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Bioimage analysis workflows: community resources to navigate through a complex ecosystem

Workflows are the keystone of bioimage analysis, and the NEUBIAS (Network of European BioImage AnalystS) community is trying to gather the actors of this field and organize the information around them.  One of its most recent outputs is the opening of the F1000Research NEUBIAS gateway, whose main ob...

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Autores principales: Paul-Gilloteaux, Perrine, Tosi, Sébastien, Hériché, Jean-Karim, Gaignard, Alban, Ménager, Hervé, Marée, Raphaël, Baecker, Volker, Klemm, Anna, Kalaš, Matúš, Zhang, Chong, Miura, Kota, Colombelli, Julien
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8182692/
https://www.ncbi.nlm.nih.gov/pubmed/34136134
http://dx.doi.org/10.12688/f1000research.52569.1
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author Paul-Gilloteaux, Perrine
Tosi, Sébastien
Hériché, Jean-Karim
Gaignard, Alban
Ménager, Hervé
Marée, Raphaël
Baecker, Volker
Klemm, Anna
Kalaš, Matúš
Zhang, Chong
Miura, Kota
Colombelli, Julien
author_facet Paul-Gilloteaux, Perrine
Tosi, Sébastien
Hériché, Jean-Karim
Gaignard, Alban
Ménager, Hervé
Marée, Raphaël
Baecker, Volker
Klemm, Anna
Kalaš, Matúš
Zhang, Chong
Miura, Kota
Colombelli, Julien
author_sort Paul-Gilloteaux, Perrine
collection PubMed
description Workflows are the keystone of bioimage analysis, and the NEUBIAS (Network of European BioImage AnalystS) community is trying to gather the actors of this field and organize the information around them.  One of its most recent outputs is the opening of the F1000Research NEUBIAS gateway, whose main objective is to offer a channel of publication for bioimage analysis workflows and associated resources. In this paper we want to express some personal opinions and recommendations related to finding, handling and developing bioimage analysis workflows.  The emergence of "big data” in bioimaging and resource-intensive analysis algorithms make local data storage and computing solutions a limiting factor. At the same time, the need for data sharing with collaborators and a general shift towards remote work, have created new challenges and avenues for the execution and sharing of bioimage analysis workflows. These challenges are to reproducibly run workflows in remote environments, in particular when their components come from different software packages, but also to document them and link their parameters and results by following the FAIR principles (Findable, Accessible, Interoperable, Reusable) to foster open and reproducible science. In this opinion paper, we focus on giving some directions to the reader to tackle these challenges and navigate through this complex ecosystem, in order to find and use workflows, and to compare workflows addressing the same problem. We also discuss tools to run workflows in the cloud and on High Performance Computing resources, and suggest ways to make these workflows FAIR.
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spelling pubmed-81826922021-06-15 Bioimage analysis workflows: community resources to navigate through a complex ecosystem Paul-Gilloteaux, Perrine Tosi, Sébastien Hériché, Jean-Karim Gaignard, Alban Ménager, Hervé Marée, Raphaël Baecker, Volker Klemm, Anna Kalaš, Matúš Zhang, Chong Miura, Kota Colombelli, Julien F1000Res Opinion Article Workflows are the keystone of bioimage analysis, and the NEUBIAS (Network of European BioImage AnalystS) community is trying to gather the actors of this field and organize the information around them.  One of its most recent outputs is the opening of the F1000Research NEUBIAS gateway, whose main objective is to offer a channel of publication for bioimage analysis workflows and associated resources. In this paper we want to express some personal opinions and recommendations related to finding, handling and developing bioimage analysis workflows.  The emergence of "big data” in bioimaging and resource-intensive analysis algorithms make local data storage and computing solutions a limiting factor. At the same time, the need for data sharing with collaborators and a general shift towards remote work, have created new challenges and avenues for the execution and sharing of bioimage analysis workflows. These challenges are to reproducibly run workflows in remote environments, in particular when their components come from different software packages, but also to document them and link their parameters and results by following the FAIR principles (Findable, Accessible, Interoperable, Reusable) to foster open and reproducible science. In this opinion paper, we focus on giving some directions to the reader to tackle these challenges and navigate through this complex ecosystem, in order to find and use workflows, and to compare workflows addressing the same problem. We also discuss tools to run workflows in the cloud and on High Performance Computing resources, and suggest ways to make these workflows FAIR. F1000 Research Limited 2021-04-26 /pmc/articles/PMC8182692/ /pubmed/34136134 http://dx.doi.org/10.12688/f1000research.52569.1 Text en Copyright: © 2021 Paul-Gilloteaux P et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Opinion Article
Paul-Gilloteaux, Perrine
Tosi, Sébastien
Hériché, Jean-Karim
Gaignard, Alban
Ménager, Hervé
Marée, Raphaël
Baecker, Volker
Klemm, Anna
Kalaš, Matúš
Zhang, Chong
Miura, Kota
Colombelli, Julien
Bioimage analysis workflows: community resources to navigate through a complex ecosystem
title Bioimage analysis workflows: community resources to navigate through a complex ecosystem
title_full Bioimage analysis workflows: community resources to navigate through a complex ecosystem
title_fullStr Bioimage analysis workflows: community resources to navigate through a complex ecosystem
title_full_unstemmed Bioimage analysis workflows: community resources to navigate through a complex ecosystem
title_short Bioimage analysis workflows: community resources to navigate through a complex ecosystem
title_sort bioimage analysis workflows: community resources to navigate through a complex ecosystem
topic Opinion Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8182692/
https://www.ncbi.nlm.nih.gov/pubmed/34136134
http://dx.doi.org/10.12688/f1000research.52569.1
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