Agent-Based Modelling in Multicellular Systems Biology

2020 ◽  
pp. 369-389
Author(s):  
Sara Montagna ◽  
Andrea Omicini

This chapter aims at discussing the content of multi-agent based simulation (MABS) applied to computational biology i.e., to modelling and simulating biological systems by means of computational models, methodologies, and frameworks. In particular, the adoption of agent-based modelling (ABM) in the field of multicellular systems biology is explored, focussing on the challenging scenarios of developmental biology. After motivating why agent-based abstractions are critical in representing multicellular systems behaviour, MABS is discussed as the source of the most natural and appropriate mechanism for analysing the self-organising behaviour of systems of cells. As a case study, an application of MABS to the development of Drosophila Melanogaster is finally presented, which exploits the ALCHEMIST platform for agent-based simulation.

Author(s):  
Sara Montagna ◽  
Andrea Omicini

This chapter aims at discussing the content of multi-agent based simulation (MABS) applied to computational biology i.e., to modelling and simulating biological systems by means of computational models, methodologies, and frameworks. In particular, the adoption of agent-based modelling (ABM) in the field of multicellular systems biology is explored, focussing on the challenging scenarios of developmental biology. After motivating why agent-based abstractions are critical in representing multicellular systems behaviour, MABS is discussed as the source of the most natural and appropriate mechanism for analysing the self-organising behaviour of systems of cells. As a case study, an application of MABS to the development of Drosophila Melanogaster is finally presented, which exploits the ALCHEMIST platform for agent-based simulation.


2019 ◽  
Vol 18 (1) ◽  
pp. 84-101 ◽  
Author(s):  
Najmeh Neshat ◽  
Hengameh Hadian ◽  
Somayeh Rahimi Alangi

Purpose Obviously, the development of a robust optimization framework is the main step in energy and climate policy. In other words, the challenge of energy policy assessment requires the application of approaches which recognize the complexity of energy systems in relation to technological, social, economic and environmental aspects. This paper aims to develop a two-sided multi-agent based modelling framework which endogenizes the technological learning mechanism to determine the optimal generation plan. In this framework, the supplier agents try to maximize their income while complying with operational, technical and market penetration rates constraints. A case study is used to illustrate the application of the proposed planning approach. The results showed that considering the endogenous technology cost reduction moves optimal investment timings to earlier planning years and influences the competitiveness of technologies. The proposed integrated approach provides not only an economical generation expansion plan but also a cleaner one compared to the traditional approach. Design/methodology/approach To the best of the authors’ knowledge, so far there has not been any agent-based generation expansion planning (GEP) incorporating technology learning mechanism into the modelling framework. The main contribution of this paper is to introduce a multi-agent based modelling for long-term GEP and undertakes to show how incorporating technological learning issues in supply agents behaviour modelling influence on renewable technology share in the optimal mix of technologies. A case study of the electric power system of Iran is used to illustrate the usefulness of the proposed planning approach and also to demonstrate its efficiency. Findings As seen, the share of the renewable technology agents (geothermal, hydropower, wind, solar, biomass and photovoltaic) in expanding generation increases from 10.2% in the traditional model to 13.5% in the proposed model over the planning horizon. Also, to incorporate technological learning in the supply agent behaviour leads to earlier involving of renewable technologies in the optimal plan. This increased share of the renewable technology agents is reasonable due to their decreasing investment cost and capability of cooperation in network reserve supply which leads to a high utilization factor. Originality/value To the best of the authors’ knowledge, so far there hasn’t been any agent-based GEP paying attention to this integrated approach. The main contribution of this paper is to introduce a multi-agent based modelling for long-term GEP and undertakes to show how incorporating technological learning issues in supply agents behaviour modelling influence on renewable technology share in the optimal mix of technologies. A case study of the electric power system of Iran is used to illustrate the usefulness of the proposed planning approach and also to demonstrate its efficiency.


2021 ◽  
Vol 12 (1) ◽  
pp. 18
Author(s):  
Lennart Adenaw ◽  
Markus Lienkamp

In order to electrify the transport sector, scores of charging stations are needed to incentivize people to buy electric vehicles. In urban areas with a high charging demand and little space, decision-makers are in need of planning tools that enable them to efficiently allocate financial and organizational resources to the promotion of electromobility. As with many other city planning tasks, simulations foster successful decision-making. This article presents a novel agent-based simulation framework for urban electromobility aimed at the analysis of charging station utilization and user behavior. The approach presented here employs a novel co-evolutionary learning model for adaptive charging behavior. The simulation framework is tested and verified by means of a case study conducted in the city of Munich. The case study shows that the presented approach realistically reproduces charging behavior and spatio-temporal charger utilization.


2019 ◽  
Vol 5 (1) ◽  
pp. 444-467
Author(s):  
Katherine A. Crawford

AbstractOstia, the ancient port of Rome, had a rich religious landscape. How processional rituals further contributed to this landscape, however, has seen little consideration. This is largely due to a lack of evidence that attests to the routes taken by processional rituals. The present study aims to address existing problems in studying processions by questioning what factors motivated processional movement routes. A novel computational approach that integrates GIS, urban network analysis, and agent-based modelling is introduced. This multi-layered approach is used to question how spectators served as attractors in the creation of a processional landscape using Ostia’s Campo della Magna Mater as a case study. The analysis of these results is subsequently used to gain new insight into how a greater processional landscape was created surrounding the sanctuary of the Magna Mater.


Author(s):  
Joseph Kim ◽  
Tomoyuki Takabatake ◽  
Ioan NISTOR ◽  
Tomoya Shibayama

Soft measures such as evacuation planning are recommended to mitigate the loss of life during tsunamis. Two types of evacuation models are widely used: (1) Agent-based modelling (ABM) defines sets of rules that individual agents in a simulation follow during a simulated evacuation. (2) Geographical information systems (GIS) are more accessible to city planners, but cannot incorporate the dynamic behaviours found in ABMs. The two evacuation modelling methodologies were compared through a case study by assessing the state of evacuation preparedness and investigating potential mitigation options. The two models showed different magnitudes for mortality rates and facility demand but had similar trends. Both models agreed on the best solution to reduce the loss of life for the community. GIS may serve as a useful tool for initial investigation or as a validation tool for ABMs. ABMs are recommended for use when modelling evacuation until GIS methodologies are further developed.


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