Bioimage analysis workflows: community resources to navigate through a complex ecosystem.
Bioimage analysis
FAIR principles
NEUBIAS
collections
components
knowledge database
remote computing
scientific workflow management systems
workflows
Journal
F1000Research
ISSN: 2046-1402
Titre abrégé: F1000Res
Pays: England
ID NLM: 101594320
Informations de publication
Date de publication:
2021
2021
Historique:
accepted:
14
04
2021
entrez:
17
6
2021
pubmed:
18
6
2021
medline:
28
7
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34136134
doi: 10.12688/f1000research.52569.1
pmc: PMC8182692
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
320Informations de copyright
Copyright: © 2021 Paul-Gilloteaux P et al.
Déclaration de conflit d'intérêts
No competing interests were disclosed.
Références
EMBO J. 2021 Mar 15;40(6):e107409
pubmed: 33565128
Curr Protoc. 2021 May;1(5):e89
pubmed: 34038030
F1000Res. 2018 Jun 14;7:
pubmed: 31543945
Nucleic Acids Res. 2020 Jul 2;48(W1):W395-W402
pubmed: 32479607
Bioinformatics. 2017 Aug 15;33(16):2580-2582
pubmed: 28379341
Patterns (N Y). 2020 Jun 03;1(3):100040
pubmed: 33205108
Brief Bioinform. 2017 May 1;18(3):530-536
pubmed: 27013646
F1000Res. 2020 Jun 16;9:613
pubmed: 32595963
Nat Methods. 2017 Dec;14(12):1141-1152
pubmed: 29083403
J Cell Biol. 2010 May 31;189(5):777-82
pubmed: 20513764
Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47
pubmed: 26538599
Genome Biol. 2006;7(10):R100
pubmed: 17076895
Bioinformatics. 2016 Apr 1;32(7):1112-4
pubmed: 26628585
Nat Methods. 2015 Nov;12(11):1065-71
pubmed: 26344046
Genome Biol. 2019 Aug 12;20(1):164
pubmed: 31405382
EMBO J. 2021 Feb 1;40(3):e105889
pubmed: 33480052
Nat Methods. 2014 Mar;11(3):281-9
pubmed: 24441936
PLoS Biol. 2019 Jun 19;17(6):e3000340
pubmed: 31216269
Front Neuroinform. 2014 Feb 20;8:13
pubmed: 24600387
Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10
pubmed: 27137889
Nat Methods. 2019 Dec;16(12):1247-1253
pubmed: 31636459
J Biotechnol. 2017 Nov 10;261:70-75
pubmed: 28757289
Bioinformatics. 2013 May 15;29(10):1325-32
pubmed: 23479348
Bioinformatics. 2012 Nov 15;28(22):3009-11
pubmed: 22962343
Nat Biotechnol. 2020 Mar;38(3):276-278
pubmed: 32055031
Sci Data. 2016 Mar 15;3:160018
pubmed: 26978244
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Front Comput Sci. 2020 Mar;2:
pubmed: 32905440
Plant Methods. 2013 Oct 09;9(1):38
pubmed: 24107223
J Cell Sci. 2021 Apr 1;134(7):
pubmed: 33795377
F1000Res. 2021 Jan 18;10:33
pubmed: 34035898
Nat Methods. 2012 Jul;9(7):671-5
pubmed: 22930834
Nat Methods. 2012 Jun 28;9(7):690-6
pubmed: 22743774