and other post-graduate trainees. The material is organized by disease category, disease location (organ system), and by patient profiles.
The foundation for MedPix was a radiology study tool that was originally developed by Dr. J.G. Smirniotopoulos in 1984. In the early 1990s, as radiology was moving from film to digital imaging, there was simultaneously a merger of the diagnostic imaging residency programs of the two premier military hospitals: Walter Reed Army Medical Center and the National Naval Medical Center. In the summer of 1999, a Web-based digital teaching file based on the radiology study tool was built at USUHS to allow the two military training programs to share teaching file cases, a training requirement. Soon, other military hospitals and several civilian institutions joined MedPix. Over the past 16 years, MedPix has amassed an impressive collection of over 53,000 images from over 13,000 cases. Continuing Medical Education (CME) and Nurse Education (CNE) were added to the MedPix system in 2001.
As a public education service, the NLM and MedPix provide the storage service, indexing, and Web server hosting. Individuals as well as institutions may participate. Contributed content may be copyrighted by the original author/contributor. No additional software is required; an Internet browser is all you need!
Precision medicine’s promise to deliver the right treatment at the right time relies on our ability to extract information from high-dimensional data sets that combine traditional clinical data in electronic health records with data generated by high- throughput technologies. To meet this challenge, new approaches for data representation, integration, analysis, visualization and sharing need to be developed collaboratively by quantitative scientists, biomedical researchers, clinicians, and bioethicists.
Fellowship applications are now being accepted for a joint Weill Cornell Medicine, Johns Hopkins Medicine, and University of Minnesota week-long Big Data Coursework for Computational Medicine (BDC4CM) funded by the U.S. National Institutes of Health (NIH). BDC4CM will emphasize how to navigate the interface between research and practice by offering participants in-depth lectures, case studies and hands-on training from leading researchers in academia and industry. The course will be held on July 11-14, 2016 at Weill Cornell Medicine, in New York City.
Applicants must be faculty, scientists, post-doctoral fellows and researchers with a PhD, MD, or equivalent in computer science, biomedical informatics, bioinformatics, statistics, health information technology or a related degree, or graduate students enrolled in a PhD, MD, or equivalent program in these fields. For additional information about the program and to apply, visit the CFA website. The deadline for application submission is March 15, 2016.
The Friends of the National Library of Medicine seek your nominations for this year’s Michael E. DeBakey Library Services Outreach Award.
- Nominees must be currently employed as a health sciences librarian and have worked in such a position for at least five years immediately preceding the award.
- Nominations may be made for contributions by the librarian as demonstrated by excellence and achievement in leadership, publications, teaching, research, special projects or any combination of these.
- Nominations must be in writing and contain at least the following elements:
- Official nomination form
- Five page description of the nominee’s achievements
- Current resume or curriculum vitae
- Any additional information (no more than 10 pages) that would assist the jury in the evaluation of the nomination and selection of the recipient.
- Self-nominations are accepted and encouraged.
- Nominations must be received by May 1, 2016, and can be submitted via mail, email or fax.
Join members of the National Library of Medicine Training Center for three quick online presentations related to teaching topics. Jessi Van Der Volgen will discuss tips and tools for creating video tutorials. Cheryl Rowan will talk about including audience culture and diversity in your training sessions and Rebecca Brown will demonstrate how to integrate Zaption into your online training to add interactive opportunities to videos. Register now for this one-hour session on Friday, February 19, at 10:00 AM PST!
On January 20, join NLM staff for a highlights tour of the 2016 Medical Subject Headings (MeSH). A 30-minute presentation will feature a MeSH tree clean-up project; a new Clinical Study publication type; changes to the trees for diet, food and nutrition; restructuring in pharmacology and toxicology; and new terms in psychology and health care. Following the presentation, Indexing and MeSH experts will be available to answer your questions.
Webinar: 2016 MeSH Highlights
Date and time: Wednesday, January 20, 2016, at 9:00 am PST
View a recording of the presentation.
For more information about 2016 MeSH, see What’s New for 2016 MeSH and the Introduction to MeSH – 2016.