Flame: an open source framework for model development, hosting, and usage in production environments

This article describes Flame, an open source software for building predictive models and supporting their use in production environments. Flame is a web application with a web-based graphic interface, which can be used as a desktop application or installed in a server receiving requests from multipl...

Descripción completa

Detalles Bibliográficos
Autores: Pastor Maeso, Manuel, Gómez-Tamayo, José C., Sanz, Ferran
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/47781
Acceso en línea:http://hdl.handle.net/10230/47781
http://dx.doi.org/10.1186/s13321-021-00509-z
Access Level:acceso abierto
Palabra clave:In-silico toxicology
Model integration
Model management
Modeling framework
Modeling tools
QSAR
Reproducibility
Web-interfaces
Workflow
id ES_5499363e12a266c1e7cafc6de1237d6d
oai_identifier_str oai:recercat.cat:10230/47781
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Flame: an open source framework for model development, hosting, and usage in production environments
title Flame: an open source framework for model development, hosting, and usage in production environments
spellingShingle Flame: an open source framework for model development, hosting, and usage in production environments
Pastor Maeso, Manuel
In-silico toxicology
Model integration
Model management
Modeling framework
Modeling tools
QSAR
Reproducibility
Web-interfaces
Workflow
title_short Flame: an open source framework for model development, hosting, and usage in production environments
title_full Flame: an open source framework for model development, hosting, and usage in production environments
title_fullStr Flame: an open source framework for model development, hosting, and usage in production environments
title_full_unstemmed Flame: an open source framework for model development, hosting, and usage in production environments
title_sort Flame: an open source framework for model development, hosting, and usage in production environments
dc.creator.none.fl_str_mv Pastor Maeso, Manuel
Gómez-Tamayo, José C.
Sanz, Ferran
author Pastor Maeso, Manuel
author_facet Pastor Maeso, Manuel
Gómez-Tamayo, José C.
Sanz, Ferran
author_role author
author2 Gómez-Tamayo, José C.
Sanz, Ferran
author2_role author
author
dc.subject.none.fl_str_mv In-silico toxicology
Model integration
Model management
Modeling framework
Modeling tools
QSAR
Reproducibility
Web-interfaces
Workflow
topic In-silico toxicology
Model integration
Model management
Modeling framework
Modeling tools
QSAR
Reproducibility
Web-interfaces
Workflow
description This article describes Flame, an open source software for building predictive models and supporting their use in production environments. Flame is a web application with a web-based graphic interface, which can be used as a desktop application or installed in a server receiving requests from multiple users. Models can be built starting from any collection of biologically annotated chemical structures since the software supports structural normalization, molecular descriptor calculation, and machine learning model generation using predefined workflows. The model building workflow can be customized from the graphic interface, selecting the type of normalization, molecular descriptors, and machine learning algorithm to be used from a panel of state-of-the-art methods implemented natively. Moreover, Flame implements a mechanism allowing to extend its source code, adding unlimited model customization. Models generated with Flame can be easily exported, facilitating collaborative model development. All models are stored in a model repository supporting model versioning. Models are identified by unique model IDs and include detailed documentation formatted using widely accepted standards. The current version is the result of nearly 3 years of development in collaboration with users from the pharmaceutical industry within the IMI eTRANSAFE project, which aims, among other objectives, to develop high-quality predictive models based on shared legacy data for assessing the safety of drug candidates.
publishDate 2021
dc.date.none.fl_str_mv 2021
2021
2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/47781
http://dx.doi.org/10.1186/s13321-021-00509-z
url http://hdl.handle.net/10230/47781
http://dx.doi.org/10.1186/s13321-021-00509-z
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv J Cheminform. 2021;13(1):31
info:eu-repo/grantAgreement/EC/H2020/777365
info:eu-repo/grantAgreement/EC/H2020/116030
info:eu-repo/grantAgreement/EC/H2020/681002
info:eu-repo/grantAgreement/EC/H2020/802750
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869408195164766208
spelling Flame: an open source framework for model development, hosting, and usage in production environmentsPastor Maeso, ManuelGómez-Tamayo, José C.Sanz, FerranIn-silico toxicologyModel integrationModel managementModeling frameworkModeling toolsQSARReproducibilityWeb-interfacesWorkflowThis article describes Flame, an open source software for building predictive models and supporting their use in production environments. Flame is a web application with a web-based graphic interface, which can be used as a desktop application or installed in a server receiving requests from multiple users. Models can be built starting from any collection of biologically annotated chemical structures since the software supports structural normalization, molecular descriptor calculation, and machine learning model generation using predefined workflows. The model building workflow can be customized from the graphic interface, selecting the type of normalization, molecular descriptors, and machine learning algorithm to be used from a panel of state-of-the-art methods implemented natively. Moreover, Flame implements a mechanism allowing to extend its source code, adding unlimited model customization. Models generated with Flame can be easily exported, facilitating collaborative model development. All models are stored in a model repository supporting model versioning. Models are identified by unique model IDs and include detailed documentation formatted using widely accepted standards. The current version is the result of nearly 3 years of development in collaboration with users from the pharmaceutical industry within the IMI eTRANSAFE project, which aims, among other objectives, to develop high-quality predictive models based on shared legacy data for assessing the safety of drug candidates.This work has received funding from the eTRANSAFE project (Grant Agreement No. 777365), developed under the Innovative Medicines Initiative Joint Undertaking (IMI2), resources of which are composed of a financial contribution from the European Union’s Seventh Framework Programme (FP7/2007–2013) and EFPIA companies’ in kind contributions. The authors of this article are also involved in other related IMI projects which contributed funding, such as TransQST (No. 116030) as well as the H2020 EU-ToxRisk project (No. 681002) and FAIRplus (No. 802750). The Research Programme on Biomedical Informatics (GRIB) is a member of the Spanish National Bioinformatics Institute (INB), funded by ISCIII and FEDER (PT17/0009/0014). The DCEXS is a ‘Unidad de Excelencia María de Maeztu’, funded by the AEI (CEX2018-000782-M). The GRIB is also supported by the Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR), Generalitat de Catalunya (2017 SGR 00519).Springer202120212021info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/47781http://dx.doi.org/10.1186/s13321-021-00509-zreponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésJ Cheminform. 2021;13(1):31info:eu-repo/grantAgreement/EC/H2020/777365info:eu-repo/grantAgreement/EC/H2020/116030info:eu-repo/grantAgreement/EC/H2020/681002info:eu-repo/grantAgreement/EC/H2020/802750© The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data mahttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/477812026-05-29T05:05:01Z
score 15.198674

Similares en LA Referencia