Archive for the ‘NLM Resources’ Category
From January 4-6, 2016, NCBI will host a genomics hackathon focusing on advanced bioinformatics analysis of next generation sequencing data. This event is for students, post-doctorates, and investigators already engaged in the use of pipelines for genomic analyses from next generation sequencing data. (Specific projects are available to other developers or mathematicians.) Working groups of 5-6 individuals will be formed for twelve teams, in the following sections: Network Analysis of Variants, Structural Variation, RNA-Seq, Streaming Data and Metadata, and Neuroscience/Immunity. The working groups will build pipelines to analyze large datasets within a cloud infrastructure. Please see the application link below for specific team projects.
After a brief organizational session, teams will spend three days analyzing a challenging set of scientific problems related to a group of datasets. Participants will analyze and combine datasets in order to work on these problems. This course will take place at the National Library of Medicine on the NIH main campus in Bethesda, MD. Datasets will come from the public repositories housed at NCBI. During the course, participants will have an opportunity to include other datasets and tools for analysis. Please note, if you use your own data during the course, you will be asked to submit it to a public database within six months of the end of the hackathon. All pipelines and other scripts, software, and programs generated in this course will be added to a public GitHub repository designed for that purpose. A manuscript outlining the design of the hackathon and describing participant processes, products and scientific outcomes will be submitted to an appropriate journal.
To apply, complete the online form, which takes approximately ten minutes. Applications are due by December 1 at 2:00pm PST. Participants will be selected from a pool of applicants; prior students and prior applicants will be given priority in the event of a tie. Please note: applicants are judged based on the motivation and experience outlined in the form itself. Accepted applicants will be notified on December 4 by 11:00am PST, and have until December 7 at 2:00pm PST to confirm their participation. Please include a monitored email address, in case there are follow-up questions.
Participants will need to bring their own laptop to this program. A working knowledge of scripting (e.g., Shell, Python) is necessary to be successful in this event. Employment of higher level scripting or programming languages may also be useful. Applicants must be willing to commit to all three days of the event. No financial support for travel, lodging or meals can be provided for this event. Also note that the course may extend into the evening hours on Monday and/or Tuesday. Please make any necessary arrangements to accommodate this possibility. Please contact email@example.com with any questions.
Health science librarians are invited to participate in a rigorous online bioinformatics training course, Fundamentals of Bioinformatics and Searching, 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). The course provides basic knowledge and skills for librarians interested in helping patrons use online molecular databases and tools from the NCBI. Attending this course will improve your ability to initiate or extend bioinformatics services at your institution. Prior knowledge of molecular biology and genetics is not required. The major goal of this course is to provide an introduction to bioinformatics theory and practice in support of developing and implementing library-based bioinformatics products and services. This material is essential for decision-making and implementation of these programs, particularly instructional and reference services.
This course is offered online (asynchronously) from January 11 – February 19, 2016. The format includes video lectures, readings, a molecular vocabulary exercise, an NCBI discovery exercise, and other hands-on exercises. The instructor is Diane Rein, Ph.D., MLS, Bioinformatics and Molecular Biology Liaison from the Health Science Library, University at Buffalo. The course is a prerequisite for the face-to-face workshop, Librarian’s Guide to NCBI. Participants who complete the required coursework and earn full continuing education credit will be eligible to apply to attend the 5-day Librarian’s Guide in the future.
Due to limited enrollment, interested participants are required to complete an application form. The deadline for completing the application is December 7, 2015; participants will be notified of acceptance on December 21, 2015. The course is offered at no cost to participants. Participants who complete all assignments and the course evaluation by the due dates will receive 25 hours of MLA CE credit. No partial CE credit is granted. For questions, contact the course organizers.
Looking for health or science related images? The National Institutes of Health (NIH) recently launched the NIH Image Gallery on Flickr. The Image Gallery offers a wide variety of scientific, biomedical and disease related imagery as well as photos of NIH leadership, labs, buildings and major historical events. Additionally, you can find NIH infographics, b-roll, and the latest research images.
The Flickr site was developed as a means to distribute images to the press and public while ensuring proper license, permissions and copyright protections are documented. The majority of the images offered are free to reuse with proper credit given. The content in the NIH Flickr site will be continuously updated. View the gallery on Flickr and follow the NIH Image Gallery to stay connected. If you cannot find the image you are looking for, you may email a request.
The Fall 2015 issue of NIH MedlinePlus the Magazine features topics including migraine headaches, planning for a healthy school year, understanding and managing head lice, delirium research, and the NIH precision medicine imitative. The cover features Cindy McCain, the wife of U.S. Senator John McCain. She discusses how she has dealt with the problems of migraines, and how she is working to raise public awareness and understanding of migraines and increase support for research.
The issue also features a health information literacy project teaching high school students to use and promote MedlinePlus. Developed by the South Carolina Area Health Education Consortium (AHEC) and the Medical University of South Carolina (MUSC), students learned to use the health information resources of the NLM to create health literacy comic books, and gained valuable experience accessing these tools to continually improve their health literacy and answer other health-related questions they or their parents will have in the future.
