Second Round of HTTPS Tests

Posted on September 21, 2016 by NCBI Staff

NCBI has scheduled the next round of HTTPS tests, following up from the initial tests performed on September 15.

The schedule for these tests is as follows (all times are EDT):

Thursday, Sept 22
8:00 AM – 12:00 PM : redirect web pages from HTTP to HTTPS, same as the first test on Sept 15.
8:00 AM – 9:00 AM : redirect CGI’s and API calls to HTTPS where possible, reject where not possible

Monday, Sept 26
8:00 AM – 10:00 AM : redirect web pages from HTTP to HTTPS with HSTS activated using a 1-hour expiration
10:00 AM – 12:00 PM : redirect web pages from HTTP to HTTPS without HSTS

Tuesday, Sept 27
8:00 AM : Start continually redirecting web pages from HTTP to HTTPS

If you use NCBI APIs, please see https://go.usa.gov/xKf8H

For more detailed information about these tests, please see https://go.usa.gov/xKH6Y

Important considerations:

If you develop software that depends on NCBI APIs or toolkits (e.g. SRA or C++), please target the 8-9 AM window on Sept 22 for testing, as we expect any problems with HTTPS to result in failures of affected applications during this test.
Some browsers may cache the HTTPS pages viewed during the test periods, and so may continue to request pages over HTTPS once the tests are complete. If this causes problems, clearing the browser’s cache and cookies will restore access over HTTP.
We will be running additional tests on CGI applications once we analyze the results of the tests on September 22.

NCBI Begins HTTPS Tests

Posted on September 14, 2016 by NCBI Staff

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.

If you experience problems with any NCBI site or service during that hour, please see our Secure Website Tests plan for advice on how to proceed.

If you use software that accesses NCBI data, and you experience problems with that software, we recommend that you contact the software vendor, as they may need to update their products to work over HTTPS.

If you use proxies to access NCBI (for example, EZProxy) and you experience problems during this period, we also recommend that you contact the proxy service to ensure that your service is ready for HTTPS.

If you develop software that accesses NCBI services or that depends on NCBI APIs (such as the E-utilities) or toolkits (such as the SRA or C++ toolkits), these tests are a great opportunity for you to see how your software will function over HTTPS.

If you have other questions or concerns, please contact us at info@ncbi.nlm.nih.gov.

The Future of Existing GI Numbers at NCBI

Posted on September 12, 2016 by NCBI Staff

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:

GIs will no longer appear on flat file or FASTA data displays after September 2016. The GIs will still exist, but they won’t be visible.
More and more new sequence records will not be assigned a GI. This means that over time, you will be missing more and more new sequences if you only use GIs.

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

Posted on September 7, 2016 by NCBI Staff

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!)

Get started now:

Visit the PubMed Journals home page to see a list of popular journals
Click a journal title to browse the most recent content and news feed
Click the “Follow” button to add to your personal journal list

To follow a journal, you’ll need to be logged in to your NCBI account. If you’re not already logged in to NCBI, you can try out our completely revamped login experience. The new NCBI login, like the old, works with any existing NCBI account or your eRA Commons, NIH, or federated university account.

PubMed Journals is an experiment of PubMed Labs, NCBI’s product incubator for delivering new features and capabilities to NCBI end users.

Have feedback for us? Please use the comments box below to ask questions, provide suggestions, or to provide any other feedback about the Journal Browser, the new login, or PubMed Labs.

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

Posted on July 15, 2016 by NCBI Staff

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:

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

Continue reading →

Fast Sequence Inspection with ORFfinder + SmartBLAST

Posted on May 16, 2016 by NCBI Staff

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.

Continue reading →

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

Posted on March 3, 2016 by NCBI Staff

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/.

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

Posted on February 17, 2016 by NCBI Staff

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!

Figure 1. The My NCBI login page.

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!

Continue reading →

Researchers identify potential alternative to CRISPR-Cas genome editing tools

Posted on January 29, 2016 by NCBI Staff

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.”

Continue reading →

The NCBI Minute: quick introductions to NCBI resources

Posted on December 17, 2015 by NCBI Staff

For over two years, NCBI has presented webinars on a wide range of topics to a growing audience. More recently, we began offering shorter webinars in a series called The NCBI Minute.

These presentations introduce a new NCBI tool or resource or provide quick tips for using a popular resource in 5-10 minutes.

screenshot of popular NCBI Minute presentations on YouTube

Figure 1. Examples of popular NCBI Minute presentations; SmartBLAST Introduction presented September 2 (YouTube), and Connecting with PubMed Commons presented May 2 (YouTube).

Each NCBI Minute is recorded and posted on our YouTube channel in the NCBI Minute playlist. Two of our most popular NCBI Minute presentations (Figure 1) are the introduction to the new SmartBLAST service, first described on NCBI Insights in July, and Connecting with PubMed Commons, our public commenting service for PubMed articles described in several NCBI Insights posts.

Missed a presentation? No problem!

If you missed any of The NCBI Minute, there are two ways you can catch up: