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

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• dc.contributor.author Pastor Maeso, Manuel
• dc.contributor.author Gómez-Tamayo, José C.
• dc.contributor.author Sanz, Ferran
• dc.date.accessioned 2021-06-07T07:32:08Z
• dc.date.available 2021-06-07T07:32:08Z
• dc.date.issued 2021
• dc.description.abstract 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.
• dc.description.sponsorship 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).
• dc.format.mimetype application/pdf
• dc.identifier.citation Pastor M, Gómez-Tamayo JC, Sanz F. Flame: an open source framework for model development, hosting, and usage in production environments. J Cheminform. 2021;13(1):31. DOI: 10.1186/s13321-021-00509-z
• dc.identifier.doi http://dx.doi.org/10.1186/s13321-021-00509-z
• dc.identifier.issn 1758-2946
• dc.identifier.uri http://hdl.handle.net/10230/47781
• dc.language.iso eng
• dc.publisher Springer
• dc.relation.ispartof J Cheminform. 2021;13(1):31
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/777365
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/116030
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/681002
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/802750
• dc.rights © 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 ma
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword In-silico toxicology
• dc.subject.keyword Model integration
• dc.subject.keyword Model management
• dc.subject.keyword Modeling framework
• dc.subject.keyword Modeling tools
• dc.subject.keyword QSAR
• dc.subject.keyword Reproducibility
• dc.subject.keyword Web-interfaces
• dc.subject.keyword Workflow
• dc.title Flame: an open source framework for model development, hosting, and usage in production environments
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion