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Archive for the ‘NCBI’ Category

NCBI Advanced Genomics Hackathon in January 2016

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 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

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.

New Videos Available on the NCBI YouTube Channel

Two new three-minute videos on the NCBI YouTube channel will provide information about how to view track sets in all of the NCBI genome browsers and Sequence Viewer displays and how to store and share custom sets of tracks in track collections. NCBI Recommended Tracks presents track sets, which allow you to instantly tailor your display to a specific need, while My NCBI Track Collections: Introduction shows how to store and share tracks in custom sets called track collections. To learn more about track sets and collections, visit the FAQ on the Sequence Viewer page. Subscribe to the NCBI YouTube channel to receive alerts about new videos ranging from quick tips to full webinar presentations.

First Offering of NCBI NOW (Next Generation Sequencing Online Workshop) Begins October 13!

NCBI will present the first iteration of NCBI NOW, a free online experience aimed at those new to next generation sequencing (NGS) analysis, from October 13-23. Enrollment in this course is limited to the first 1,000 participants who sign up through the ORAU Portal. Since enrollment is on a first-come, first-served basis, please only sign up for this educational opportunity if you will be able to participate fully. Learners will watch 6-7 videos (average video duration: 45-60 minutes) online during the first seven days of the course. These videos will cover the basics of NGS data, preprocessing, quality control and alignment strategies for both DNA-Seq and RNA-Seq, as well as a brief discussion of downstream analysis. Additionally, there will be demonstrations about leveraging BLAST tools for NGS analysis.

Next, participants will apply a selection of RNA-Seq alignment algorithms over three days (1-2 hours per day), mapping RNA-Seq data to GRCh38 chromosome 20. Finally, participants will compare the results of these mappers for specific genes. Throughout the course, participants will be able to post questions at Biostars; experts from NCBI and elsewhere will be available online to answer questions. Learners will emerge from the course equipped to map their own RNA-Seq or DNA-Seq data to the human genome, understand the options for downstream analysis, and use their understanding of the basic steps of data processing to interact more effectively with bioinformatician collaborators.

NLM Theater Presentations at MLA 2015

The NLM exhibit booth at the 2015 Annual Meeting of the Medical Library Association in Austin, TX, featured theater presentations to bring users up-to-date on several NLM products and services. The presentation recordings are captioned and accessible from the NLM Distance Education Program Resources page. The presentations include:

Note: To listen to the voice recordings and view the captions you may need the latest version of Flash® Player (download for free from the Adobe Web site). To maximize the presentation, use the Full Screen button. For more information, go to the NLM Technical Bulletin page.

NCBI Homepage Update: Action Buttons and Category Pages

The NCBI homepage has six new buttons on it: Submit, Download, Learn, Develop, Analyze, and Research. Each of these leads to an action page devoted to a particular set of services. These action pages allow easy access to the pages and resources you need to complete tasks. For instance, you can: Find information about the Entrez API; Find an upcoming NCBI webinar, Find an NCBI tool that designs PCR primers, and much more! On the new action pages, you’ll also see six categories in the header: Literature, Health, Genomes, Genes, Proteins, and Chemicals. These category pages highlight useful databases, tools and resources for each of the topics all in one place.

Also included is a blue Feedback button on the left side of the Download, Learn, Develop, and Analyze pages so that you can send comments to NCBI. More information about the new homepage will be released on NCBI News and to the blog, NCBI Insights.

Nucleic Acids Research Database 2015 Issue Features NCBI Databases

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.

SciENcv Enhancements: NIH and NSF Biographical Sketch Formats

SciENcv enhancements will include the new NIH biographical sketch format as a choice for creating SciENcv profiles. SciENcv will continue to support the current NIH biographical sketch format; however, NIH encourages researchers to use the new format with their grant submissions. Researchers will be required to employ the new NIH biographical sketch starting May 25, 2015. Users will be able to utilize their existing Science Experts Network Curriculum Vitae (SciENcv) profiles to create profiles in the new NIH biographical sketch format, as well as be able to select the new NIH biographical sketch format when creating profiles manually or through a data feed from an external source. The Personal Statement section of the NIH biographical sketch has been updated to include an option to list up to four peer-reviewed citations. A new section, Contribution to Science, replaces the former section Selected Peer-Reviewed Publications, and it aims to give researchers a place where they can describe five of their most significant contributions to science.

SciENcv users will also soon be able to create profiles in the National Science Foundation (NSF) biographical sketch format. This newly added format will be available to download in PDF, MS Word or XML, and users will be able to share their SciENcv NSF profiles through a public URL. In addition, by linking your NSF account to an NCBI account, you will be able to populate SciENcv profiles with information stored in your NSF account. The NSF biographical sketch is the official format used for grant submissions to the NSF and consists of five sections: Professional Preparation, Appointments, Products, Synergistic Activities, and Collaborators & Other Affiliations.

For more information visit the NLM Technical Bulletin articles: My NCBI – New NIH Biographical Sketch Available in SciENcv and My NCBI – National Science Foundation Biographical Sketch and Data Integration with SciENcv.

NCBI HIV-1 Website Updated

The HIV-1, human interaction database has been updated and is now on an improved page. The improved interface includes help documentation and supports structured queries against Gene, as well as browsing, filtering and downloading the protein and replication interaction data sets. The most recent data release (June 2014) includes 12,785 HIV-1, human protein-protein interactions for 3,142 human genes and 1,316 replication interactions for 1,250 human genes. The HIV-1, human interactions project, collates published reports of two types of interactions – HIV-1, human protein interactions, and human gene knock-downs that affect virus replication which are reported as “replication interactions.”