Archive for the ‘Informatics’ Category
The 22nd annual edition of the Nucleic Acids Research Database Issue features nine free full-text papers from NCBI staff that present recent updates to the databases, including GenBank, Gene, and RefSeq. These papers describe the state of NCBI databases as well as future plans to improve their use, from new reference resources created to improve the usability of viral sequence data to in-house curation efforts in the Conserved Domain Database, and much more. The articles are all available from PubMed.
The Robert B. Greenblatt, M.D. Library, Georgia Regents University, has announced that applications are now being accepted for the Spring and Fall 2015 sessions of the NLM Georgia Biomedical Informatics Course, to be held April 12-18 and September 27-October 3, 2015, at the Brasstown Valley Resort & Spa in Young Harris, GA. The course, previously held at the Marine Biological Laboratory in Woods Hole, MA, offers participants a week-long immersive experience in biomedical informatics and provides continuing education to health care professionals interested in the application of computer technologies to medicine. The application deadline for both sessions is December 15, 2014.
Biomedical administrators, faculty, and others who can become change agents for their institutions are strongly encouraged to apply. All costs for the course including travel, housing, and per diem are supported by NLM. The application is open to US citizens and US permanent residents. Enrollment is limited to 30 attendees. The course will provide attendees a diverse set of skills and experiences incorporating concepts, theories and building blocks of biomedical informatics; ability to use informatics for solving current health care challenges; application and policies related to computer technologies and information science; hands-on experience during evening workshops; and networking with nationally known bioinformatics educators and thought leaders.
The National Library of Medicine is saddened at the passing of Dr. Morris F. Collen, known around the world as “Mr. Medical Informatics,” on September 27, 2014. He was 100 years old. In addition to his wide-ranging contributions to medical informatics, Dr. Collen was a valued advisor to NLM. He was a member of the Lister Hill Board of Scientific Counselors from 1984 to 1987. He served on the Literature Selection Technical Review Committee, which advises NLM on the journals to be indexed in MEDLINE/PubMed, from 1997 to 2002, chairing the Committee from 2000 to 2002. He also contributed to NLM Long Range planning.
Morris Collen earned his bachelor’s degree in electrical engineering from the University of Minnesota and graduated from the University of Minnesota School of Medicine in 1938. His residency at the University of Southern California/Los Angeles County General Hospital took him to California, where he started what would become a legendary career at Kaiser (later Kaiser Permanente). He served as chief of medical services at Kaiser’s Oakland hospital from 1942 to 1952, and medical director the following year. From 1953 to 1961, Dr. Collen served as physician-in-chief at Kaiser Permanente (KP) in San Francisco.
During World War II, Dr. Collen was one of the first doctors to experiment with the use of a new wonder drug–penicillin–for the treatment of pneumonia in shipyard workers, at a time when most of the drug was shipped overseas for members of the armed forces. Dr. Collen’s interest in the use of computers as a way to improve medical care developed during a 1961 conference on biomedical electronics. Soon afterward, he founded Kaiser Permanente’s research division and created a prototype electronic health record fed by punch card into a huge IBM mainframe computer. The record included information from patient screenings and lab results. One of Dr. Collen’s major achievements at KP was the development of the multiphasic health checkup, which addressed the physician shortage of the 1950s, post-World War II. This series of procedures and tests, given to thousands of KP members, screened for conditions such as heart disease, diabetes, and cancer. Not only did these revolutionary tests save physicians’ time; they constituted a significant experiment in preventive care. Dr. Collen eventually automated the multiphasic health checkups, moving them onto a punch card system in 1964.
Electronic health records are in the headlines today, but their bloodlines run back to Dr. Collen. Kaiser Permanente’s early EHR system became internationally known because of his groundbreaking efforts. In fact, he predicted that the computer would have “the greatest technological impact on medical science since the invention of the microscope,” as noted in a 2008 Kaiser Permanente publication.
Health science librarians in the United States 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). 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. Instructors will be NCBI staff and Diane Rein, Ph.D., MLS, Bioinformatics and Molecular Biology Liaison from the Health Science Library, University at Buffalo. There is no charge for the classes. Travel and lodging costs for the in-person class are at the expense of the participant.
There are two parts to A Librarian’s Guide to NCBI, 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 is an online (asynchronous) course, January 12-February 13, 2015, and Part 2 is a 5-day in-person course offered on-site at the National Library of Medicine in Bethesda, MD, March 9-13, 2015. Students successfully completing the Fundamentals course (Part 1) will earn 18 MLA CE credits. Those successfully completing the 5-day in-person class (Part 2) will earn 36 additional MLA CE credits.
