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Literature DB >> 28968637

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

Fabiano B Menegidio¹, Daniela L Jabes¹, Regina Costa de Oliveira¹, Luiz R Nunes².

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.

Entities: Species

Mesh：

Year: 2018 PMID： 28968637 DOI： 10.1093/bioinformatics/btx554

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

Keyword Cloud
Cited

11 in total

1. dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data.

Authors: Jhih-Hua Jhong; Yu-Hsiang Chi; Wen-Chi Li; Tsai-Hsuan Lin; Kai-Yao Huang; Tzong-Yi Lee
Journal: Nucleic Acids Res Date: 2019-01-08 Impact factor: 16.971

2. Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing.

Authors: David Aciole Barbosa; Bruno C Araújo; Giovana Souza Branco; Alexandre S Simeone; Alexandre W S Hilsdorf; Daniela L Jabes; Luiz R Nunes; Renata G Moreira; Fabiano B Menegidio
Journal: Mar Biotechnol (NY) Date: 2021-12-02 Impact factor: 3.619

3. The democratization of bioinformatics: A software engineering perspective.

Authors: Brendan Lawlor; Roy D Sleator
Journal: Gigascience Date: 2020-06-01 Impact factor: 6.524

4. Bioportainer Workbench: a versatile and user-friendly system that integrates implementation, management, and use of bioinformatics resources in Docker environments.

Authors: Fabiano B Menegidio; David Aciole Barbosa; Rafael Dos S Gonçalves; Marcio M Nishime; Daniela L Jabes; Regina Costa de Oliveira; Luiz R Nunes
Journal: Gigascience Date: 2019-04-01 Impact factor: 6.524

5. ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.

Authors: David Aciole Barbosa; Fabiano Bezerra Menegidio; Valquíria Campos Alencar; Rafael S Gonçalves; Juliana de Fátima Santos Silva; Renata Ozelami Vilas Boas; Yara Natércia Lima Faustino de Maria; Daniela Leite Jabes; Regina Costa de Oliveira; Luiz R Nunes
Journal: PLoS Negl Trop Dis Date: 2019-07-15

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

1. dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data.

2. Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing.

3. The democratization of bioinformatics: A software engineering perspective.

4. Bioportainer Workbench: a versatile and user-friendly system that integrates implementation, management, and use of bioinformatics resources in Docker environments.

5. ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.

6. ORCA: a comprehensive bioinformatics container environment for education and research.

Review 7. Towards reproducible computational drug discovery.

8. Editorial: Curriculum Applications in Microbiology: Bioinformatics in the Classroom.

9. Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines.

10. Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2.