NCBI’s Bryant and Bolton receive 2016 Herman Skolnik Award for PubChem database


On August 23, Drs. Stephen Bryant and Evan Bolton received the American Chemical Society (ACS) 2016 Herman Skolnik Award for their work in developing, maintaining, and expanding the National Center for Biotechnology Information’s PubChem database of chemical substances and their biological activities. The award was presented at the ACS 252nd National Meeting & Exposition in Philadelphia.

Figure 1. Drs. Bryant and Bolton receive the American Chemical Society 2016 Herman Skolnik Award.

Figure 1. Drs. Bryant and Bolton receive the American Chemical Society 2016 Herman Skolnik Award.

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NCBI Begins HTTPS Tests


You may have heard that NCBI, along with the rest of the Federal Government, is switching to HTTPS-only access. To help prepare for this, NCBI is beginning a series of tests. During these tests, all traffic to NCBI will be redirected from HTTP to HTTPS to simulate our system’s behavior once the HTTPS transition is complete.

The first test will be Thursday, September 15, from 8:00-9:00 AM EDT.

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The Future of Existing GI Numbers at NCBI


NCBI has announced that we will be changing the way we handle GI numbers for sequence records in September 2016. (Read more, in case you missed it).

In this post, we’ll address a key question:

What is the future of existing GI numbers?

The short answer is that nothing is happening to these GI numbers.

If a nucleotide or protein record already has a GI, it will continue to have that GI indefinitely. You will also be able to retrieve such a record using its GI either on the NCBI web site or using the E-utilities.

Moreover, GIs will remain part of the XML and ASN.1 formats of sequence records.

If not GIs, then what?

Accession.version identifiers. All sequence records, both new and old, will have a unique accession.version identifier.

Existing records will keep the accessions they already have; new sequences will only receive an accession.version identifier.

So what’s all the fuss about?

Two things:

Stay tuned for additional posts about this topic, and please contact us if you have questions.

Find, Browse and Follow Biomedical Literature with PubMed Journals


Following the latest biomedical literature can be a challenge, but NCBI’s new PubMed Journals will help you keep up-to-date.

PubMed Journals lets you:

  • Easily find and follow journals of interest
  • Browse new articles in your favorite journals
  • Keep up-to-date with a Journal News Feed containing new arrivals, news links, trending articles, and important article updates (retractions and more!)

The PubMed Journals home page.

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NCBI is Phasing Out Sequence GIs – Here’s What You Need to Know


You may have heard that NCBI is changing the way we handle GI numbers for sequence records in September 2016. Well, you heard right! Here’s the announcement, in case you missed it.

There are a number of issues raised by these changes, but we’re going to answer two questions in this post:

  1. What pieces of your code will break in September?
  2. Are GI numbers gone for good?

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Fast Sequence Inspection with ORFfinder + SmartBLAST


intro pic

This blog post is intended for all BLAST users.

ORFfinder is a graphical analysis tool for finding open reading frames (ORFs). We’ve been working on a few updates, and we’d like to find out what you think about them. Read on to find out what you can do with the new ORFfinder.

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Streptococcus pyogenes “A to Zs” Covered in New Book, Freely Available on NCBI Bookshelf


The University of Oklahoma Health Sciences Center has published an open-access book called “Streptococcus pyogenes: Basic Biology to Clinical Manifestations” that provides a comprehensive review of research on the bacteria. The university’s first online, open-access book, “Streptococcus pyogenes” is freely available on NCBI’s Bookshelf, at http://www.ncbi.nlm.nih.gov/books/NBK333424/.
S.pyogenes Book on the NCBI Bookshelf

Streptococcus pyogenes (Group A Streptococcus) is responsible for diseases such as scarlet fever, pharyngitis, impetigo, cellulitis, necrotizing fasciitis and toxic shock syndrome, as well as the sequelae of rheumatic fever and acute poststreptococcal glomerulonephritis. The book aims to provide an up-to-date and comprehensive review of research on Streptococcus pyogenes, including its basic biology, epidemiology, genetics and pathways that facilitate group A streptococcal infections. Continue reading

Professors:  NCBI can help you streamline your teaching and research efforts


Professors, you’re busy – really busy. You have to develop and teach your courses and laboratory sessions, coordinate your lab’s research efforts, write grants and publications, and stay current on everything related to your teaching and research topics.

NCBI has information that would help most of these efforts – but there are so many interesting records and so little time to organize them for efficient use. Sign up for a free NCBI Account and let us help you organize your important lists!

my ncbi login page

Figure 1. The My NCBI login page.

Sign up for an NCBI Account – or sign in to your account if you already have one – and:

  • Store and automate your searches;
  • Save and manage collections of important records for use in coursework, research projects and federal grants;
  • Create public lists for students in your courses and your own Faculty Profile;
  • And keep track of everything – right on your My NCBI dashboard.

Read on to find out how to do all of these things and more!

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Researchers identify potential alternative to CRISPR-Cas genome editing tools


An international team of CRISPR-Cas researchers has identified three new naturally-occurring systems that show potential for genome editing. The discovery and characterization of these systems is expected to further expand the genome editing toolbox, opening new avenues for biomedical research. The research, published October 22nd in the journal Molecular Cell, was supported in part by the National Institutes of Health.

“This work shows a path to discovery of novel CRISPR-Cas systems with diverse properties, which are demonstrated here in direct experiments,” said Eugene Koonin, Ph.D., senior investigator at the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), part of the NIH. “The most remarkable aspect of the story is how evolution has achieved a broad repertoire of biological activities, a feat we can take advantage of for new genome manipulation tools.”

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