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

2015 ◽  
Author(s):  
Patrick Smadbeck ◽  
Michael P.H. Stumpf
Keyword(s):  
Developmental Biology ◽  
Population Genetics ◽  
Large Scale ◽  
Cell Tracking ◽  
Temporal Dynamics ◽  
Growth Models ◽  
Tissue Growth ◽  
Lineage Tracing ◽  
Space And Time ◽  
Spatio Temporal

Development is a process that needs to 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 in both space and time. A generic feature of developing (as well as 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 fairly quickly. This has spurned the interest also of computational and theoretical biologists/physicists who have developed a range of modelling -- perhaps most notably are the agent-based modelling (ABM) --- approaches. These can become computationally prohibitively expensive but seem to capture some of the features observed in experiments. Here we develop a complementary perspective that allows us to understand the dynamics leading to the formation of a tissue (or colony of cells). Borrowing from the rich population genetics literature we develop genealogical models of tissue development that trace the ancestry of cells in a tissue back to their most recent common ancestors. We apply this approach to tissues that grow under confined conditions --- as would, for example, be appropriate for the neural crest --- and unbounded growth --- illustrative of the behaviour of 2D tumours or bacterial colonies. The classical coalescent model from population genetics is readily adapted to capture tissue genealogies for different models of tissue growth and development. We show that simple but universal scaling relationships allow us to establish relationships between the coalescent and different fractal growth models that have been extensively studied in many different contexts, including developmental biology. Using our genealogical perspective we are able to study the statistical properties of the processes that give rise to tissues of cells, without the need for large-scale simulations.

Improving the Efficiency of Large-Scale Agent-Based Models Using Compression Techniques

2012 ◽  
pp. 301-326
Author(s):  
Mitchell Welch ◽  
Paul Kwan ◽  
A.S.M. Sajeev ◽  
Graeme Garner
Keyword(s):  
Large Scale ◽  
Agent Based Models ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Livestock Disease ◽  
Interacting Agents ◽  
National Model ◽  
Complex Phenomena ◽  
Modelling System

Agent-based modelling is becoming a widely used approach for simulating complex phenomena. By making use of emergent behaviour, agent based models can simulate systems right down to the most minute interactions that affect a system’s behaviour. In order to capture the level of detail desired by users, many agent based models now contain hundreds of thousands and even millions of interacting agents. The scale of these models makes them computationally expensive to operate in terms of memory and CPU time, limiting their practicality and use. This chapter details the techniques for applying Dynamic Hierarchical Agent Compression to agent based modelling systems, with the aim of reducing the amount of memory and number of CPU cycles required to manage a set of agents within a model. The scheme outlined extracts the state data stored within a model’s agents and takes advantage of redundancy in this data to reduce the memory required to represent this information. The techniques show how a hierarchical data structure can be used to achieve compression of this data and the techniques for implementing this type of structure within an existing modelling system. The chapter includes a case study that outlines the practical considerations related to the application of this scheme to Australia’s National Model for Emerging Livestock Disease Threats that is currently being developed.

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.

scholarly journals Arctic avian predators synchronise their spring migration with the northern progression of snowmelt

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Teja Curk ◽  
Ivan Pokrovsky ◽  
Nicolas Lecomte ◽  
Tomas Aarvak ◽  
David F. Brinker ◽  
...  
Keyword(s):  
Large Scale ◽  
Temporal Dynamics ◽  
The Arctic ◽  
Migratory Species ◽  
Migration Patterns ◽  
Predator Species ◽  
Movement Data ◽  
Breeding Grounds ◽  
Spatio Temporal ◽  
Spring Snowmelt

Abstract Migratory species display a range of migration patterns between irruptive (facultative) to regular (obligate), as a response to different predictability of resources. In the Arctic, snow directly influences resource availability. The causes and consequences of different migration patterns of migratory species as a response to the snow conditions remains however unexplored. Birds migrating to the Arctic are expected to follow the spring snowmelt to optimise their arrival time and select for snow-free areas to maximise prey encounter en-route. Based on large-scale movement data, we compared the migration patterns of three top predator species of the tundra in relation to the spatio-temporal dynamics of snow cover. The snowy owl, an irruptive migrant, the rough-legged buzzard, with an intermediary migration pattern, and the peregrine falcon as a regular migrant, all followed, as expected, the spring snowmelt during their migrations. However, the owl stayed ahead, the buzzard stayed on, and the falcon stayed behind the spatio-temporal peak in snowmelt. Although none of the species avoided snow-covered areas, they presumably used snow presence as a cue to time their arrival at their breeding grounds. We show the importance of environmental cues for species with different migration patterns.

scholarly journals Early alterations of large-scale brain networks temporal dynamics in young children with autism

