A workflow management system for reproducible and interoperable high-throughput self-driving experiments

Autores
Mione, Federico Martin; Kaspersetz, Lucas; Luna, Martín Francisco; Aizpuru, Judit; Scholz, Randolf; Borisyak, Maxim; Kemmer, Annina; Schermeyer, M. Therese; Martínez, Ernesto Carlos; Neubauer, Peter; Cruz Bournazou, M. Nicolas
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
To foster self-driving experimentation and address the reproducibility crisis in bioprocess development in a collaborative environment, a modular Workflow Management System (WMS) is required. In this work, a WMS based on Directed Acyclic Graphs that offers a modular and flexible design for plug-and-play integration of computational tools is presented. A case study is used to demonstrate that the implementation of a computational WMS in robotic experimental facilities promotes the application of Findable, Accessible, Interoperable and Re-usable principles, allowing researchers to readily share protocols, models, methods and data. As a proof of concept, we integrated three different computational workflows for online re-design of feeding rates in 24 parallel E. coli fed-batch cultivations producing elastin-like proteins. This approach provides a solid foundation for increasing scientific data generation in robotic experimental facilities, fostering open collaboration, and addressing the challenges of reproducibility in research.
Fil: Mione, Federico Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentina
Fil: Kaspersetz, Lucas. Technishe Universitat Berlin; Alemania
Fil: Luna, Martín Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentina
Fil: Aizpuru, Judit. Technishe Universitat Berlin; Alemania
Fil: Scholz, Randolf. University of Hildesheim; Alemania
Fil: Borisyak, Maxim. Technishe Universitat Berlin; Alemania
Fil: Kemmer, Annina. Technishe Universitat Berlin; Alemania
Fil: Schermeyer, M. Therese. Technishe Universitat Berlin; Alemania
Fil: Martínez, Ernesto Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentina
Fil: Neubauer, Peter. Technishe Universitat Berlin; Alemania
Fil: Cruz Bournazou, M. Nicolas. Technishe Universitat Berlin; Alemania
Materia
FAIR data
High-throughput
Bioprocess development
Self-driving experimentation
Workflow automation
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/243892
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/243892
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling A workflow management system for reproducible and interoperable high-throughput self-driving experimentsMione, Federico MartinKaspersetz, LucasLuna, Martín FranciscoAizpuru, JuditScholz, RandolfBorisyak, MaximKemmer, AnninaSchermeyer, M. ThereseMartínez, Ernesto CarlosNeubauer, PeterCruz Bournazou, M. NicolasFAIR dataHigh-throughputBioprocess developmentSelf-driving experimentationWorkflow automationhttps://purl.org/becyt/ford/2.9https://purl.org/becyt/ford/2To foster self-driving experimentation and address the reproducibility crisis in bioprocess development in a collaborative environment, a modular Workflow Management System (WMS) is required. In this work, a WMS based on Directed Acyclic Graphs that offers a modular and flexible design for plug-and-play integration of computational tools is presented. A case study is used to demonstrate that the implementation of a computational WMS in robotic experimental facilities promotes the application of Findable, Accessible, Interoperable and Re-usable principles, allowing researchers to readily share protocols, models, methods and data. As a proof of concept, we integrated three different computational workflows for online re-design of feeding rates in 24 parallel E. coli fed-batch cultivations producing elastin-like proteins. This approach provides a solid foundation for increasing scientific data generation in robotic experimental facilities, fostering open collaboration, and addressing the challenges of reproducibility in research.Fil: Mione, Federico Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; ArgentinaFil: Kaspersetz, Lucas. Technishe Universitat Berlin; AlemaniaFil: Luna, Martín Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; ArgentinaFil: Aizpuru, Judit. Technishe Universitat Berlin; AlemaniaFil: Scholz, Randolf. University of Hildesheim; AlemaniaFil: Borisyak, Maxim. Technishe Universitat Berlin; AlemaniaFil: Kemmer, Annina. Technishe Universitat Berlin; AlemaniaFil: Schermeyer, M. Therese. Technishe Universitat Berlin; AlemaniaFil: Martínez, Ernesto Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; ArgentinaFil: Neubauer, Peter. Technishe Universitat Berlin; AlemaniaFil: Cruz Bournazou, M. Nicolas. Technishe Universitat Berlin; AlemaniaPergamon-Elsevier Science Ltd2024-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/243892Mione, Federico Martin; Kaspersetz, Lucas; Luna, Martín Francisco; Aizpuru, Judit; Scholz, Randolf; et al.; A workflow management system for reproducible and interoperable high-throughput self-driving experiments; Pergamon-Elsevier Science Ltd; Computers and Chemical Engineering; 187; 5-2024; 1-430098-1354CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S0098135424001388info:eu-repo/semantics/altIdentifier/doi/10.1016/j.compchemeng.2024.108720info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:13:36Zoai:ri.conicet.gov.ar:11336/243892instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:13:37.16CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A workflow management system for reproducible and interoperable high-throughput self-driving experiments
title A workflow management system for reproducible and interoperable high-throughput self-driving experiments
spellingShingle A workflow management system for reproducible and interoperable high-throughput self-driving experiments
Mione, Federico Martin
FAIR data
