NCBI staff to present 3 posters at Advances in Genome Biology and Technology (AGBT), February 2020

Next week, NCBI staff will attend AGBT in Marco Island, Florida. On Tuesday, February 25, 2020, three posters from NCBI staff will be on display from 4:40 p.m. – 6:10 p.m. during the Poster Session and Wine Reception in the Banyan and Calusa Ballroom Foyers, Levels 1 and 3. Read on to learn a little bit about what we’ll be presenting.

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NCBI on YouTube: Get the most out of NCBI resources with these videos

Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.

Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips

This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.

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Bulk track hub settings now in Genome Data Viewer

You now have access to bulk settings options for track hubs  in the Genome Data Viewer (GDV) and Sequence Viewer. These settings allow you to pick the default tracks that load into the viewer from your chosen track hub.  You can access the bulk options menu for by clicking on the collapsed menu  or “hamburger” icon (stack of horizontal bars) at the right end of the track grouping in the Configure Track Hubs dialog (Figure 1).Bulk_SettingsFigure 1. The Configure Track Hubs dialog in GDV. You can activate the bulk settings menu for a connected track hub by clicking on hamburger icon at the right of the track grouping.  Clicking Select Default tracks checks on all of the tracks in that grouping, Smoothed PhyloCSF in this case.  Continue reading

Presentation on NCBI’s genome browser at Rocky Mountain Genomics Hackcon

On June 18, 2019, NCBI’s Sanjida Rangwala will demonstrate the rich data visualization capabilities of NCBI’s genome browser at a conference that is part of the Rocky Mountain Genomics Hackcon.  As mentioned in a previous post, NCBI staff will also participate in an NCBI-style Hackathon  as part of the larger event.  The genome browser presentation and demonstration will show you how to create visuals that provide insights and show connections among genes, transcripts, variation,  epigenomics and GWAS data from NCBI sources. You will also see  how you can upload your own data and embed NCBI viewers on your own pages.

Join NCBI at PAG in San Diego, January 12–16, 2019

Next week, NCBI staff will attend the Plant and Animal Genome (PAG) Conference. We have several activities planned, including 1 booth (#223), 4 workshops, 1 talk and 2 posters.

Read on to learn more about what you can look forward to if you’re attending PAG this year. (Note: The listed times are Pacific time.)

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See improvements in NCBI’s genome visualization and analysis tools at ASHG

GDV_homepage

In 2016, NCBI introduced the Genome Data Viewer (GDV). This past May, the GDV replaced the aging Map Viewer. Over the past year, NCBI has kept you updated about GDV through announcements, webinars, and blogs. Now you can gather information and get an overview of all the changes to GDV in person at ASHG!

Check out Poster 1670F “What’s new with NCBI tools for genome visualization and analysis.” on Friday, Oct. 19 from 3 PM to 4 PM
(Exhibit Hall, Ground Level)

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NCBI at ASHG 2018: Data and Clinical CoLabs introduce interactive graphical displays and medical genetics resources

As you know, NCBI will be attending American Society of Human Genetics (ASHG) 2018 in San Diego.

This year, we have two CoLabs – interactive sessions where you can learn about freely available NCBI tools and resources. Read on below for a description of each CoLab and join us at ASHG in two weeks!

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NCBI’s Genome Data Viewer now displays data from track hubs

The Genome Data Viewer’s (GDV) browser display now supports content provided in track hubs. This new GDV feature, summarized in this short video, extends the genome browser’s capability when it comes to viewing user-supplied data tracks alongside NCBI-provided tracks.  You now have multiple options to analyze your data that include uploading your data (file/URL), streaming individual files from a remote location and/or connecting to a track hub. In all instances, GDV recognizes a variety of popular file formats with support for additional file formats planned. In the display, you can now also easily distinguish user-supplied tracks by their green-tinted track labels. Continue reading

NCBI to retire Clone DB web interface

Starting in April 2019, the sequence content of Clone DB will be frozen, and its web interfaces will no longer be available. NCBI will continue to produce and make genomic clone placements available as annotations in NCBI’s Genome Data Viewer (GDV) using the sequence data currently in Clone DB. These placements and their corresponding underlying (now static) library and sequence data will also be accessible on the Clone DB FTP site.

The collection of Clone DB records for cell-based (integrated) gene targeting and gene trap libraries will also be retired in January. These data were provided to Clone DB by MGI.  Clone DB users should refer to MGI for their continuing research needs.

Please contact us with any comments, concerns, or if you need help with the use of Clone DB data.

Clone DB was originally implemented as the Clone Registry during the human and mouse genome projects. In subsequent years, it expanded to represent clone-associated data for a broad range of organisms. Clone DB has been a valuable resource connecting users with information and reagents for genomic and cell-based clones. However, with the advent of short read sequencing, fewer and fewer genomic clone end and insert sequences are submitted to NCBI every year, and the usage of and need for Clone DB has dropped significantly.