NCBI’s Genome Remapping Service assists in the transition to the new human genome reference assembly (GRCh38)

In late December 2013, the Genome Reference Consortium (GRC) released an updated version of the human reference genome assembly, GRCh38, and submitted these new sequences to GenBank. This is the first time in four years that a new major version of the human genome has become available to the genomics community.

Perhaps you’ve been working on data mapped to the previous assembly (GRCh37) that became available in March 2009, or maybe you are still using an even earlier version, such as NCBI36 from March 2006. Is there a way to reduce the amount of time and effort required to reanalyze your data in the context of the new assembly?

Yes! It’s NCBI’s Genome Remapping Service, or NCBI Remap for short.

Continue reading

A Librarian’s Guide to NCBI — an intensive training course for medical librarians to be offered April 2014

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 (NCBI Insights April 11 and May 6, 2013). After the course, we will post lecture slides and hands-on practical exercises 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 available, as well as lecture videos for the expression module.
Continue reading

Introducing the New Human Genome Assembly: GRCh38

This month marks a major event in the realm of human genome research: the release of a new assembly of the genome, GRCh38. It has been over four years since the last major release (GRCh37 in March 2009), and we are going to explore several aspects of this new assembly in a series of blog posts over the coming weeks. In this initial post, we will give an overview of the data flow so that you will understand how NCBI received the data, where the data are at NCBI and what genome annotations you can expect from NCBI in the near future.
Continue reading

NCBI’s 25th Anniversary and The Jim Gray eScience Award

November 2013 marks 25 years since the founding of the National Center for Biotechnology Information (NCBI).

Cardin Congressional Record Statement

In honor of NCBI’s 25th anniversary, United States Senator Ben Cardin read a statement into the Congressional Record recognizing years of service in providing access to biomedical and genomic information to enhance the world’s science and health.

On November 1st an awards and recognition program was held on the NIH Campus in Bethesda, Maryland to commemorate this occasion.

Presentation of the Jim Gray eScience Award

Tony Hey, Ph.D., Vice President of Microsoft Research, presenting the Jim Gray eScience award to David Lipman, M.D., Director of the NCBI.

At this event, Tony Hey, PhD, Vice President of Microsoft Research, presented NCBI Director David Lipman, MD, with the Jim Gray eScience Award which recognizes researchers who have made outstanding contributions to the field of data-intensive computing in the pursuit of open, supportive, and collaborative research models. Continue reading

PubMed Commons: A New Forum for Scientific Discourse

NCBI has released a pilot version of a new service in PubMed that allows researchers to post comments on individual PubMed abstracts. Called PubMed Commons, this service is an initiative of the NIH leadership in response to repeated requests by the scientific community for such a forum to be part of PubMed. We hope that PubMed Commons will leverage the social power of the internet to encourage constructive criticism and high quality discussions of scientific issues that will both enhance understanding and provide new avenues of collaboration within the community.

Continue reading

New Pandoravirus Sequences are Accessible in GenBank

In the July 19, 2013 issue of the journal Science, an interesting article describes the discovery and characterization of two “giant” viruses that are proposed to comprise the first members of the “Pandoravirus” genus.

Nadege Philippe and co-workers obtained the viruses from sediment samples in Chile and Australia and found that they have no morphological resemblance to any previously defined virus families. The investigators isolated the genomes of these viruses and sequenced them using a variety of NextGen methodologies. They then assembled the reads into contigs and characterized them using various sequence similarity algorithms (including NCBI’s BLAST and CD-Search). Interestingly, while related to each other, the genomes were not similar to those of any other organism or virus. Additionally, 93% of protein-coding sequences had no recognizable homologs.

Continue reading

A Librarian’s Guide to NCBI: Course Follow-up

NCBI, in collaboration with NLM and the National Network of Libraries of Medicine NLM Training Center (NTC) at the University of Utah, recently presented A Librarian’s Guide to NCBI. Thisnew course was designed to prepare health science librarians for supporting and training patrons about NCBI molecular databases and tools at their own institutions.

Participants, instructors, and organizers in the first offering of “A Librarian’s Guide to NCBI” outside the National Library of Medicine.

Participants, instructors, and organizers in the first offering of “A Librarian’s Guide to NCBI” outside the National Library of Medicine.

We have made all of the course materials available. Feel free to learn from these, adapt them for your own teaching, or share them with others. You can use the links below access the course materials, which include the slide sets with quizzes, demonstrations and practice problems, or visit the FTP site to get all the materials.

Continue reading

A Librarian’s Guide to NCBI – A New Education Initiative

Next week NCBI will premiere A Librarian’s Guide to NCBIa new course aimed at teaching health science librarians about NCBI resources. The course is sponsored by the NCBI, the National Library of Medicine (NLM), and the National Network of Libraries of Medicine’s NLM Training Center (NNLM/NTC) at the University of Utah. The initial offering of this course will be held from April 15-19, 2013.

Continue reading

New PubReader View For Full-Text Articles

NCBI’s new PubReader display format in PubMed Central (PMC) makes full-text research papers not only more readable but also more portable.

Whether you’re using a desktop, laptop, tablet or smart phone, PubReader adapts to your device, displaying full-text articles in a user-friendly format that minimizes scrolling and maximizes intuitive navigation and portability (see Figure 1).

NCBI’s new PubReader display format in PubMed Central (PMC) makes full-text research papers not only more readable but also more portable.  Whether you’re using a desktop, laptop, tablet or smart phone, PubReader adapts to your device, displaying full-text articles in a user-friendly format that minimizes scrolling and maximizes intuitive navigation and portability (see Figure 1).

Figure 1. The PubReader format as seen in three common displays (widescreen desktop, smart phone and tablet).

Continue reading