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Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases

Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communiti...

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Autores principales: Spoor, Shawna, Wytko, Connor, Soto, Brian, Chen, Ming, Almsaeed, Abdullah, Condon, Bradford, Herndon, Nic, Hough, Heidi, Jung, Sook, Staton, Meg, Wegrzyn, Jill, Main, Dorrie, Feltus, F Alex, Ficklin, Stephen P
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334887/
https://www.ncbi.nlm.nih.gov/pubmed/32621602
http://dx.doi.org/10.1093/database/baaa032
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author Spoor, Shawna
Wytko, Connor
Soto, Brian
Chen, Ming
Almsaeed, Abdullah
Condon, Bradford
Herndon, Nic
Hough, Heidi
Jung, Sook
Staton, Meg
Wegrzyn, Jill
Main, Dorrie
Feltus, F Alex
Ficklin, Stephen P
author_facet Spoor, Shawna
Wytko, Connor
Soto, Brian
Chen, Ming
Almsaeed, Abdullah
Condon, Bradford
Herndon, Nic
Hough, Heidi
Jung, Sook
Staton, Meg
Wegrzyn, Jill
Main, Dorrie
Feltus, F Alex
Ficklin, Stephen P
author_sort Spoor, Shawna
collection PubMed
description Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a ‘plug-in’ for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications.
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spelling pubmed-73348872020-07-13 Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases Spoor, Shawna Wytko, Connor Soto, Brian Chen, Ming Almsaeed, Abdullah Condon, Bradford Herndon, Nic Hough, Heidi Jung, Sook Staton, Meg Wegrzyn, Jill Main, Dorrie Feltus, F Alex Ficklin, Stephen P Database (Oxford) Original Article Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a ‘plug-in’ for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications. Oxford University Press 2020-07-04 /pmc/articles/PMC7334887/ /pubmed/32621602 http://dx.doi.org/10.1093/database/baaa032 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Spoor, Shawna
Wytko, Connor
Soto, Brian
Chen, Ming
Almsaeed, Abdullah
Condon, Bradford
Herndon, Nic
Hough, Heidi
Jung, Sook
Staton, Meg
Wegrzyn, Jill
Main, Dorrie
Feltus, F Alex
Ficklin, Stephen P
Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases
title Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases
title_full Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases
title_fullStr Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases
title_full_unstemmed Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases
title_short Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases
title_sort tripal and galaxy: supporting reproducible scientific workflows for community biological databases
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334887/
https://www.ncbi.nlm.nih.gov/pubmed/32621602
http://dx.doi.org/10.1093/database/baaa032
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