Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses
- PMID: 28968637
- DOI: 10.1093/bioinformatics/btx554
Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses
Abstract
Summary: This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects.
Availability and implementation: Source code and instructions for local installation are available at https://github.com/DugongBioinformatics, under the MIT open source license.
Contact: Luiz.nunes@ufabc.edu.br.
© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
Similar articles
-
ORCA: a comprehensive bioinformatics container environment for education and research.Bioinformatics. 2019 Nov 1;35(21):4448-4450. doi: 10.1093/bioinformatics/btz278. Bioinformatics. 2019. PMID: 31004474 Free PMC article.
-
Bioportainer Workbench: a versatile and user-friendly system that integrates implementation, management, and use of bioinformatics resources in Docker environments.Gigascience. 2019 Apr 1;8(4):giz041. doi: 10.1093/gigascience/giz041. Gigascience. 2019. PMID: 31222200 Free PMC article.
-
AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.Bioinformatics. 2016 Aug 1;32(15):2396-8. doi: 10.1093/bioinformatics/btw120. Epub 2016 Mar 2. Bioinformatics. 2016. PMID: 27153722 Free PMC article.
-
A Bioinformatics Primer to Data Science, with Examples for Metabolomics.Methods Mol Biol. 2020;2104:245-263. doi: 10.1007/978-1-0716-0239-3_14. Methods Mol Biol. 2020. PMID: 31953822 Review.
-
Container-Based Clinical Solutions for Portable and Reproducible Image Analysis.J Digit Imaging. 2018 Jun;31(3):315-320. doi: 10.1007/s10278-018-0089-4. J Digit Imaging. 2018. PMID: 29740715 Free PMC article. Review.
Cited by
-
dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data.Nucleic Acids Res. 2019 Jan 8;47(D1):D285-D297. doi: 10.1093/nar/gky1030. Nucleic Acids Res. 2019. PMID: 30380085 Free PMC article.
-
The democratization of bioinformatics: A software engineering perspective.Gigascience. 2020 Jun 1;9(6):giaa063. doi: 10.1093/gigascience/giaa063. Gigascience. 2020. PMID: 32562490 Free PMC article.
-
Towards reproducible computational drug discovery.J Cheminform. 2020 Jan 28;12(1):9. doi: 10.1186/s13321-020-0408-x. J Cheminform. 2020. PMID: 33430992 Free PMC article. Review.
-
Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines.BMC Bioinformatics. 2018 Oct 15;19(Suppl 10):349. doi: 10.1186/s12859-018-2296-x. BMC Bioinformatics. 2018. PMID: 30367595 Free PMC article.
-
NPARS-A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science.Front Big Data. 2021 Sep 27;4:725095. doi: 10.3389/fdata.2021.725095. eCollection 2021. Front Big Data. 2021. PMID: 34647017 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources
