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NCBI News, July 2015

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New NCBI Insights blog post: Introducing PubMed Labs, an NCBI initiative to include user community in product development from beginning

Wednesday, July 29, 2015

Today on NCBI Insights, we announced PubMed Labs, an initiative for creating innovative and relevant products by involving you, our user community, from the start.

PubMed Labs is centered upon our user community, experimentation, learning and conversation. In "Introducing PubMed Labs", we describe what you can expect from PubMed Labs, how to find our first new experimental features, SmartBLAST and PubMed also-viewed, and how you can provide us with feedback, which we'll use to improve our services for our users.

To read about SmartBLAST and PubMed also-viewed and try them out, visit NCBI Insights. We look forward to hearing your thoughts on PubMed Labs.

August 12th NCBI Minute: Using Variation Reporter to Map and Annotate Your Own Variant Calls

Tuesday, July 28, 2015

In two weeks, NCBI staff will show you how to use Variation Reporter to submit your own variant calls for analysis and quickly view and interpret mapping results. Variation Reporter is an interface to NCBI's variation resources that quickly provides genomic context, phenotypic assertions and allele frequency for known variants in your data. It also maps and predicts consequences for genes and gene products for variants not in the NCBI databases.

Date and Time: August 12, 2015 12 PM EDT

Registration URL: https://attendee.gotowebinar.com/register/6563285440761995778

After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. The webinar and any materials will also be archived on the Webinars and Courses page, where you can also find information about future webinars.

Sequence Viewer 3.9 adds data upload options to API, improved response time and more

Tuesday, July 28, 2015

Recent updates to Sequence Viewer bring the following features and improvements to version 3.9:

  • Data upload option added to track and data upload API
  • Improved response time
  • Improved HTTPS compliance

A full list of features, improvements and bug fixes is available in the release notes.

Sequence Viewer is a graphical view of sequences and color-coded annotations on regions of sequences stored in the Nucleotide and Protein databases.

August 5th NCBI Minute: "Using EDirect's Xtract Utility to Parse NCBI BLAST XML Output"

Wednesday, July 22, 2015

The next NCBI Minute will introduce the EDirect Xtract XML parser, a useful tool for processing NCBI BLAST XML output. Future NCBI Minute webinars will show additional ways to use the EDirect suite to enhance and customize standalone BLAST.

Date: Wednesday, August 5, 2015

Time: 12:00PM EDT

Registration

After the live presentation, this webinar will be uploaded to the NCBI YouTube channel. The webinar and any relevant materials will also be archived on the Webinars and Courses page, where you can also find information about upcoming webinars. For an introduction to EDirect, you can watch our webinar from June 15th on YouTube.

July 30th webinar: "Using SciENcv to Create Your NIH Biosketch"

Wednesday, July 15, 2015

In two weeks, NCBI staff will present a webinar on SciENcv, our platform for maintaining your record of research accomplishment in the form of a CV. In this webinar, we'll show you how to use SciENcv to maintain your scientific record and generate the new BioSketch. Register here: https://bit.ly/1f7wWC8.

A recording will be posted on the NCBI YouTube account after the live presentation; subscribe to our YouTube channel to be notified. To see upcoming webinars and materials from past presentations, visit the Webinars and Courses page.

July 22nd NCBI Minute webinar: Find disease-related variants in ClinVar

Wednesday, July 15, 2015

Next Wednesday, July 22, NCBI staff will show you how to quickly find variants related to human disease in the NCBI ClinVar resource, as well as how to download batches of variants and related information in .xml and .vcf formats. To sign up, go here: https://bit.ly/1gxkBYY

ClinVar is NCBI's repository for human variation and its relationship to health and disease. ClinVar is an essential resource for basic researchers, clinicians and genetic counselors.

To see upcoming webinars and materials from past presentations, visit the Webinars and Courses page.

RefSeq Release 71 is now available!

Monday, July 13, 2015

RefSeq Release 71 is now available online, on the FTP site, and through NCBI's programming utilities, with 77,730,891 records describing 52,494,032 proteins, 11,803,354 RNAs, and sequences from 55,267 organisms. More information can be found in the Release Notes.

Please note that we plan to comprehensively re-annotate bacterial and archaeal genomes for RefSeq Release 72 (September 2015). This re-annotation is being carried out to reflect improvements in a) management of partial, very short, and fragmented genes and proteins and b) protein name management. It will also result in increased consistency of some textual information applied to RefSeq records. To learn more about the re-annotation project and what NCBI is doing to help users in transitioning to using this new data, please see the RefSeq Re-annotation Project page.

More information about the RefSeq project, pipelines and data, please take a look at the RefSeq homepage.

July 15th webinar: "EDirect: Bringing the E-Utilities to the UNIX Command Line"

Wednesday, July 01, 2015

In two weeks, NCBI staff will introduce EDirect, a simple, easy-to-use command-line interface for E-Utilities, the NCBI Entrez API. In this webinar, you will learn how to use EDirect to search, retrieve and process literature and molecular data from NCBI. You will also learn how to set up pipelines for common tasks.

To sign up for this webinar, go here: https://attendee.gotowebinar.com/register/6848186495038667265. Like all of our webinars, this presentation will be posted on the NCBI YouTube account after the live presentation; subscribe to our YouTube channel to be notified of all of our new videos.

To see upcoming webinars, as well as related materials and recordings from past webinars, visit the NCBI Webinars page.