Archive for the ‘Events’ 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 firstname.lastname@example.org with any questions.
November is National Native American Heritage Month (NNAHM), a time to recognize the accomplishments of this country’s first inhabitants. As the early inhabitants of this land, the native peoples of North America have their own tribal orientations, language origins, and cultural histories. Today, many healing techniques that are practiced have been adopted from traditions that originate from various Native American tribes. This year’s NNAHM theme, Tribal Diversity: Weaving Together Our Traditions, highlights spirituality as an inseparable element of healing in medicine. Healing the physical parts of a patient is not enough; one must acknowledge the importance of emotional wellness, as influenced by Native American rituals and traditions.
This month is dedicated to building new avenues of opportunity for Native Americans by making critical investments to improve health, to strengthen tribal communities, and to promote educational opportunities at the NIH. Maintaining an inclusive biomedical research workforce with a diversity of talent is critical to the NIH mission of fostering new discoveries and promoting the highest level of scientific integrity to improve the nation’s health. NNAHM allows the opportunity for every individual to learn more about the distinctive backgrounds and heritages of Native Americans. You can show support during National Native American Heritage Month by actively engaging with the Office of Equity, Diversity and Inclusion’s (EDI’s) social media campaign, including the month-long NIH Twitter campaign. More information is located on the Strategist for the Native American Portfolio website.
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.
The next session of the National Library of Medicine Informatics Lecture Series will be held on November 4, at 11:00am-12:00pm PST, with the feature presentation Use of Clinical Big Data to Inform Precision Medicine. The speaker will be Joshua Denny, MD, Associate Professor in the Departments of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. This talk will be broadcast live and archived.
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). 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.
Dr. Denny 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 a 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.
Video recordings and slide presentations for most sessions of the 2015 Science Boot Camp West for Librarians are now available. The meeting was held July 27-29, 2015, at Stanford University. Video files are large and best viewed by downloading rather than watching online. The full meeting agenda is also available.
The National Library of Medicine is pleased to announce the first annual Donald A.B. Lindberg & Donald West King Lecture on Wednesday, October 7, at 10:00 AM PDT in Bethesda, MD, and will be videocast (and archived for later viewing). The inaugural lecture, which honors recently retired NLM Director Dr. Lindberg and former NLM Deputy Director of Research and Education Dr. King, is titled, Integrating Multi-scale Data for Biomedical Discovery and Clinical Implementation. It will be given by Russell Altman, MD, PhD, of Stanford University. Dr. Altman’s primary interests are in the field of bioinformatics. He is particularly interested in the analysis of protein and RNA structure and function, both in an individual problem-centered manner and on a functional genomic scale. Dr. Altman currently serves as a member of the Advisory Committee to the NIH Director (ACD).
The NIH Big Data to Knowledge (BD2K) program and the NIH Library are pleased to join the Johns Hopkins (JHU) Bloomberg School of Public Health Department of Biostatistics in announcing the first JHU DaSH, Data Science Hackathon, on September 21-23, 2015, in Baltimore.
The event 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, and provides a local opportunity for NIH scientists and trainees to participate in a data science Hackathon. For questions about the Hackathon, contact Lisa Federer at the NIH Library.
The Banner Alzheimer’s Institute Native American Program will host the first National Native American Conference on Alzheimer’s Disease and Dementia in Native American Communities on Thursday and Friday, October 15-16, at the Scottsdale (AZ) Plaza Resort. Targeting urban and tribal health care and social service professionals, this two-day conference will provide eight plenary and more than 30 concurrent sessions from stellar Native American and dementia specialists from across the U.S. This conference is designed to provide the opportunity to learn best practices in the diagnosis, treatment and care available for Native American families affected by Alzheimer’s disease.
Registration and agenda information for the National Library of Medicine’s third annual DailyMed/RxNorm Jamboree Workshop is now available. The Jamboree is a free public meeting to be held on September 24, 2015, 9:30 am to 4:15 pm EDT, at the Lister Hill Auditorium on the NLM campus in Bethesda, MD. The session will also be webcast and archived for future viewing. Registration is required for attendance. Since 2015 marks the 10th anniversary of DailyMed, the meeting will feature a retrospective look at how industry has made use of DailyMed during that time.
Featured speakers will include representatives from the federal government, industry, academia and non-profit sectors. Speakers from the U.S. Food and Drug Administration, U.S. Pharmacopeial Convention, and Avalere Health will talk about biosimilars naming. Ed Millikan, representing the American Society of Health-System Pharmacists, will present an extended look at Risk Evaluation and Mediation Strategies. The meeting emphasis is on practical and novel ways to use and understand this free drug information, which is produced and consumed by a number of federal agencies.
The Institute of Medicine Roundtable on Population Health Improvement will be hosting a workshop, Metrics that Matter for Population Health Action, on July 30, 2015, at the Oakland Conference Center of the California Endowment in Oakland, CA. This workshop will:
- highlight existing and emerging population health metrics sets and explore their purposes, areas of overlap and gaps
- highlight population health metrics with attention to equity/disparities
- discuss characteristics of metrics necessary for stakeholder action (across multiple sectors whose engagement is needed to transform the conditions for health in communities)
- highlight population health metrics useful to addressing health beyond health care and engaging “total population health” (again, across multiple sectors)
The workshop is open to the public and will also be webcast live on the Institute of Medicine website. Register for the workshop and/or webcast, and follow the conversation on Twitter: #pophealthRT.