High-throughput
Bioprocess development
Self-driving experimentation
Workflow automation
title_short A workflow management system for reproducible and interoperable high-throughput self-driving experiments
title_full A workflow management system for reproducible and interoperable high-throughput self-driving experiments
title_fullStr A workflow management system for reproducible and interoperable high-throughput self-driving experiments
title_full_unstemmed A workflow management system for reproducible and interoperable high-throughput self-driving experiments
title_sort A workflow management system for reproducible and interoperable high-throughput self-driving experiments
dc.creator.none.fl_str_mv Mione, Federico Martin
Kaspersetz, Lucas
Luna, Martín Francisco
Aizpuru, Judit
Scholz, Randolf
Borisyak, Maxim
Kemmer, Annina
Schermeyer, M. Therese
Martínez, Ernesto Carlos
Neubauer, Peter
Cruz Bournazou, M. Nicolas
author Mione, Federico Martin
author_facet Mione, Federico Martin
Kaspersetz, Lucas
Luna, Martín Francisco
Aizpuru, Judit
Scholz, Randolf
Borisyak, Maxim
Kemmer, Annina
Schermeyer, M. Therese
Martínez, Ernesto Carlos
Neubauer, Peter
Cruz Bournazou, M. Nicolas
author_role author
author2 Kaspersetz, Lucas
Luna, Martín Francisco
Aizpuru, Judit
Scholz, Randolf
Borisyak, Maxim
Kemmer, Annina
Schermeyer, M. Therese
Martínez, Ernesto Carlos
Neubauer, Peter
Cruz Bournazou, M. Nicolas
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv FAIR data
High-throughput
Bioprocess development
Self-driving experimentation
Workflow automation
topic FAIR data
High-throughput
Bioprocess development
Self-driving experimentation
Workflow automation
purl_subject.fl_str_mv https://purl.org/becyt/ford/2.9
https://purl.org/becyt/ford/2
dc.description.none.fl_txt_mv To foster self-driving experimentation and address the reproducibility crisis in bioprocess development in a collaborative environment, a modular Workflow Management System (WMS) is required. In this work, a WMS based on Directed Acyclic Graphs that offers a modular and flexible design for plug-and-play integration of computational tools is presented. A case study is used to demonstrate that the implementation of a computational WMS in robotic experimental facilities promotes the application of Findable, Accessible, Interoperable and Re-usable principles, allowing researchers to readily share protocols, models, methods and data. As a proof of concept, we integrated three different computational workflows for online re-design of feeding rates in 24 parallel E. coli fed-batch cultivations producing elastin-like proteins. This approach provides a solid foundation for increasing scientific data generation in robotic experimental facilities, fostering open collaboration, and addressing the challenges of reproducibility in research.
Fil: Mione, Federico Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentina
Fil: Kaspersetz, Lucas. Technishe Universitat Berlin; Alemania
Fil: Luna, Martín Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentina
Fil: Aizpuru, Judit. Technishe Universitat Berlin; Alemania
Fil: Scholz, Randolf. University of Hildesheim; Alemania
Fil: Borisyak, Maxim. Technishe Universitat Berlin; Alemania
Fil: Kemmer, Annina. Technishe Universitat Berlin; Alemania
Fil: Schermeyer, M. Therese. Technishe Universitat Berlin; Alemania
Fil: Martínez, Ernesto Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentina
Fil: Neubauer, Peter. Technishe Universitat Berlin; Alemania
Fil: Cruz Bournazou, M. Nicolas. Technishe Universitat Berlin; Alemania
description To foster self-driving experimentation and address the reproducibility crisis in bioprocess development in a collaborative environment, a modular Workflow Management System (WMS) is required. In this work, a WMS based on Directed Acyclic Graphs that offers a modular and flexible design for plug-and-play integration of computational tools is presented. A case study is used to demonstrate that the implementation of a computational WMS in robotic experimental facilities promotes the application of Findable, Accessible, Interoperable and Re-usable principles, allowing researchers to readily share protocols, models, methods and data. As a proof of concept, we integrated three different computational workflows for online re-design of feeding rates in 24 parallel E. coli fed-batch cultivations producing elastin-like proteins. This approach provides a solid foundation for increasing scientific data generation in robotic experimental facilities, fostering open collaboration, and addressing the challenges of reproducibility in research.
publishDate 2024
dc.date.none.fl_str_mv 2024-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/243892
Mione, Federico Martin; Kaspersetz, Lucas; Luna, Martín Francisco; Aizpuru, Judit; Scholz, Randolf; et al.; A workflow management system for reproducible and interoperable high-throughput self-driving experiments; Pergamon-Elsevier Science Ltd; Computers and Chemical Engineering; 187; 5-2024; 1-43
0098-1354
CONICET Digital
CONICET
url http://hdl.handle.net/11336/243892
identifier_str_mv Mione, Federico Martin; Kaspersetz, Lucas; Luna, Martín Francisco; Aizpuru, Judit; Scholz, Randolf; et al.; A workflow management system for reproducible and interoperable high-throughput self-driving experiments; Pergamon-Elsevier Science Ltd; Computers and Chemical Engineering; 187; 5-2024; 1-43
0098-1354
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S0098135424001388
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.compchemeng.2024.108720
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Pergamon-Elsevier Science Ltd
publisher.none.fl_str_mv Pergamon-Elsevier Science Ltd
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1844614055520632832
score 13.069144

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