Bioflow: A web based workflow management system for design and execution of genomics pipelines
The cost required for the process of sequencing genomes has decreased drastically in the last few years. The knowledge of full genomes has increased the pace of the advancements in the field of functional genomics. Computational genomics, which analyses these sequences, has seen a similar growth. Th...
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ndltd-VTETD-oai-vtechworks.lib.vt.edu-10919-248092020-09-29T05:43:53Z Bioflow: A web based workflow management system for design and execution of genomics pipelines Puthige, Ashwin Acharya Computer Science Garner, Harold Ray Mittelman, David Alexander Zhang, Liqing genomics pipeline workflow automation web development workflow designer ruby on rails genomics workflow. The cost required for the process of sequencing genomes has decreased drastically in the last few years. The knowledge of full genomes has increased the pace of the advancements in the field of functional genomics. Computational genomics, which analyses these sequences, has seen a similar growth. The multitude of sequencing technologies has resulted in various formats for storing the sequences. This has resulted in the creation of many tools for DNA analysis. There are various tools for sorting, indexing, analyzing read groups and other tasks. The analysis of genomics often requires the creation of pipelines, which processes the DNA sequences by chaining together many tools. This results in the creation of complex scripts that glue together these tools and pass the output from one stage to the other. Also, there are tools which allow creation of these pipelines with a graphical user interface. But these are complex to use and it is difficult to quickly add the new tools being developed to existing workflows. To solve these issues, we developed BioFlow; a web based genomic workflow management system. The use of BioFlow does not require any programming skills. The integrated workflow designer allows creation and saving workflows. The pipeline is created by connecting the tools with a visual connector. BioFlow provides an easy and simple interface that allows users to quickly add tools for use in any workflow. Audit logs are maintained at each stage, which helps users to easily identify errors and fix them. Master of Science 2014-01-12T09:00:18Z 2014-01-12T09:00:18Z 2014-01-11 Thesis vt_gsexam:1903 http://hdl.handle.net/10919/24809 In Copyright http://rightsstatements.org/vocab/InC/1.0/ ETD application/pdf Virginia Tech |
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genomics pipeline workflow automation web development workflow designer ruby on rails genomics workflow. |
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genomics pipeline workflow automation web development workflow designer ruby on rails genomics workflow. Puthige, Ashwin Acharya Bioflow: A web based workflow management system for design and execution of genomics pipelines |
description |
The cost required for the process of sequencing genomes has decreased drastically in the last few years. The knowledge of full genomes has increased the pace of the advancements in the field of functional genomics. Computational genomics, which analyses these sequences, has seen a similar growth. The multitude of sequencing technologies has resulted in various formats for storing the sequences. This has resulted in the creation of many tools for DNA analysis. There are various tools for sorting, indexing, analyzing read groups and other tasks. The analysis of genomics often requires the creation of pipelines, which processes the DNA sequences by chaining together many tools. This results in the creation of complex scripts that glue together these tools and pass the output from one stage to the other. Also, there are tools which allow creation of these pipelines with a graphical user interface. But these are complex to use and it is difficult to quickly add the new tools being developed to existing workflows.
To solve these issues, we developed BioFlow; a web based genomic workflow management system. The use of BioFlow does not require any programming skills. The integrated workflow designer allows creation and saving workflows. The pipeline is created by connecting the tools with a visual connector. BioFlow provides an easy and simple interface that allows users to quickly add tools for use in any workflow. Audit logs are maintained at each stage, which helps users to easily identify errors and fix them. === Master of Science |
author2 |
Computer Science |
author_facet |
Computer Science Puthige, Ashwin Acharya |
author |
Puthige, Ashwin Acharya |
author_sort |
Puthige, Ashwin Acharya |
title |
Bioflow: A web based workflow management system for design and execution of genomics pipelines |
title_short |
Bioflow: A web based workflow management system for design and execution of genomics pipelines |
title_full |
Bioflow: A web based workflow management system for design and execution of genomics pipelines |
title_fullStr |
Bioflow: A web based workflow management system for design and execution of genomics pipelines |
title_full_unstemmed |
Bioflow: A web based workflow management system for design and execution of genomics pipelines |
title_sort |
bioflow: a web based workflow management system for design and execution of genomics pipelines |
publisher |
Virginia Tech |
publishDate |
2014 |
url |
http://hdl.handle.net/10919/24809 |
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AT puthigeashwinacharya bioflowawebbasedworkflowmanagementsystemfordesignandexecutionofgenomicspipelines |
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