Applications are open to health science librarians in the United States. Applicants will be accepted both from libraries currently providing bioinformatics services as well as from those desiring to implement services. Enrollment is limited to 25 participants. The application deadline is November 17, 2014, and acceptance notification will be on or about December 15, 2014. Visit the A Librarian’s Guide to NCBI course page for additional information.
NCBI Discovery Workshops, consisting of four 2.5-hour hands-on training sessions emphasizing NCBI resources such as BLAST and Nucleotide, will be presented by NCBI staff at the University of California, Davis, on September 15-16, and at the University of California, Berkeley, on September 17-18:
- Session 1: Navigating NCBI Molecular Data Through the Integrated Entrez System. 9 am – 11:30 am, 9/15 (UC Davis) & 9/17 (UC Berkeley)
- Session 2: NCBI Genomes, Assemblies and Annotation Products: Microbes to Human. 1 pm – 3:30 pm, 9/15 (UC Davis) & 9/17 (UC Berkeley)
- Session 3: Advanced NCBI BLAST. 9 am – 11:30 am, 9/16 (UC Davis) & 9/18 (UC Berkeley)
- Session 4: Gene Expression Resources at NCBI. 1 pm – 3:30 pm, 9/16 (UC Davis) & 9/18 (UC Berkeley)
For more information or to register:
A collaborative project between the National Library of Medicine’s National Center for Biotechnology Information (NCBI) and several other federal and state partners, to reduce the time and improve the accuracy of detecting foodborne pathogens by using whole genome sequencing (WGS) techniques, received the HHSinnovates award on July 21, 2014. The HHSinnovates program was initiated in 2010 to recognize new ideas and solutions developed by HHS employees and their collaborators. Six finalist teams were recognized at the awards ceremony. The WGS Food Safety Project, which also involved the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA), the US Department of Agriculture (USDA), and state public health laboratories, was one of three projects to be honored as “Secretary’s Picks” by HHS Secretary Sylvia Mathews Burwell. The award went to the specific individuals leading the project in the various agencies; in the case of NCBI, Senior Scientist William Klimke, PhD, was honored for his work in heading NCBI’s part of the project.
WGS provides greater specificity than other techniques, such as the commonly used pulsed-field gel electrophoresis (PFGE), in identifying the DNA fingerprint of bacteria. It also can more rapidly determine whether isolates are related to a foodborne disease outbreak. The demonstration project involves real-time sequencing of Listeria monocytogenes isolates from human DNA as well as the food supply chain. In the project, the whole genomes of isolates are sequenced and the sequencing data are sent to NCBI, which performs assembly, annotation and analysis, and then sends results back to CDC, FDA, USDA and the labs. Collaborative projects using WGS for other pathogens related to food safety are also underway.
The National Library of Medicine has announced that Georgia Regents University (GRU) will serve as the host organization for the NLM-sponsored biomedical informatics course. The NLM Biomedical Informatics Course, now entering its 22nd year, offers participants a week-long immersive experience in biomedical informatics taught by experts in the field. The course was previously held at the Marine Biological Laboratory (MBL) in Woods Hole, MA, with Cathy Norton, MLS, as the MBL principal investigator. NLM plans to take the skills shaped over the past two decades at MBL to its new colleagues at GRU. The first course organized at Georgia Regents University will be held September 14-20, 2014, followed by an additional session April 12-18, 2015. The course will be held at a conference center at the Brasstown Resort in Young Harris, GA, at no cost to participants.
Application to the course is open to anyone, but space is limited. Preference will be given to American applicants who demonstrate, through a brief application letter, that they have the significant need for an understanding of the informatics solutions that are available to address their biomedical research, practice and education challenges and that, through their official position, they are significant “change agents” who can influence the adoption of best practices in their own environment and expand the influence of the course to others through teaching or by example. The application deadline is July 7.
The course, co-directed by James J. Cimino, MD, Chief, Laboratory for Informatics Development at the National Library of Medicine and the NIH Clinical Center, and NLM Director Donald Lindberg, MD, will guide participants through topics including biomedical informatics methods, clinical informatics, big data and imaging, genomics, consumer health informatics, mathematical modeling, and telemedicine and telehealth. The co-principal investigators from GRU are Brenda L. Seago, MLS, MA, PhD, Professor and Director of Libraries, and Kathy J. Davies, MLS, Chair, Research and Education Services, Robert B. Greenblatt, MD Library.
NCBI has just released Entrez Direct, a new software suite that allows you to use the UNIX command line to directly access NCBI’s data servers, as well as parse and format data to create customized data files. The latest NCBI News story discusses Entrez Direct and gives several examples of how the programs may be used, as well as links to the suite on FTP and documentation. Entrez Direct is available as a simple FTP download and has extensive documentation on the NCBI web site.