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Aurélie Bochet ◽  
Holger Franz Sperdin ◽  
Tonia Anahi Rihs ◽  
Nada Kojovic ◽  
Martina Franchini ◽  
...  
Keyword(s):  
Large Scale ◽  
Developmental Stages ◽  
Temporal Dynamics ◽  
Brain Networks ◽  
Autism Spectrum ◽  
Brain Network ◽  
Clustering Methods ◽  
Early Developmental Stages ◽  
Spatio Temporal ◽  
Early Developmental

AbstractAutism spectrum disorders (ASD) are associated with disruption of large-scale brain network. Recently, we found that directed functional connectivity alterations of social brain networks are a core component of atypical brain development at early developmental stages in ASD. Here, we investigated the spatio-temporal dynamics of whole-brain neuronal networks at a subsecond scale in 113 toddlers and preschoolers (66 with ASD) using an EEG microstate approach. We first determined the predominant microstates using established clustering methods. We identified five predominant microstate (labeled as microstate classes A–E) with significant differences in the temporal dynamics of microstate class B between the groups in terms of increased appearance and prolonged duration. Using Markov chains, we found differences in the dynamic syntax between several maps in toddlers and preschoolers with ASD compared to their TD peers. Finally, exploratory analysis of brain–behavioral relationships within the ASD group suggested that the temporal dynamics of some maps were related to conditions comorbid to ASD during early developmental stages.

scholarly journals Spatio-Temporal Dynamics of Feed Grain Demand of Dairy Cows in China

2020 ◽  
Vol 12 (2) ◽  
pp. 663 ◽  
Author(s):  
Chao Yang Dong ◽  
Bei Bei Ma ◽  
Chun Xia LU
Keyword(s):  
Dairy Cows ◽  
Dairy Cow ◽  
Large Scale ◽  
Temporal Dynamics ◽  
Hot Spot ◽  
Market Environment ◽  
Relative Level ◽  
Resource Endowment ◽  
Spatio Temporal ◽  
Feeding Technology

As the income of urban and rural residents has increased in recent decades in China, dairy products have become an important part of the Chinese diet. Therefore, keeping up with the growing demand for feed grain for dairy cows is a critical issue of feed grain security. Utilizing traditional statistical and spatial statistical methods, this study analyzes the spatio-temporal dynamics of dairy cow feed grain (DCFG) demand on the provincial, regional, and national levels across China from 1990 to 2016. Additionally, this paper explores the impacts of various factors on the spatio-temporal dynamics of DCFG demand using the Geo-Detector method. The results demonstrate that: (1) the temporal dynamics of DCFG demand can be divided into three stages of slow growth, rapid growth, and high-level stability, and the relative level of DCFG demand in the whole animal husbandry tends to decline; (2) at the regional and national levels, the spatial concentration of high DCFG demand has intensified; in particular, North China was the region where the largest demand for DCFG was localized and was increasing at the highest rate; (3) based on the hot spot analysis of provincial DCFG demand, the high and low demand provinces of DCFG have sharp characteristic contrast from north to south China; (4) the spatio-temporal dynamics of DCFG demand in China were essentially co-affected by the four groups of factors (e.g., resource endowment, feeding scale, feeding technology, and market environment), of which resource endowment and feeding scale were the dominant factors. Therefore, in the future, dairy cow feeding in China should promote grain-saving feeding technology, improve the utilization of forage, expand large-scale feeding, and create a good market environment to ensure the reasonable development and sustainability of DCFG demand.

An Analysis Technique of Evacuation Simulation Using an Array DBMS

2018 ◽  
Vol 13 (2) ◽  
pp. 338-346
Author(s):  
Yusuke Kawai ◽  
Jing Zhao ◽  
Kento Sugiura ◽  
Yoshiharu Ishikawa ◽  
Yukiko Wakita ◽  
...  
Keyword(s):  
Query Processing ◽  
Large Scale ◽  
Evacuation Simulation ◽  
Array Data ◽  
Interactive Analysis ◽  
Large Scale Data ◽  
Analysis Technique ◽  
Spatio Temporal ◽  
Efficient Query Processing ◽  
Large Scale Simulations

Today, large-scale simulations are thriving because of the increase of computating performance and storage capacity. Understanding the results of these simulations is not easy, and hence, support for interactive and exploratory analysis is becoming more important. This study focuses on spatio-temporal simulations and attempts to develop an analysis technology to support them. It uses a database system for supporting interactive analysis of large-scale data. Since the data gained via spatio-temporal simulations is not suitable for management in a relational DBMS (RDBMS), this study uses an array DBMS, a type of DBMS that has been garnering increased attention in recent years. An array DBMS is designed for the management of large-scale array data; it provides a logical model for array data, yet it also supports efficient query processing. SciDB is used as our specific array DBMS in this paper. This study targets disaster evacuation simulation data and demonstrates via experimentation that the query-processing functions offered by an array DBMS provide effective analysis support.

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