scholarly journals Adapting principles of developmental biology and agent-based modelling for automated urban residential layout design

2017 ◽  
Vol 45 (5) ◽  
pp. 973-993 ◽  
Author(s):  
Yuchao Sun ◽  
John Taplin
Keyword(s):  
Developmental Biology ◽  
Layout Design ◽  
Residential Density ◽  
Local Interactions ◽  
Agent Based ◽  
Gene Set ◽  
Agent Based Modelling ◽  
Full Development ◽  
Local Contexts ◽  
Cell Expression

The objective is to automate the design of residential layouts as an aid for planners dealing with complex situations. The algorithm COmputational Urban Layout Design, applied to sites with various shapes, is guided by the goal of many mutually accessible residences and can be set to generate orthogonal or irregular road layouts. Using biological principles of genomic equivalence, conditional differentiation and induction, it grows from an embryonic ‘adaptive cell’ into a plan. Cells are ‘genetically identical’ with full development potential and can simultaneously lay roads and residential lots, using the gene set to change cell expression and adapt to local contexts. Cells can be seen as self-propagating agents that sort out their dependencies through local interactions. When COmputational Urban Layout Design is set to grow a non-orthogonal layout, the plan has winding roads and irregular residential lots. Such a plan achieves the objective of relatively high residential density and accessibility, leading to walkable and coherent communities.

Agent-Based Modelling in Multicellular Systems Biology

2020 ◽  
pp. 369-389
Author(s):  
Sara Montagna ◽  
Andrea Omicini
Keyword(s):  
Developmental Biology ◽  
Drosophila Melanogaster ◽  
Systems Biology ◽  
Computational Models ◽  
The Self ◽  
Agent Based Simulation ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Multi Agent

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.

Agent-Based Modelling in Multicellular Systems Biology

2017 ◽  
pp. 159-178 ◽  
Author(s):  
Sara Montagna ◽  
Andrea Omicini
Keyword(s):  
Developmental Biology ◽  
Drosophila Melanogaster ◽  
Systems Biology ◽  
Computational Models ◽  
The Self ◽  
Agent Based Simulation ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Multi Agent

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.

scholarly journals Coalescent models for developmental biology and the spatio-temporal dynamics of growing tissues

2016 ◽  
Vol 13 (117) ◽  
pp. 20160112 ◽  
Author(s):  
Patrick Smadbeck ◽  
Michael P. H. Stumpf
Keyword(s):  
Developmental Biology ◽  
Large Scale ◽  
Cell Tracking ◽  
Temporal Dynamics ◽  
Growth Models ◽  
Lineage Tracing ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Spatio Temporal ◽  
Large Scale Simulations

Development is a process that needs to be tightly coordinated in both space and time. Cell tracking and lineage tracing have become important experimental techniques in developmental biology and allow us to map the fate of cells and their progeny. A generic feature of developing and homeostatic tissues that these analyses have revealed is that relatively few cells give rise to the bulk of the cells in a tissue; the lineages of most cells come to an end quickly. Computational and theoretical biologists/physicists have, in response, developed a range of modelling approaches, most notably agent-based modelling. These models seem to capture features observed in experiments, but can also become computationally expensive. Here, we develop complementary genealogical models of tissue development that trace the ancestry of cells in a tissue back to their most recent common ancestors. We show that with both bounded and unbounded growth simple, but universal scaling relationships allow us to connect coalescent theory with the fractal growth models extensively used in developmental biology. Using our genealogical perspective, it is possible to study bulk statistical properties of the processes that give rise to tissues of cells, without the need for large-scale simulations.

scholarly journals Agent-based Modelling and Simulation for Circular Business Model Experimentation

2021 ◽  
pp. 200055
Author(s):  
Kasper P.H. Lange ◽  
Gijsbert Korevaar ◽  
Inge F. Oskam ◽  
Igor Nikolic ◽  
Paulien M. Herder
Keyword(s):  
Business Model ◽  
Modelling And Simulation ◽  
Agent Based ◽  
Agent Based Modelling

scholarly journals Skin Stem Cell Hypotheses and Long Term Clone Survival – Explored Using Agent-based Modelling

2013 ◽  
Vol 3 (1) ◽  
Author(s):  
X. Li ◽  
A. K. Upadhyay ◽  
A. J. Bullock ◽  
T. Dicolandrea ◽  
J. Xu ◽  
...  
Keyword(s):  
Stem Cell ◽  
Agent Based ◽  
Agent Based Modelling

scholarly journals Visualising Ostia’s Processional Landscape Through a Multi-Layered Computational Approach: Case Study of the Cult of the Magna Mater

2019 ◽  
Vol 5 (1) ◽  
pp. 444-467
Author(s):  
Katherine A. Crawford
Keyword(s):  
Network Analysis ◽  
Computational Approach ◽  
Urban Network ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Existing Problems ◽  
Layered Approach ◽  
Religious Landscape ◽  
Insight Into

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.

A Comparison between Agent-Based and GIS-Based Tsunami Evacuation Simulations: A Case Study for Tofino, BC

2021 ◽  
Author(s):  
Joseph Kim ◽  
Tomoyuki Takabatake ◽  
Ioan NISTOR ◽  
Tomoya Shibayama
Keyword(s):  
Information Systems ◽  
Geographical Information Systems ◽  
Mortality Rates ◽  
Geographical Information ◽  
Evacuation Planning ◽  
Loss Of Life ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Validation Tool

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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