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From the GMR: NCBI Announcements

FYI: NCBI Upcoming events and honors
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BLAST in the Cloud webinar July 30th

In one week, NCBI will offer a webinar entitled "BLAST in the Cloud". This presentation will show you how to log on to AWS and deploy the NCBI-BLAST Amazon Machine Image (AMI) quickly. Prior knowledge of using web and standalone BLAST is required.

To register, please go to this link: https://attendee.gotowebinar.com/register/8126572163773355778.

* NCBI News: http://www.ncbi.nlm.nih.gov/news/07-01-2014-BLAST-in-cloud-July-webinar/

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NCBI webinar "Using the New NCBI Variation Viewer to Explore Human Genetic Variation" on August 13th

On August 13th, NCBI will host a webinar entitled "Using the New NCBI Variation Viewer to Explore Human Genetic Variation". This presentation will show you how to find human sequence variants by chromosome position, gene, disease names and database identifiers (RefSNP, Variant region IDs) using NCBI's new Variation Viewer.

You will learn how to browse the genome, navigate by gene or exon, filter results by one or more categories including allele frequencies from 1000 Genomes or GO-ESP, and link to related information in NCBI's molecular databases and medical genetic resources such as ClinVar, MedGen, and GTR. You will also be shown how to upload your own data to add to the display and download results.

Anyone who works with clinical or research variation data will find that the Variation Viewer provides a convenient and powerful way to access human variation data in a genomic context that is fully integrated with all other NCBI tools and databases.

To register, please go to this link https://attendee.gotowebinar.com/register/2762824590748330498.

Related Links:
• Variation Viewer: http://www.ncbi.nlm.nih.gov/variation/view
• 1000 Genomes: http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/
• GO-ESP: http://www.ncbi.nlm.nih.gov/bioproject/165957
• ClinVar: http://www.ncbi.nlm.nih.gov/clinvar/
• MedGen: http://www.ncbi.nlm.nih.gov/medgen/
• GTR: http://www.ncbi.nlm.nih.gov/gtr/?

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Announcing major revision of the NCBI genomes FTP site

Within the next two weeks, NCBI will make a major revision to the genomes FTP site. This redesign will expand available content and facilitate data access through an organized, predictable directory hierarchy. The updated site will also provide greater support for downloading assembled genome sequences and/or corresponding annotation data. To give those with automated tools time to update, we plan to maintain the older content and structure of the preexisting /genomes/ FTP site in parallel with the new structure for six months.

The new FTP site structure provides a single entry point to access content representing either GenBank or RefSeq data. Advantages of the updated genomes FTP site include the comprehensive provision of data through a single process flow that is reliant on content in NCBI's Assembly database (which excludes viruses at this time), integration of quality assurance regression tests, and provision of a consistent core set of files for all organisms and assemblies.

Stay tuned for more information about the changes to come and the official launch of the revamped genomes FTP site.

. Current Genomes FTP site: ftp://ftp.ncbi.nlm.nih.gov/genomes/
. GenBank: http://www.ncbi.nlm.nih.gov/genbank/
. RefSeq: http://www.ncbi.nlm.nih.gov/refseq/
. Assembly: http://www.ncbi.nlm.nih.gov/assembly/

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NCBI/CDC/FDA/USDA collaboration using whole genome sequencing (WGS) to improve food safety is honored with an HHSinnovates award

A collaborative project between NCBI and several other Federal and state partners to reduce the time and improve the accuracy of detecting foodborne pathogens by using whole genome sequencing (WGS) techniques received an HHSinnovates award on July 21.

The HHSinnovates program was initiated in 2010 to recognize new ideas and solutions developed by HHS employees and their collaborators. Six finalist teams were recognized at the awards ceremony. The WGS Food Safety Project, which also involved the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA), the U.S. Department of Agriculture (USDA), and state public health laboratories, was one of three projects to be honored as "Secretary's Picks" by HHS Secretary Sylvia Mathews Burwell.

Presenting the award, HHS Deputy Secretary Bill Corr said: "Together all these folks engaged in a demonstration project to showcase the benefits of using whole genome sequencing for food surveillance and detection purposes. They showed that whole genome sequencing can produce faster detection of foodborne pathogens than the traditional method, helping us stop an outbreak of disease in its tracks, and for that we deeply appreciate your work." The award went to the specific individuals leading the project in the various agencies; in the case of NCBI, Senior Scientist William Klimke, Ph.D., was honored for his work in heading NCBI's part of the project.

WGS provides greater specificity than other techniques, such as the commonly used pulsed-field gel electrophoresis (PFGE), in identifying the DNA fingerprint of bacteria. It also can more rapidly determine whether isolates are related to a foodborne disease outbreak.

The demonstration project involves real-time sequencing of Listeria monocytogenes isolates from human DNA as well as the food supply chain. In the project, the whole genomes of isolates are sequenced and the sequencing data are sent to NCBI, which performs assembly, annotation, and analysis and then sends results back to CDC, FDA, USDA, and the labs.

Collaborative projects using WGS for other pathogens related to food safety are also underway.

* HHSinnovates: http://www.hhs.gov/idealab/pathways/hhs-innovates/

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