Archive for the ‘E-Science’ Category
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 Center for Advancing Translational Sciences (NCATS) has announced the Toxicology in the 21st Century (Tox21) Data Challenge 2014 competition.
The goal of the challenge is to crowdsource data analysis by independent researchers in order to develop computational models that can better predict chemical toxicity. It is designed to improve current toxicity assessment methods, which are often slow and costly. The model submission deadline is November 14, 2014. NCATS will showcase the winning models in January 2015. Registration for the challenge and more information is available on the web site.
Tox21 scientists are currently testing a library of more than 10,000 chemical compounds in NCATS’s high-throughput robotic screening system. To date, the team has produced nearly 50 million data points from screening the chemical library against cell-based assays. Data generated from twelve of these assays form the basis of the 2014 challenge. For more information on the Tox21 Modeling Challenge and Tox21 Program, contact Anna Rossoshek.
On April 8, 2014, the inaugural cohort of National Digital Stewardship Residents will present a symposium entitled Emerging Trends in Digital Stewardship at the National Library of Medicine (NLM), on the NIH campus in Bethesda, MD. The symposium will consist of panel presentations on topics including preserving social media and collaborative workspaces, open government and open data, and digital strategies for public and non-profit institutions. It will also feature a demonstration of BitCurator, an environment of digital forensics tools designed to help collecting institutions manage born-digital materials, developed by the School of Information and Library Science at the University of North Carolina, Chapel Hill (SILS), and the Maryland Institute for Technology in the Humanities (MITH). The symposium is free and open to the public. Pre-registration is encouraged.
The National Digital Stewardship Residency (NDSR) is an initiative of the Library of Congress (LC) and Institute of Museum and Library Services (IMLS), to “provide a robust, hands-on learning experience to complement graduate-level training and education.” The inaugural cohort began their residency at Washington, DC area libraries, museums, and cultural institutions in September 2013. Ten residents are embedded in institutions around the area, each completing a project related to an aspect of digital preservation and stewardship. The NDSR program aims to “serve the American people by developing the next generation of stewards to collect, manage, preserve, and make accessible our digital assets.” NLM serves as a host institution for the National Digital Stewardship Residency, and since September has worked with its NDSR Resident Maureen Harlow to develop a thematic Web archive collection. This project builds on a pilot Web archive collection completed by NLM and featured in The Signal blog of the Library of Congress, in October 2012.
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 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.
The NIH Big Data to Knowledge (BD2K) initiative has released a Funding Opportunity Announcement (FOA) to support a U24 resource award for Development of an NIH BD2K Data Discovery Index Coordination Consortium. The purpose of this FOA is to create a consortium to begin development of an NIH Data Discovery Index (DDI) to allow discovery, access, and citation of biomedical data. Letters of intent to apply are due by February 6, 2014, and completed applications are due by March 6, 2014. Budgets are limited to $2,000,000 in direct costs per year but must reflect the actual needs of the proposed project. The maximum project period is three years.
As part of the NIH Big Data to Knowledge (BD2K) initiative, the DDI seeks to fulfill the recommendation from the Data and Informatics Working Group (DIWG) Report to the Advisory Council to the Director to “Promote Data Sharing Through Central and Federated Catalogues.” The awardee in response to this FOA will constitute a DDI Coordination Consortium (DDICC, U24) to conduct outreach, fund small pilot projects, manage communication with stakeholders, constitute and coordinate Task Forces to study relevant questions related to access, discoverability, citation for all biomedical data and assure community engagement in the development, testing, and validation of an NIH DDI. Part of this effort will be to assemble a user interface (website) through which the results of development and testing of models for an NIH DDI may be communicated.
November 2013 marks 25 years that the National Center for Biotechnology Information (NCBI) has been providing access to biomedical and genomic information to advance science and health. Established in 1988 as a division of the National Library of Medicine (NLM) at the National Institutes of Health (NIH), NCBI has grown into a leading source for public biomedical databases, software tools for analyzing molecular and genomic data, and research in computational biology. NCBI’s resources rank among the most heavily used government web sites in the United States, with approximately 3 million users every day.
In recognition of NCBI’s achievements, an awards and recognition program was held November 1 on the NIH campus in Bethesda, Maryland. At that event Tony Hey, PhD, Vice President of Microsoft Research, presented NCBI Director David Lipman, MD, with the Jim Gray eScience Award. Named for Jim Gray, a technical fellow for Microsoft Research and an A.M. Turing Award winner who disappeared at sea in 2007, the annual award recognizes researchers who have made outstanding contributions to the field of data-intensive computing and made “science easier for scientists,” according to Microsoft.
Gray was very familiar with the work of NCBI. He was a member of the NLM Board of Regents in 2006 and met a number of times with Dr. Lipman, NCBI Information Engineering Branch Chief Jim Ostell, PhD, and other staff to discuss issues such as organization of and access to biomedical literature and data. His interest in NCBI’s work is evidenced by his final lecture, in January 2007, in which he highlighted the importance of NCBI/NLM biomedical literature databases like PubMed and PubMed Central, genomic databases such as GenBank, and NCBI’s Entrez system for searching across these and many other databases. An edited version of Gray’s lecture can be read in The Fourth Paradigm, available on Microsoft Research’s web site.
The NCBI awards program also featured presentations by Sir Richard Roberts, PhD, chief scientific officer of New England Biolabs, who provided the keynote address, entitled “A personal recollection of GenBank and NCBI.” NLM Director Donald A.B. Lindberg, MD, recounted the planning process that led to the formation of NCBI, and NIH Deputy Director for Intramural Research Michael M. Gottesman, MD, provided introductory remarks for the awards ceremony. Dr. Lipman closed the event by recognizing the dedicated and hard-working staff of NCBI who have enabled the progress that has transpired over the last 25 years.
The New England Collaborative Data Management Curriculum (NECDMC) offers openly available materials that librarians can use to teach research data management (RDM) 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. The project has been led by the Lamar Soutter Library at the University of Massachusetts Medical School with funding from the National Network of Libraries of Medicine, New England Region.
The Lamar Soutter Library developed the Frameworks for a Data Management Curriculum with Worcester Polytechnic Institute in 2011. Over the past year the Soutter Library has partnered with librarians from Tufts University, University of Massachusetts Amherst, Northeastern University, and the Marine Biological Laboratory and Woods Hole Oceanographic Institute, to fully develop the curriculum’s lecture content, readings, activities, and slide presentations.
Some libraries will be piloting the curriculum at their institutions and conducting evaluations with students of the learning modules. If you are teaching or plan to teach RDM, you are invited to pilot the NECDMC. For more information about being a pilot partner, please contact Donna Kafel.
The 9th International Digital Curation Conference (IDCC) will be held from February 24-27, 2014, at the Omni San Francisco Hotel, and registration is now open. This year the IDCC will focus on how data-driven developments are changing the world around us, recognizing that the growing volume and complexity of data provides institutions, researchers, businesses, and communities with a range of exciting opportunities and challenges. The Conference will explore the expanding portfolio of tools and data services, as well as the diverse skills that are essential to explore, manage, use, and benefit from valuable data assets. The program will reflect cultural, technical, and economic perspectives, and will illustrate the progress made in this arena in recent months.
IDCC14 will be organized by the Digital Curation Centre UK, in partnership with the University of California Curation Center (UC3) at the California Digital Library and the Coalition for Networked Information (CNI). The draft program is now available.