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elastic-blast

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

https://github.com/ncbi/elastic-blast

Science Score: 75.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: pubmed.ncbi, ncbi.nlm.nih.gov
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization ncbi has institutional domain (www.ncbi.nlm.nih.gov)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.6%) to scientific vocabulary

Keywords

bioinformatics blast ncbi
Last synced: 6 months ago · JSON representation ·

Repository

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

Basic Info
Statistics
  • Stars: 61
  • Watchers: 15
  • Forks: 18
  • Open Issues: 3
  • Releases: 24
Topics
bioinformatics blast ncbi
Created almost 5 years ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

ElasticBLAST

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PyPI version

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective.

ElasticBLAST is ideal for users who have a large number (thousands or more) of queries to BLAST or who prefer to use cloud infrastructure for their searches. It can run BLAST searches that cannot be done on NCBI WebBLAST and runs them more quickly than stand-alone BLAST+.

ElasticBLAST speeds up your work by distributing your BLAST+ searches across multiple cloud instances. The ability to scale resources in this way allows larger numbers of queries to be searched in a shorter time than you could with BLAST+ on a single host.

The National Center for Biotechnology Information (NCBI), part of the National Library of Medicine at the NIH, developed and maintains ElasticBLAST.

The NCBI is making the source code for ElasticBLAST available on GitHub as an Open Distribution to allow the user community to easily obtain and examine that code. GitHub also provides a means for users to report issues and suggest modifications through pull requests.

The NCBI will use internal source code control as the repository of record and push regular releases of the ElasticBLAST source code to GitHub. The BLAST developers will work to ensure that ElasticBLAST continues to function in changing environments and, when possible, integrate user feedback into ElasticBLAST. Owing to resource constraints, they cannot absolutely commit to act on all issue reports, except critical security vulnerabilities.

End-user documentation

Please visit https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/

How to get ElasticBLAST

There are several ways to obtain ElasticBLAST, please select the one that is most suitable to you:

Publication:

Camacho C, Boratyn GM, Joukov V, Vera Alvarez R, Madden TL. ElasticBLAST: accelerating sequence search via cloud computing. BMC Bioinformatics. 2023 Mar 26;24(1):117. doi: 10.1186/s12859-023-05245-9. PMID: 36967390; PMCID: PMC10040096.

Developer information

How to build ElasticBLAST

make elastic-blast

Requirements for building ElasticBLAST

In addition to the requirements listed in the documentation, the AWS Command Line Interface is required.

Owner

  • Name: NCBI - National Center for Biotechnology Information/NLM/NIH
  • Login: ncbi
  • Kind: organization
  • Email: github-tools@ncbi.nlm.nih.gov

Citation (CITATION.cff) 

cff-version: "1.2.0"
message: "If you use this software, please cite it using these metadata."
title: ElasticBLAST
version: "1.4.0"
date-released: 2025-03-17
license: "NCBI Public Domain"
repository-code: "https://github.com/ncbi/elastic-blast/"
url: "https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/"
authors: 
- family-names: Camacho
  given-names: Christiam E.
  orcid: https://orcid.org/0000-0002-6709-8298
- family-names: Boratyn
  given-names: Greg
- family-names: Joukov
  given-names: Victor
  orcid: https://orcid.org/0000-0003-2962-8902
- family-names: Merezhuk
  given-names: Yuri
- family-names: Madden
  given-names: Thomas
  orcid: https://orcid.org/0000-0003-1641-7321
preferred-citation:
  type: article
  authors:
  - family-names: Camacho
    given-names: Christiam
    orcid: https://orcid.org/0000-0002-6709-8298
  - family-names: Boratyn
    given-names: Grzegorz M
  - family-names: Joukov
    given-names: Victor
    orcid: https://orcid.org/0000-0003-2962-8902
  - family-names: Vera Alvarez
    given-names: Roberto
  - family-names: Madden
    given-names: Thomas L
    orcid: https://orcid.org/0000-0003-1641-7321
  doi: 10.1186/s12859-023-05245-9
  journal: BMC Bioinformatics
  month: 3
  start: 117
  title: "ElasticBLAST: accelerating sequence search via cloud computing"
  issue: 1
  volume: 24
  year: 2023

