Literature DB >> 31521606

Building Containerized Workflows Using the BioDepot-Workflow-Builder.

Ling-Hong Hung1, Jiaming Hu1, Trevor Meiss1, Alyssa Ingersoll1, Wes Lloyd1, Daniel Kristiyanto1, Yuguang Xiong2, Eric Sobie2, Ka Yee Yeung3.   

Abstract

We present the BioDepot-workflow-builder (Bwb), a software tool that allows users to create and execute reproducible bioinformatics workflows using a drag-and-drop interface. Graphical widgets represent Docker containers executing a modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains a form-based user interface to facilitate parameter entry and a console to display intermediate results. Bwb provides tools for rapid customization of widgets, containers, and workflows. Saved workflows can be shared using Bwb's native format or exported as shell scripts.
Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Docker; RNA sequencing; bioinformatics workflows; reproducibility of research; software development

Year:  2019        PMID： 31521606      PMCID： PMC6883158          DOI： 10.1016/j.cels.2019.08.007

Source DB:  PubMed          Journal:  Cell Syst        ISSN： 2405-4712            Impact factor:   10.304


  19 in total

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  4 in total

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Journal:  BMC Genomics       Date:  2021-08-23       Impact factor: 4.547

2.  Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data.

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  4 in total

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