Limits...
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

The Prokaryo cytoplasm. A snapshot from an interactive simulation with DNA structure, water, ribosomes, RNA polymerases, β-galactosidase and lactose. In this scene over 70,000 particles are rendered in realtime. Compare Fig. 11 for protein shapes and colour representations
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: The Prokaryo cytoplasm. A snapshot from an interactive simulation with DNA structure, water, ribosomes, RNA polymerases, β-galactosidase and lactose. In this scene over 70,000 particles are rendered in realtime. Compare Fig. 11 for protein shapes and colour representations

Mentions: Motivated by Goodsell’s visuals, we have taken his highly detailed, illustrative “snapshots” one step further: we bring the biomolecular interactions of a bacterial cell alive as 3-dimensional computer simulations (Fig. 1). The output from our Prokaryo model is similar to the animations generated through Harvard University’s BioVisions project [2]. In order to visualize the inner workings of a eukaryotic cell, Harvard BioVisions produced an eight-minute animation entitled “The Inner Life of a Cell” [3]. Unlike Goodsell’s static illustrations, BioVisions enhances the understanding of structural and cellular biology by providing movement, flow, and a sense of real dynamics. However, an important element is missing in these animations: a way to interact with and explore the models in real time.Fig. 1


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)

The Prokaryo cytoplasm. A snapshot from an interactive simulation with DNA structure, water, ribosomes, RNA polymerases, β-galactosidase and lactose. In this scene over 70,000 particles are rendered in realtime. Compare Fig. 11 for protein shapes and colour representations
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: The Prokaryo cytoplasm. A snapshot from an interactive simulation with DNA structure, water, ribosomes, RNA polymerases, β-galactosidase and lactose. In this scene over 70,000 particles are rendered in realtime. Compare Fig. 11 for protein shapes and colour representations
Mentions: Motivated by Goodsell’s visuals, we have taken his highly detailed, illustrative “snapshots” one step further: we bring the biomolecular interactions of a bacterial cell alive as 3-dimensional computer simulations (Fig. 1). The output from our Prokaryo model is similar to the animations generated through Harvard University’s BioVisions project [2]. In order to visualize the inner workings of a eukaryotic cell, Harvard BioVisions produced an eight-minute animation entitled “The Inner Life of a Cell” [3]. Unlike Goodsell’s static illustrations, BioVisions enhances the understanding of structural and cellular biology by providing movement, flow, and a sense of real dynamics. However, an important element is missing in these animations: a way to interact with and explore the models in real time.Fig. 1

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