Biomolecular swarms ? an agent-based model of the lactose operon

Jacob, Christian; Burleigh, Ian

doi:10.1007/s11047-004-2638-7

Cited by 27 publications

(10 citation statements)

References 6 publications

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“…In agent-based modeling (ABM), each entity is considered to be an agent in a multi agent system (MAS) that interacts locally with its neighbors as well as the environment [44][45][46]. For example, Shirazi et.al., [46] presented a multi-agent approach to model the MAPK signaling pathway, which defines each substrate in a signaling pathway as an independent entity (agent).…”

Section: Agent-based Models(abm)mentioning

confidence: 99%

Review of the computational models for the signaling pathway

Kong

Wang

Zhang

2016

Proceedings of the 2nd Information Technology and Mechatronics Engineering Conference (ITOEC 2016TOEC 2016)

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Abstract.In the past few years, systems biology methods have been widely used to explore the mechanism of cancer. Various signaling pathways play the important role in cancer. And a large number of computational methods are used to model the signaling pathway. Here, we reviewed many existing mechanisms and modeling techniques, which are used to model different signaling pathways. Then we introduced the systematic workflow of a system biology approach and some fundamental analysis methods. Finally we discuss some known challenges in the process of modeling signaling pathways and what we should handle in our future work.

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Section: Agent-based Models(abm)mentioning

confidence: 99%

Review of the computational models for the signaling pathway

Kong

Wang

Zhang

2016

Proceedings of the 2nd Information Technology and Mechatronics Engineering Conference (ITOEC 2016TOEC 2016)

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“…However, much work needs to be done to refine these models to realize biological evolution of even simple mutation problems, e.g., transferring DNA fro m one organism and express it in a d ifferent organism to introduce specific new features, [7,28],e.g., those involving skin color changes in animals. Th is will require the bioinformatics machinery to be integrated along with agent based paradigm to explore the system biology in great details, [12,13,27] . The present best technology available is a blend of object oriented and agent-based programming approaches that aid simulation and animation.…”

Section: Multi-agent Architecture and Toolkitsmentioning

confidence: 99%

Agent-based Models in Synthetic Biology: Tools for Simulation and Prospects

Krishnamurthy¹

2012

IJISA

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Abstract-We describe a mult iset of agents based modeling and simulation paradig m for synthetic biology. The mu ltiset of agents -based programming paradig m, can be interpreted as the outcome arising out of deterministic, nondetermin istic or stochastic interaction among elements in a mult iset object space, that includes the environment. These interactions are like chemical reactions and the evolution of the mu ltiset can emulate the system biological functions. Since the reaction rules are inherently parallel, any number of actions can be performed cooperatively or competit ively among the subsets of elements, so that the elements evolve toward equilibriu m or emergent state. Pract ical realization of this paradigm for system biological simulat ion is achieved through the concept of transactional style programming with agents, as well as soft computing (neural-network) principles. Also we briefly describe currently available tools for agent-based-modeling, simu lation and animat ion.

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“…It seems to be necessary to explore a completely new mindset for programming, system control, and design. But not only engineers, physicists, computer scientists or biologists can profit from the study of complex systems and simulation tools currently being built and investigated (e.g., [20,14,4,11]). Artists can help tremendously in opening up new ways of approaching, presenting, and utilizing emergent system phenomena-in particular when interactive installations are involved, as is the case for our two SwarmArt exhibitions (Section 4).…”

Section: The Swarm Mindsetmentioning

confidence: 99%

SwarmArt

Boyd

Hushlak

Jacob

2004

Proceedings of the 12th Annual ACM International Conference on Multimedia

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This paper describes SwarmArt, a collaborative project between computer science and art, which resulted in two installations of interactive art that incorporates swarm intelligence. We describe the scientific context of the artwork, technical details of the video system, through which user interaction is controlled, and the realization of the swarmbased simulations, which were projected onto a large screen. Finally, we explain and illustrate our two recent SwarmArt installations in a Calgary gallery.

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Biomolecular swarms ? an agent-based model of the lactose operon

Cited by 27 publications

References 6 publications

Review of the computational models for the signaling pathway

Review of the computational models for the signaling pathway

Agent-based Models in Synthetic Biology: Tools for Simulation and Prospects

SwarmArt

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