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BGFit: management and automated fitting of biological growth curves
BACKGROUND: Existing tools to model cell growth curves do not offer a flexible integrative approach to manage large datasets and automatically estimate parameters. Due to the increase of experimental time-series from microbiology and oncology, the need for a software that allows researchers to easil...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848918/ https://www.ncbi.nlm.nih.gov/pubmed/24067087 http://dx.doi.org/10.1186/1471-2105-14-283 |
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author | Veríssimo, André Paixão, Laura Neves, Ana Rute Vinga, Susana |
author_facet | Veríssimo, André Paixão, Laura Neves, Ana Rute Vinga, Susana |
author_sort | Veríssimo, André |
collection | PubMed |
description | BACKGROUND: Existing tools to model cell growth curves do not offer a flexible integrative approach to manage large datasets and automatically estimate parameters. Due to the increase of experimental time-series from microbiology and oncology, the need for a software that allows researchers to easily organize experimental data and simultaneously extract relevant parameters in an efficient way is crucial. RESULTS: BGFit provides a web-based unified platform, where a rich set of dynamic models can be fitted to experimental time-series data, further allowing to efficiently manage the results in a structured and hierarchical way. The data managing system allows to organize projects, experiments and measurements data and also to define teams with different editing and viewing permission. Several dynamic and algebraic models are already implemented, such as polynomial regression, Gompertz, Baranyi, Logistic and Live Cell Fraction models and the user can add easily new models thus expanding current ones. CONCLUSIONS: BGFit allows users to easily manage their data and models in an integrated way, even if they are not familiar with databases or existing computational tools for parameter estimation. BGFit is designed with a flexible architecture that focus on extensibility and leverages free software with existing tools and methods, allowing to compare and evaluate different data modeling techniques. The application is described in the context of bacterial and tumor cells growth data fitting, but it is also applicable to any type of two-dimensional data, e.g. physical chemistry and macroeconomic time series, being fully scalable to high number of projects, data and model complexity. |
format | Online Article Text |
id | pubmed-3848918 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-38489182013-12-06 BGFit: management and automated fitting of biological growth curves Veríssimo, André Paixão, Laura Neves, Ana Rute Vinga, Susana BMC Bioinformatics Software BACKGROUND: Existing tools to model cell growth curves do not offer a flexible integrative approach to manage large datasets and automatically estimate parameters. Due to the increase of experimental time-series from microbiology and oncology, the need for a software that allows researchers to easily organize experimental data and simultaneously extract relevant parameters in an efficient way is crucial. RESULTS: BGFit provides a web-based unified platform, where a rich set of dynamic models can be fitted to experimental time-series data, further allowing to efficiently manage the results in a structured and hierarchical way. The data managing system allows to organize projects, experiments and measurements data and also to define teams with different editing and viewing permission. Several dynamic and algebraic models are already implemented, such as polynomial regression, Gompertz, Baranyi, Logistic and Live Cell Fraction models and the user can add easily new models thus expanding current ones. CONCLUSIONS: BGFit allows users to easily manage their data and models in an integrated way, even if they are not familiar with databases or existing computational tools for parameter estimation. BGFit is designed with a flexible architecture that focus on extensibility and leverages free software with existing tools and methods, allowing to compare and evaluate different data modeling techniques. The application is described in the context of bacterial and tumor cells growth data fitting, but it is also applicable to any type of two-dimensional data, e.g. physical chemistry and macroeconomic time series, being fully scalable to high number of projects, data and model complexity. BioMed Central 2013-09-25 /pmc/articles/PMC3848918/ /pubmed/24067087 http://dx.doi.org/10.1186/1471-2105-14-283 Text en Copyright © 2013 Veríssimo et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Veríssimo, André Paixão, Laura Neves, Ana Rute Vinga, Susana BGFit: management and automated fitting of biological growth curves |
title | BGFit: management and automated fitting of biological growth curves |
title_full | BGFit: management and automated fitting of biological growth curves |
title_fullStr | BGFit: management and automated fitting of biological growth curves |
title_full_unstemmed | BGFit: management and automated fitting of biological growth curves |
title_short | BGFit: management and automated fitting of biological growth curves |
title_sort | bgfit: management and automated fitting of biological growth curves |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848918/ https://www.ncbi.nlm.nih.gov/pubmed/24067087 http://dx.doi.org/10.1186/1471-2105-14-283 |
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