Tag: Conferences

NCBI events at the Bioinformatics Open Science Conference 2021 (BOSC 2021)

NCBI events at the Bioinformatics Open Science Conference 2021 (BOSC 2021)

Come visit us virtually to learn about new NCBI data access, tools and best practices at the Bioinformatics Open Science Conference  part of the ISMB/ECCB online conference from July 29 – 30, 2021. We will be presenting virtual posters on NCBI resources, offering a Birds of a Feather discussion, and participating in the BOSC  (CoFest) following the conference where you can take part in a hands-on evaluation of ElasticBLAST.

NCBI Posters, July 29, 2021, 11:20 – 12:20 PM EDT

All posters will be presented on Thursday afternoon. You can see complete abstracts on the ISMB/ECCB BOSC schedule.

Nuala O’Leary will talk about NCBI Datasets, a new resource for fast, easy access to NCBI sequence data.  You will learn about the new interface and new tools to access reference genomes, genes, and orthologs using web-based and programmatic tools.

Adelaide Rhodes will present Open access NCBI cloud resources to accelerate scientific insights where you can learn about recent developments in transferring > 20 petabytes of NCBI Sequence Read Archive (SRA) data to the cloud.

Deacon Sweeney will describe the web RAPT service for assembling and annotating bacterial genomes at the click of a button in RAPT, The Read assembly and Annotation Pipeline Tool: building a prokaryotic genome annotation package for users of all backgrounds.

Roberto Vera Alvarez will talk about best practices for using cloud tools for transcriptomics in his poster Transcriptome annotation in the cloud: complexity, best practices, and cost.

Greg Boratyn will discuss improvements to the BLAST-based short read aligner, Magic-Blast, in Recent improvements in Magic-BLAST 1.6.

Visit Christiam Camacho’s poster ElasticBLAST: Using the power of the cloud to speed up science to get an introduction to  ElasticBLAST, a Kubernetes-based approach for high throughput BLAST tasks. Join us following the conference in the CoFest to try out ElasticBLAST yourself and provide input. See the section on the CoFest below and our companion post.

Birds of a Feather, July 29, 2021, 11:20 – 12:20 PM EDT

We will host a Birds of Feather public feedback session on Thursday, where you can provide feedback and participate in discussions on all aspects of NCBI’s new data access options: NCBI Datasets, SRA, BLAST, and the Genome Data Viewer (GDV) — our genome browser for sequence visualization. We welcome your input!  Come and see us!

CollaborationFest (CoFest), July 31 – August 1, 2021

The ElasticBlast team will attend the BOSC CoFest following the conference. Sign up to participate on July 31 and August 1 to get an in-depth orientation and opportunity to test the capabilities of ElasticBlast on the Amazon Web Services (AWS) cloud. You do not have to register for the conference to attend the CoFest. See our post on the CoFest for more information.

 

Try out ElasticBLAST at the BOSC2021 CoFest!

Try out ElasticBLAST at the BOSC2021 CoFest!

Join the BLAST team at the virtual CollaborationFest (July 31 -August 1, 2021) after the BOSC 2021 conference to help test and improve ElasticBLAST, a new cloud-based tool designed to speed up high throughput BLAST searches. We would love to have your help with real world testing of our alpha release of ElasticBLAST with you own workflows and data. You may sign up for the CoFest even if you aren’t registered for BOSC 2021.

Here are suggestions for how you can participate. See the FAQs below for additional information.

  1. Try it out and let us know how well it works. You can be blunt.
  2. Help us improve the documentation.
  3. Write a script to make ElasticBLAST part of your workflow.
  4. Try to process ElasticBLAST results with cloud-native tools. Here is an example.
  5. Bring your own high throughput BLAST search problem to use with ElasticBLAST!  Please discuss it with us first to make sure you don’t blow our budget and get the ElasticBLAST team in trouble!

Continue reading “Try out ElasticBLAST at the BOSC2021 CoFest!”

NCBI to present on SRA and cloud computing at the 2021 Galaxy Community Conference

NCBI to present on SRA and cloud computing at the 2021 Galaxy Community Conference

 

We’re bringing exciting developments to our user community at the 2021 Galaxy Community Conference (GCC 2021), which is virtual this year!

Dr. Jon Trow, SRA Subject Matter Expert
Dr. Adelaide Rhodes, Cloud Subject Matter Expert

 

 

 

 

 

 

 

 

 

 

We start with hosting NCBI’s first ever GCC training week tutorial co-written by Jon Trow, Ph.D. – Sequence Read Archive (SRA): Subject Matter Expert and Adelaide Rhodes, Ph.D. – Cloud: Subject Matter Expert. This tutorial will become a permanent addition to the Galaxy Training Network. The tutorial, “SRA Aligned Read Format (SARF) to Speed Up SARS-CoV-2 Data Analysis”, has detailed instructions and a video demonstration on how to search SRA metadata for SARFs and download them into Galaxy workflows. We will be available via Slack during Office Hours for live virtual interactions.

Continue reading “NCBI to present on SRA and cloud computing at the 2021 Galaxy Community Conference”

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021

NCBI staff will be presenting virtual posters at the Cold Spring Harbor Laboratory  Biology of Genomes Meeting, May 11 -14, 2021. The posters will cover the following topics: 1) a cloud-ready suite of tools (PGAP, RAPT , and SKESA) for assembling and annotating prokaryotic genomes,  2) Datasets — a new set of services for downloading genome assemblies and annotations, and 3) updates on NCBI RefSeq eukaryotic genome annotation, and the Genome Data Viewer (GDV). Read more below for the full abstracts.

The virtual poster gallery opens Tuesday, May 11 at 9:00 a.m. with dedicated time for poster viewing and discussion at 1:00 to 2:00 p.m. through Slack each day. The poster gallery will be open for entire the conference and remain available for six weeks afterwards.  Continue reading “NCBI at CSHL Biology of Genomes, May 11 – 14, 2021”

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.

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

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

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.

NCBI at the ACMG meeting in Seattle  next week (April 2-6, 2019)

NCBI at the ACMG meeting in Seattle next week (April 2-6, 2019)

In about a week, NCBI staff will join GeneReviews® on their home turf, Seattle, at the Annual Clinical Genetics Meeting hosted by the American College of Medical Genetics and Genomics (ACMG). While there we will have an exhibit booth (#531) where you can meet our staff, get answers to your questions, and pick-up informative handouts on our various resources for clinical practice.

Also, be sure to visit our two posters on Friday, April 5 from 10:30 AM to 12 PM.

Continue reading “NCBI at the ACMG meeting in Seattle next week (April 2-6, 2019)”

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.)

Continue reading “Join NCBI at PAG in San Diego, January 12–16, 2019”

Matched Annotation by NCBI and EMBL-EBI (MANE): a new joint venture to define a set of representative transcripts for human protein-coding genes

The RefSeq project at the NCBI and the Ensembl/GENCODE project at EMBL-EBI have provided independent high-quality human reference gene datasets to biologists since the sequencing of the human genome.

Now we’re joining together on an exciting new project we’re calling Matched Annotation from the NCBI and EMBL-EBI or MANE, to provide a matched set of well-supported transcripts for human protein-coding genes and define one representative transcript for each gene. Both RefSeq and Ensembl will continue to provide a rich set of alternate transcripts per gene.

Continue reading “Matched Annotation by NCBI and EMBL-EBI (MANE): a new joint venture to define a set of representative transcripts for human protein-coding genes”