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VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models

In order for mathematical models to make credible contributions, it is essential for them to be verified and validated. Currently, verification and validation (V&V) of these models does not meet the expectations of the system biology and systems pharmacology communities. Partially as a result of...

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Detalles Bibliográficos
Autores principales: Parker, Christopher, Nelson, Erik, Zhang, Tongli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9777964/
https://www.ncbi.nlm.nih.gov/pubmed/36554152
http://dx.doi.org/10.3390/e24121747
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author Parker, Christopher
Nelson, Erik
Zhang, Tongli
author_facet Parker, Christopher
Nelson, Erik
Zhang, Tongli
author_sort Parker, Christopher
collection PubMed
description In order for mathematical models to make credible contributions, it is essential for them to be verified and validated. Currently, verification and validation (V&V) of these models does not meet the expectations of the system biology and systems pharmacology communities. Partially as a result of this shortfall, systemic V&V of existing models currently requires a lot of time and effort. In order to facilitate systemic V&V of chosen hypothalamic-pituitary-adrenal (HPA) axis models, we have developed a computational framework named VeVaPy—taking care to follow the recommended best practices regarding the development of mathematical models. VeVaPy includes four functional modules coded in Python, and the source code is publicly available. We demonstrate that VeVaPy can help us efficiently verify and validate the five HPA axis models we have chosen. Supplied with new and independent data, VeVaPy outputs objective V&V benchmarks for each model. We believe that VeVaPy will help future researchers with basic modeling and programming experience to efficiently verify and validate mathematical models from the fields of systems biology and systems pharmacology.
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spelling pubmed-97779642022-12-23 VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models Parker, Christopher Nelson, Erik Zhang, Tongli Entropy (Basel) Article In order for mathematical models to make credible contributions, it is essential for them to be verified and validated. Currently, verification and validation (V&V) of these models does not meet the expectations of the system biology and systems pharmacology communities. Partially as a result of this shortfall, systemic V&V of existing models currently requires a lot of time and effort. In order to facilitate systemic V&V of chosen hypothalamic-pituitary-adrenal (HPA) axis models, we have developed a computational framework named VeVaPy—taking care to follow the recommended best practices regarding the development of mathematical models. VeVaPy includes four functional modules coded in Python, and the source code is publicly available. We demonstrate that VeVaPy can help us efficiently verify and validate the five HPA axis models we have chosen. Supplied with new and independent data, VeVaPy outputs objective V&V benchmarks for each model. We believe that VeVaPy will help future researchers with basic modeling and programming experience to efficiently verify and validate mathematical models from the fields of systems biology and systems pharmacology. MDPI 2022-11-29 /pmc/articles/PMC9777964/ /pubmed/36554152 http://dx.doi.org/10.3390/e24121747 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Parker, Christopher
Nelson, Erik
Zhang, Tongli
VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models
title VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models
title_full VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models
title_fullStr VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models
title_full_unstemmed VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models
title_short VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models
title_sort vevapy, a python platform for efficient verification and validation of systems biology models with demonstrations using hypothalamic-pituitary-adrenal axis models
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9777964/
https://www.ncbi.nlm.nih.gov/pubmed/36554152
http://dx.doi.org/10.3390/e24121747
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