Tag: ElasticBLAST

Try out Datasets and ElasticBLAST at the BOSC 2022 CoFest!

Try out Datasets and ElasticBLAST at the BOSC 2022 CoFest!

Join NLM’s NCBI at the virtual CollaborationFest on July 15 from 08:00 – 11:00 CDT and 12:00 – 16:00 CDT following the BOSC 2022 conference. Get an in-depth orientation and opportunity to test the capabilities of Datasets and ElasticBLAST.

What is Datasets?

Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download gene, transcript, protein and genome sequences, annotation and metadata. We invite you to try the Datasets command line tool in your bioinformatic workflows! Continue reading “Try out Datasets and ElasticBLAST at the BOSC 2022 CoFest!”

Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022

Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022

Come visit NCBI at the Bioinformatics Open Science Conference (BOSC), part of the Intelligent Systems for Molecular Biology Conference (ISMB), July 13-16, taking place both in person in Madison, Wisconsin and virtually! We’ll be presenting talks and posters on the latest updates to the NCBI Datasets, BLAST, and Protein resources. You can also join us at the Birds of a Feather (BoF) discussion and the BOSC CollaborationFest (CoFest) to explore these resources and discuss workflows with NCBI staff. Continue reading “Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022”

Introducing ElasticBLAST – BLAST® is now easier, bigger, and faster on the Cloud!

Introducing ElasticBLAST – BLAST® is now easier, bigger, and faster on the Cloud!

ElasticBLAST is a new tool that helps you run BLAST searches on the cloud. ElasticBLAST is perfect for you if you have thousands to millions of queries to our Basic Local Alignment Search Tool (BLAST ®), or if you want to use cloud infrastructure for your searches. ElasticBLAST can handle large searches that are not appropriate for NCBI web BLAST, and it runs them more quickly than stand-alone BLAST+.

ElasticBLAST works on two of the current NIH Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) partners- Amazon Web Services (AWS) and Google Cloud Platform (GCP).  ElasticBLAST works by distributing your searches across multiple cloud instances to process them in tandem. The ability to scale resources in this way allows you to process large numbers of queries in a shorter time than you could with BLAST+. ElasticBLAST can handle millions of queries, and it also supports most BLAST+ options and programs.

Making it easier to run BLAST on the cloud

ElasticBLAST reduces the barrier to using the cloud by creating and managing cloud resources for you. It manages the software and database installation, handles partitioning of the BLAST workload among the various instances and deallocates cloud resources when the searches are done. For example, ElasticBLAST will select the best cloud instance type for your search based on the database metadata that provides database size and memory needs (Figure 1). You can also manually select the instance type if you prefer.

Fig. 1: JSON metadata for the 16S_ribosomal_RNA database. The “bytes-to-cache” information helps ElasticBLAST pick out an instance with the appropriate capacity.

Selecting Databases

ElasticBLAST can access the 28 NCBI databases available on AWS and GCP. These are the same databases that are also available from the NCBI FTP site. For instance, databases available on the two cloud providers include the RefSeq Eukaryotic Representative Genomes database, 16S database based on Targeted Loci, and Human and mouse genomes databases.

You can also provide your own databases, and you can produce the metadata needed to select an instance through a Python script that comes with ElasticBLAST.

Example Runs

ElasticBLAST can perform a variety of searches with query sets that range from hundreds to millions of sequences and BLAST databases of all sizes.  Table 1 shows ElasticBLAST searches with query sets that range up to billions of letters using a variety of BLAST databases.

Table 1: Sample ElasticBLAST searches.  This table demonstrates the breadth of searches supported by ElasticBLAST.  Additionally, the first row demonstrates the ability of ElasticBLAST to use many CPUs (3200) on a cloud provider at once to complete a task in hours that would have taken days on a single machine.

Costs

Because ElasticBLAST runs on cloud providers, using it will incur some cost. Based on current cost structures on AWS and GCP, in most cases these costs are quite small. For example, a protein search with a query of about 20 million residues against a database of about 20 billion residues can cost less than $5. Even a larger search with a query of 3-4 billion DNA bases can cost only around $50. Both cloud services include the option to bid on instances for less than full price, which can result in significant savings. ElasticBLAST can be configured to request such instances. Your costs will obviously vary based on many factors, and we encourage you to explore these options with the individual cloud providers. Also, both AWS and GCP offer a free tier or time-limited trial of their cloud services, and you can find information about using ElasticBLAST with the free tiers here.

Welcome to ElasticBLAST!

Go ahead and run your first ElasticBLAST search! We are sure you’ll love how ElasticBLAST accelerates your research.

Your feedback is crucial to the development and support of ElasticBLAST. If you have any questions or suggestions, please reach out to us at blast-help@ncbi.nlm.nih.gov. We’d love to hear from you.

ElasticBLAST is a cloud-native package developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) with support from the NIH Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative.

Feb 16 Webinar: accelerating your alignments in the Cloud with ElasticBLAST

Feb 16 Webinar: accelerating your alignments in the Cloud with ElasticBLAST

Join us on February 16, 2022 at 12 PM US eastern time to learn about ElasticBLAST, a new tool that runs your BLAST searches on cloud hardware, using the standard BLAST command-line package. You will hear about the benefits of ElasticBLAST, which include speed and ease of use. You will also see some practical applications of this tool and how you can try it out yourself.

    • Date: Wed, February 16, 2022
    • Time: 12:00 PM – 12:45 PM EDT
    • Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI webinars playlist on the NLM YouTube channel. You can learn about future webinars on the Outreach Events page.

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!”