The NLM exhibit booth at the Annual Meeting of the Medical Library Association (MLA) featured theater presentations to bring users up-to-date on several NLM products and services. Presentation recordings are now accessible from the NLM web site. The average video length is 20 minutes.
Archive for the ‘NCBI’ Category
NCBI has a new Twitter feed, @ncbibooks, to announce new books and documents available on the NCBI Bookshelf. An online resource providing free access to the full text of books and documents in life sciences and health care, the Bookshelf currently provides access to over 4,500 titles.
The Bookshelf is continuously expanding with new materials as well as receiving updates to existing books & documents. Between May 16 and May 20, 2016, for example, 19 new titles were added. Among the new titles are several Agency for Healthcare Research and Quality reports, health technology assessments and systematic reviews from Canadian Agency for Drugs and Technologies in Health and National Institute for Health Research (UK), and World Health Organization guidelines on daily iron supplementation.
NCBI will assist the University of California Davis in hosting a biomedical data science hackathon June 13-15 at the School of Veterinary Medicine in Davis, CA, focusing on advanced bioinformatics analysis of next generation sequencing data and metadata. This event is for students, postdocs, investigators and other researchers already engaged in the use of pipelines for genomic analyses from next-generation sequencing data or metadata. The event is open to anyone selected for the hackathon, and able to travel to Davis. Working groups of 5-6 individuals will be formed into five or six teams. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure.
Applications are due by May 5 at 5:00PM EDT. Participants will be selected from a pool of applicants based on the experience and motivation they provide on the form. Prior participants and applicants are especially encouraged to reapply. Applicants must be willing to commit to all three days of the event. No financial support for travel, lodging or meals is available.
The newest video on the NCBI YouTube channel, Navigating the NIH Manuscript Submission Process, covers details about submitting, reviewing and approving your manuscript in the NIH Manuscript Submission (NIHMS) system in ten minutes. The NIHMS system supports manuscript depositing into PubMed Central (PMC) as required by the public access policies of NIH and other participating funding agencies. Subscribe to the NCBI YouTube channel to receive alerts about new videos ranging from quick tips to full webinar presentations.
The NCBI Zika virus resource page has been updated with a specialized database. This database uses pipelines to annotate genes, proteins and mature peptides, and standardize sample metadata. Using this database, you can:
- Find sequences easily using standardized annotations and normalized metadata terms.
- Construct alignments and phylogenetic trees using a suite of online tools.
- Download sequences and metadata in a variety of formats and create customized titles/description lines (deflines) for FASTA file downloads.
NIH Director Francis Collins, MD., Ph.D., has announced that David J. Lipman, M.D., will continue in his leadership role as Director of the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM). In addition, he will take on an important additional position as Associate NIH Director for Biomedical Information Resources. Together, these actions will further strengthen NLM’s and NCBI’s efforts to expand their trans-NIH mission, as envisioned in the recent report of the NLM Working Group of the Advisory Committee to the NIH Director.
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.
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.
Apply by December 7 to attend the Winter 2016 NLM online class “Fundamentals of Bioinformatics and Searching”
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.
Upcoming NCBI Webinars: PubMed for Scientists, The New ClinVar Submission Wizard, Finding Genes in PubMed
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.