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PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli
BACKGROUND: We are creating software for agent-based simulation and visualization of bio-molecular processes in bacterial and eukaryotic cells. As a first example, we have built a 3-dimensional, interactive computer model of an Escherichia coli bacterium and its associated biomolecular processes. Ou...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587781/ https://www.ncbi.nlm.nih.gov/pubmed/26415599 http://dx.doi.org/10.1186/s12859-015-0720-z |
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author | Esmaeili, Afshin Davison, Timothy Wu, Andrew Alcantara, Joenel Jacob, Christian |
author_facet | Esmaeili, Afshin Davison, Timothy Wu, Andrew Alcantara, Joenel Jacob, Christian |
author_sort | Esmaeili, Afshin |
collection | PubMed |
description | BACKGROUND: We are creating software for agent-based simulation and visualization of bio-molecular processes in bacterial and eukaryotic cells. As a first example, we have built a 3-dimensional, interactive computer model of an Escherichia coli bacterium and its associated biomolecular processes. Our illustrative model focuses on the gene regulatory processes that control the expression of genes involved in the lactose operon. Prokaryo, our agent-based cell simulator, incorporates cellular structures, such as plasma membranes and cytoplasm, as well as elements of the molecular machinery, including RNA polymerase, messenger RNA, lactose permease, and ribosomes. RESULTS: The dynamics of cellular ’agents’ are defined by their rules of interaction, implemented as finite state machines. The agents are embedded within a 3-dimensional virtual environment with simulated physical and electrochemical properties. The hybrid model is driven by a combination of (1) mathematical equations (DEQs) to capture higher-scale phenomena and (2) agent-based rules to implement localized interactions among a small number of molecular elements. Consequently, our model is able to capture phenomena across multiple spatial scales, from changing concentration gradients to one-on-one molecular interactions. We use the classic gene regulatory mechanism of the lactose operon to demonstrate our model’s resolution, visual presentation, and real-time interactivity. Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model’s scientific validity. CONCLUSION: We believe that through illustration and interactive exploratory learning a model system like Prokaryo can enhance the general understanding and perception of biomolecular processes. Our agent-DEQ hybrid modeling approach can also be of value to conceptualize, illustrate, and—eventually—validate cell experiments in the wet lab. |
format | Online Article Text |
id | pubmed-4587781 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-45877812015-09-30 PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli Esmaeili, Afshin Davison, Timothy Wu, Andrew Alcantara, Joenel Jacob, Christian BMC Bioinformatics Research Article BACKGROUND: We are creating software for agent-based simulation and visualization of bio-molecular processes in bacterial and eukaryotic cells. As a first example, we have built a 3-dimensional, interactive computer model of an Escherichia coli bacterium and its associated biomolecular processes. Our illustrative model focuses on the gene regulatory processes that control the expression of genes involved in the lactose operon. Prokaryo, our agent-based cell simulator, incorporates cellular structures, such as plasma membranes and cytoplasm, as well as elements of the molecular machinery, including RNA polymerase, messenger RNA, lactose permease, and ribosomes. RESULTS: The dynamics of cellular ’agents’ are defined by their rules of interaction, implemented as finite state machines. The agents are embedded within a 3-dimensional virtual environment with simulated physical and electrochemical properties. The hybrid model is driven by a combination of (1) mathematical equations (DEQs) to capture higher-scale phenomena and (2) agent-based rules to implement localized interactions among a small number of molecular elements. Consequently, our model is able to capture phenomena across multiple spatial scales, from changing concentration gradients to one-on-one molecular interactions. We use the classic gene regulatory mechanism of the lactose operon to demonstrate our model’s resolution, visual presentation, and real-time interactivity. Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model’s scientific validity. CONCLUSION: We believe that through illustration and interactive exploratory learning a model system like Prokaryo can enhance the general understanding and perception of biomolecular processes. Our agent-DEQ hybrid modeling approach can also be of value to conceptualize, illustrate, and—eventually—validate cell experiments in the wet lab. BioMed Central 2015-09-29 /pmc/articles/PMC4587781/ /pubmed/26415599 http://dx.doi.org/10.1186/s12859-015-0720-z Text en © Esmaeili et al. 2015 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Esmaeili, Afshin Davison, Timothy Wu, Andrew Alcantara, Joenel Jacob, Christian PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli |
title | PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli |
title_full | PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli |
title_fullStr | PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli |
title_full_unstemmed | PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli |
title_short | PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli |
title_sort | prokaryo: an illustrative and interactive computational model of the lactose operon in the bacterium escherichia coli |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587781/ https://www.ncbi.nlm.nih.gov/pubmed/26415599 http://dx.doi.org/10.1186/s12859-015-0720-z |
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