GitHub Events

Total
  • Create event: 4
  • Release event: 1
  • Issues event: 4
  • Watch event: 11
  • Delete event: 4
  • Issue comment event: 11
  • Push event: 4
  • Pull request review event: 3
  • Pull request event: 6
  • Fork event: 4
Last Year
  • Create event: 4
  • Release event: 1
  • Issues event: 4
  • Watch event: 11
  • Delete event: 4
  • Issue comment event: 11
  • Push event: 4
  • Pull request review event: 3
  • Pull request event: 6
  • Fork event: 4

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 16
  • Total pull requests: 14
  • Average time to close issues: 3 months
  • Average time to close pull requests: 11 days
  • Total issue authors: 14
  • Total pull request authors: 5
  • Average comments per issue: 4.0
  • Average comments per pull request: 0.07
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 8
Past Year
  • Issues: 1
  • Pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 18 days
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 7.0
  • Average comments per pull request: 0.11
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 6
View more stats
Top Authors
Issue Authors
  • christiam (3)
  • merezhuk (1)
  • phlatphish (1)
  • shreyas-a-s (1)
  • dikiprawisuda (1)
  • arminmm91 (1)
  • nikkiing (1)
  • alexsanyum (1)
  • sean-bam (1)
  • snamburi3 (1)
  • mayla-abrahim (1)
  • elasekness (1)
  • pipaber (1)
  • NickShanyt (1)
  • Soph36 (1)
Pull Request Authors
  • dependabot[bot] (9)
  • boratyng (3)
  • christiam (3)
  • dotnetpower (1)
  • tom6931 (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (9) python (4)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 178 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 23
  • Total maintainers: 1
pypi.org: elastic-blast

ElasticBLAST runs BLAST searches faster by distributing its work to multiple cloud instances. This allows larger numbers of queries to be searched in less time compared to BLAST+ on a single host. Use of the cloud facilitates collaboration, sharing of results, datasets and pipelines on a common platform. The National Center for Biotechnology Information ([NCBI](https://www.ncbi.nlm.nih.gov)), part of the National Library of Medicine at the NIH, developed and maintains ElasticBLAST.

  • Versions: 23
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 178 Last month
Rankings
Dependent repos count: 9.0%
Dependent packages count: 10.1%
Stargazers count: 10.8%
Forks count: 10.9%
Average: 11.1%
Downloads: 14.8%
Maintainers (1)
ncbi
Last synced: 6 months ago

Dependencies

setup.py pypi
docker-blast/requirements.txt pypi
  • awscli *
  • boto3 *
  • ec2_metadata ==2.4.0
  • filelock *
  • requests ==2.25.1
docker-demo/requirements.txt pypi
  • awscli *
  • elastic-blast *
docker-janitor/requirements.txt pypi
  • elastic-blast *
docker-job-submit/requirements.txt pypi
  • elastic-blast *
docker-qs/requirements.txt pypi
  • awscli *
  • elastic-blast *
lambda-janitor/requirements-for-testing.txt pypi
  • elastic-blast ==0.0.80 test
lambda-janitor/requirements.txt pypi
  • elastic-blast *
requirements/base.txt pypi
  • awslimitchecker ==12.0.0
  • boto3 ==1.24.49
  • botocore ==1.27.49
  • dataclasses-json ==0.5.7
  • importlib-metadata ==4.12.0
  • importlib-resources ==5.9.0
  • pex ==2.1.103
  • setuptools ==56.0.0
  • tenacity ==8.0.1
  • types-pkg-resources ==0.1.3
  • wheel ==0.37.0
requirements/test.txt pypi
  • cfn-lint ==0.61.4 test
  • docker ==5.0.3 test
  • moto ==3.1.17 test
  • mypy ==0.971 test
  • pylint ==2.7.4 test
  • pytest ==7.1.2 test
  • pytest-cov ==3.0.0 test
  • pytest-mock ==3.8.2 test
  • teamcity-messages ==1.31 test
  • tox ==3.25.1 test
  • yamllint ==1.27.1 test
.github/workflows/build-multi-pex.yml actions
  • actions/checkout v2 composite
  • actions/download-artifact v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v2 composite
docker-blast/Dockerfile docker
  • google/cloud-sdk slim build
  • ncbi/blast latest build
docker-demo/Dockerfile docker
  • google/cloud-sdk slim build
docker-qs/Dockerfile docker
  • google/cloud-sdk alpine build