The Coalition for Networked Information (CNI), the Association of Research Libraries (ARL), and EDUCAUSE have announced that Donald A.B. Lindberg, Director of the National Library of Medicine, has been named the 2014 recipient of the Paul Evan Peters Award. The award recognizes notable, lasting achievements in the creation and innovative use of network-based information resources and services that advance scholarship and intellectual productivity. Named for CNI’s founding director, the award honors the memory and accomplishments of Paul Evan Peters (1947–1996), a visionary and a coalition builder in higher education and the world of scholarly communication, who led CNI from its founding in 1990. The award will be presented during the CNI membership meeting in St. Louis, MO, to be held March 31–April 1, 2014, where Dr. Lindberg will deliver the Paul Evan Peters Memorial Lecture. The talk will be recorded and made available on CNI’s YouTube and Vimeo channels after the meeting concludes.
Dr. Lindberg’s interest in the potential intersection between information technology and the biological sciences stretches back to the early days of his career. He joined the pathology faculty at the University of Missouri in 1960, where he developed the first automated lab system and an automated patient history acquisition system. He implemented an automated statewide system for interpreting electrocardiograms, as well as other medical applications for the computer. Around this time, he also began publishing articles in a field that would come to be known as medical informatics, including The Computer and Medical Care, which appeared in 1968.
Dr. Lindberg has worked as a scientist for over 50 years, becoming widely recognized as an innovator in applying computer technology to health care, medical diagnosis, artificial intelligence, and educational programs. In 1984 he was appointed director of the National Library of Medicine (NLM), the world’s largest biomedical library, a post that he still holds. As NLM’s Director, Dr. Lindberg convinced the United States Congress that the Library was an essential information conduit, facilitating the decision-making process of scientists and pharmaceutical companies, and, ultimately, benefiting patients and the general public, thereby securing the organization’s robust future. He has spearheaded countless transformative programs in medical informatics, including the Unified Medical Language System, making it possible to link health information, medical terms, drug names and billing codes across different computer systems; the Visible Human Project, a digital image library of complete, anatomically detailed, three-dimensional representations of the normal male and female human bodies; the production and implementation of ClinicalTrials.gov, a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world; and, the establishment of the National Center for Biotechnology Information, a national resource for molecular biology information and genetic processes that control health and disease. Today, NLM has a budget of $327 million, more than 800 employees, and digital information services that are used billions of times a year by millions of scientists, health professionals, and members of the public.
Dr. Lindberg is a member of the Institute of Medicine of the National Academy of Sciences, and has received numerous honors and awards, including the prestigious Morris F. Collen, MD, Award of Excellence of the American College of Medical Informatics, and the Surgeon General’s Medallion of the US Public Health Service. He received his medical degree from the College of Physicians and Surgeons, Columbia University, and an undergraduate degree from Amherst College. A four-member committee selected Dr. Lindberg for the award: the late Ann J. Wolpert, director of libraries at the Massachusetts Institute of Technology; George O. Strawn, director of the Federal Networking and Information Technology Research and Development (NITRD) National Coordination Office (NCO); Sally Jackson, professor of communication at the University of Illinois at Urbana-Champaign; and Joan Lippincott, associate executive director of the Coalition for Networked Information.
The NCBI, in partnership with the National Library of Medicine Training Center (NTC), will offer the Librarian’s Guide to NCBI course on the NIH campus in April 2014. This will be the second presentation of the course; it was previously offered in the spring of 2013. After the course, lecture slides and hands-on practical exercises will be posted on the education area of the NCBI FTP site and video tutorials of the course lectures will be available on the NCBI YouTube channel. Materials from the 2013 course are currently available.
A Librarian’s Guide is an intense five-day exploration of modern molecular biology, genetic, and other biomedical data as represented at the NCBI. The course explains how and why these data are generated, their importance in modern biomedical research, and how to access them through the NCBI Web site. It is intended for medical librarians in the United States who currently are offering bioinformatics education and support services to their patrons or are planning to offer such services in the future. More information is available in the newest NCBI Insights blog post.
All applicants for A Librarian’s Guide must have successfully completed the asynchronous online Fundamentals of Bioinformatics and Searching class, which is a six-week introduction to molecular biology and bioinformatics taught by Diane Rein, Ph.D., MLS, and offered through the NTC. The Fundamentals course is open to any medical librarian in the United States interested in an introduction to bioinformatics and NCBI resources. A winter 2014 Fundamentals class, which runs from February 10 – March 21, 2014, is open for applications. Only people who have successfully completed the Fundamentals class may apply to A Librarian’s Guide to NCBI. The application process for eligible Fundamentals candidates will be announced in February 2014.