NIH MedlinePlus the Magazine is the free, trusted consumer guide to the vast array of authoritative online health and medical information in MedlinePlus. Published four times a year, the magazine showcases the National Institutes of Health’s (NIH) latest medical research and healthcare information. NIH MedlinePlus the Magazine is freely available as a print subscription, e-mail alerts, and online.
Join NCBI staff for the upcoming webinars on PubMed and ClinVar:
PubMed for Scientists
Thu, Nov 12, 2015 9:30 AM – 10:30 AM PST
Search the biomedical literature more efficiently with PubMed. In this Webinar designed for scientists you will learn to search by author; explore a subject; use filters to narrow your search; find the full text article; and set up an e-mail alert for new research on your topic. Bring your questions about searching PubMed.
NCBI Minute: The New ClinVar Submission Wizard
Wed, Nov 18, 2015 9:00 AM – 9:30 AM PST
ClinVar is the NCBI archive of submitted interpretations of variants relative to diseases and other phenotypes. Submission to ClinVar has been through the Variation Submission Portal, which is useful for groups who frequently submit large number of variants but may not be convenient for infrequent submitters of small numbers of variants. This webinar will introduce and demonstrate the new ClinVar Submission Wizard, a guided interface for direct data entry, targeted to research laboratories that infrequently want to submit a small number of records. The Submission Wizard is designed to support all types of submissions to ClinVar, including structural variants, pharmacogenomics variants, somatic variants, as well as interpretations based on functional rather than clinical significance.
NCBI Minute: Finding Genes in PubMed
Wed, Dec 2, 2015 9:00 AM – 9:15 AM PST
Learn to quickly find literature about a gene of interest using PubMed. Take advantage of the links between gene data and literature, and leverage the vocabulary used to describe gene information in PubMed to build a better search.
Visit the NCBI Webinars and Courses webpage to view archived webinars and materials, and to learn about future webinars. Archived webinars can also be accessed on the NCBI YouTube channel.
The National Library of Medicine (NLM) has updated its list of structured abstract labels. This updated list, along with the NLM-assigned broader category mappings, can be downloaded for free from the Structured Abstracts resource page which also provides NLM guidelines and other background information to assist licensees or researchers. A grand total of 4,702 citations (whether in process, MEDLINE, or PubMed-not-MEDLINE status) were revised so that the new labels include the NLM Category mapping in the XML data, effective on or about October 26, 2015. Of interest, the new label ‘TWEETABLE ABSTRACT’ (mapped to the NLM Category ‘CONCLUSIONS’) illustrates the impact of social media. Read more about Structured Abstracts in MEDLINE/PubMed.
The Office of Dietary Supplements (ODS) at the National Institutes of Health, in partnership with the National Library of Medicine, is inviting public comment on the Dietary Supplement Label Database (DSLD). Launched in June 2013, DSLD now provides all the information from the labels of 50,000 dietary supplement products marketed in the United States. ODS is particularly interested in comments about features to add and functionality improvements that would make the DSLD a more useful tool to users. A federal stakeholder panel for the DSLD will consider all comments received. ODS welcomes input from academic researchers, government agencies, the dietary supplement industry, and other interested parties, including consumers.
ODS would like would like to receive ideas and suggestions for how the DSLD might evolve. What features might be added, improved, or enhanced—for example, in capabilities related to search, sorting, organization, and downloading of information that would make it a more valuable tool for users? All comments should be sent to ODS@nih.gov, and must be received by 11:59 p.m. eastern time, November 27, 2015. The full announcement is available in the Federal Register notice: Notice of Opportunity for Public Comment on the Dietary Supplement Label Database.
The Exhibition Program at the National Library of Medicine has announced booking availability for its newest traveling exhibition, For All the People: A Century of Citizen Action in Health Care Reform. When requesting booking, please provide 3 to 4 booking dates which are of interest. NLM will make every effort to find the best fit for your institution on the exhibition itinerary. The online exhibition incorporates education resources, including a K-12 lesson plan that investigates the exhibition content; a higher education module; an online activity, and a robust selection of resources including K-12 suggested readings. In addition, the Web feature, “Related Resources at NLM,” includes a selection of published articles on health care access, policy, and disparities, available through PubMed Central, which provides free access to over 3.1 million full-text biomedical and life science journal articles.
Health care reform has been a contentious political issue in the United States for more than one hundred years. From the beginning of the 20th century to today, citizens have made their voices heard in the debates. For All the People tells the lesser-known story of how movements of ordinary people helped shape the changing American health care system. The six-banner traveling exhibition highlights images from over one hundred years of citizen action for health care reform.
A recent post in the National Library of Medicine’s Circulating Now blog highlights the fifty years since the Medical Library Assistance Act was signed into law by President Lyndon B. Johnson in October, 1965, establishing the Regional Medical Library Program, now known as the National Network of Libraries of Medicine. The first RML to be selected was the Countway Library of Medicine at Harvard Medical School; the second, the library of the New York Academy of Medicine; and the third, the library of the College of Physicians of Philadelphia. In all, eleven RMLs were initially established. The number of regions was later reduced to seven due to federal budget cuts, and then expanded to its current configuration of eight regions.