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ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists
BACKGROUND: New mathematical models of complex biological structures and computer simulation software allow modelers to simulate and analyze biochemical systems in silico and form mathematical predictions. Due to this potential predictive ability, the use of these models and software has the possibi...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705353/ https://www.ncbi.nlm.nih.gov/pubmed/19500393 http://dx.doi.org/10.1186/1752-0509-3-58 |
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author | Helikar, Tomáš Rogers, Jim A |
author_facet | Helikar, Tomáš Rogers, Jim A |
author_sort | Helikar, Tomáš |
collection | PubMed |
description | BACKGROUND: New mathematical models of complex biological structures and computer simulation software allow modelers to simulate and analyze biochemical systems in silico and form mathematical predictions. Due to this potential predictive ability, the use of these models and software has the possibility to compliment laboratory investigations and help refine, or even develop, new hypotheses. However, the existing mathematical modeling techniques and simulation tools are often difficult to use by laboratory biologists without training in high-level mathematics, limiting their use to trained modelers. RESULTS: We have developed a Boolean network-based simulation and analysis software tool, ChemChains, which combines the advantages of the parameter-free nature of logical models while providing the ability for users to interact with their models in a continuous manner, similar to the way laboratory biologists interact with laboratory data. ChemChains allows users to simulate models in an automatic fashion under tens of thousands of different external environments, as well as perform various mutational studies. CONCLUSION: ChemChains combines the advantages of logical and continuous modeling and provides a way for laboratory biologists to perform in silico experiments on mathematical models easily, a necessary component of laboratory research in the systems biology era. |
format | Text |
id | pubmed-2705353 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-27053532009-07-03 ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists Helikar, Tomáš Rogers, Jim A BMC Syst Biol Software BACKGROUND: New mathematical models of complex biological structures and computer simulation software allow modelers to simulate and analyze biochemical systems in silico and form mathematical predictions. Due to this potential predictive ability, the use of these models and software has the possibility to compliment laboratory investigations and help refine, or even develop, new hypotheses. However, the existing mathematical modeling techniques and simulation tools are often difficult to use by laboratory biologists without training in high-level mathematics, limiting their use to trained modelers. RESULTS: We have developed a Boolean network-based simulation and analysis software tool, ChemChains, which combines the advantages of the parameter-free nature of logical models while providing the ability for users to interact with their models in a continuous manner, similar to the way laboratory biologists interact with laboratory data. ChemChains allows users to simulate models in an automatic fashion under tens of thousands of different external environments, as well as perform various mutational studies. CONCLUSION: ChemChains combines the advantages of logical and continuous modeling and provides a way for laboratory biologists to perform in silico experiments on mathematical models easily, a necessary component of laboratory research in the systems biology era. BioMed Central 2009-06-06 /pmc/articles/PMC2705353/ /pubmed/19500393 http://dx.doi.org/10.1186/1752-0509-3-58 Text en Copyright © 2009 Helikar and Rogers; 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 Helikar, Tomáš Rogers, Jim A ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists |
title | ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists |
title_full | ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists |
title_fullStr | ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists |
title_full_unstemmed | ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists |
title_short | ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists |
title_sort | chemchains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705353/ https://www.ncbi.nlm.nih.gov/pubmed/19500393 http://dx.doi.org/10.1186/1752-0509-3-58 |
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