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PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli.

Esmaeili A, Davison T, Wu A, Alcantara J, Jacob C - BMC Bioinformatics (2015)

Bottom Line: Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model's scientific validity.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Faculty of Science, University of Calgary, 2500 University Drive NW, Calgary, T2N 1N4, Canada. afshin@invistaware.com.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Application on mobile devices. Prokaryo running on an iPhone, making use of the touch interface for easy navigation
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Fig17: Application on mobile devices. Prokaryo running on an iPhone, making use of the touch interface for easy navigation

Mentions: Our article also demonstrates how interactivity and illustrations, in the form of detailed graphical representations in 3-dimensional scenes, can enhance the understanding of biological systems through exploration and visualization. We have implemented our Prokaryo model on desktop computers, but also on mobile devices with touch interfaces (Fig. 17). Mobile computing devices make such models more accessible. Touch interfaces greatly facilitate navigation through and exploration of such models.Fig. 17


PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli.

Esmaeili A, Davison T, Wu A, Alcantara J, Jacob C - BMC Bioinformatics (2015)

Application on mobile devices. Prokaryo running on an iPhone, making use of the touch interface for easy navigation
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4587781&req=5

Fig17: Application on mobile devices. Prokaryo running on an iPhone, making use of the touch interface for easy navigation
Mentions: Our article also demonstrates how interactivity and illustrations, in the form of detailed graphical representations in 3-dimensional scenes, can enhance the understanding of biological systems through exploration and visualization. We have implemented our Prokaryo model on desktop computers, but also on mobile devices with touch interfaces (Fig. 17). Mobile computing devices make such models more accessible. Touch interfaces greatly facilitate navigation through and exploration of such models.Fig. 17

Bottom Line: Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model's scientific validity.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Faculty of Science, University of Calgary, 2500 University Drive NW, Calgary, T2N 1N4, Canada. afshin@invistaware.com.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus