scholarly journals PhysiBoSS: a multi-scale agent based modelling framework integrating physical dimension and cell signalling

2018 ◽  
Author(s):  
Gaelle Letort ◽  
Arnau Montagud ◽  
Gautier Stoll ◽  
Randy Heiland ◽  
Emmanuel Barillot ◽  
...  
Keyword(s):  
Open Source ◽  
Cell Population ◽  
Cell Signalling ◽  
Genetic Alterations ◽  
Computationally Efficient ◽  
Agent Based ◽  
Cell Fate Decisions ◽  
Agent Based Modelling ◽  
Multi Scale ◽  
Link Type

AbstractDue to the complexity of biological systems, their heterogeneity, and the internal regulation of each cell and its surrounding, mathematical models that take into account cell signalling, cell population behaviour and the extracellular environment are particularly helpful to understand such complex systems. However, very few of these tools, freely available and computationally efficient, are currently available. To fill this gap, we present here our open-source software, PhysiBoSS, which is built on two available software packages that focus on different scales: intracellular signalling using continuous-time markovian Boolean modelling (MaBoSS) and multicellular behaviour using agent-based modelling (PhysiCell).The multi-scale feature of PhysiBoSS - its agent-based structure and the possibility to integrate any Boolean network to it - provide a flexible and computationally efficient framework to study heterogeneous cell population growth in diverse experimental set-ups. This tool allows one to explore the effect of environmental and genetic alterations of individual cells at the population level, bridging the critical gap from genotype to phenotype. PhysiBoSS thus becomes very useful when studying population response to treatment, mutations effects, cell modes of invasion or isomorphic morphogenesis events.To illustrate potential use of PhysiBoSS, we studied heterogeneous cell fate decisions in response to TNF treatment in a 2-D cell population and in a tumour cell 3-D spheroid. We explored the effect of different treatment regimes and the behaviour and selection of several resistant mutants. We highlighted the importance of spatial information on the population dynamics by considering the effect of competition for resources like oxygen. PhysiBoSS is freely available on GitHub (https://github.com/gletort/PhysiBoSS), and is distributed open source under the BSD 3-clause license. It is compatible with most Unix systems, and a Docker package (https://hub.docker.com/r/gletort/physiboss/) is provided to ease its deployment in other systems.

scholarly journals PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling

2018 ◽  
Vol 35 (7) ◽  
pp. 1188-1196 ◽  
Author(s):  
Gaelle Letort ◽  
Arnau Montagud ◽  
Gautier Stoll ◽  
Randy Heiland ◽  
Emmanuel Barillot ◽  
...  
Keyword(s):  
Cell Signalling ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Multi Scale ◽  
Modelling Framework

scholarly journals A multi-scale agent-based modelling framework for urban freight distribution

2017 ◽  
Vol 27 ◽  
pp. 188-196 ◽  
Author(s):  
André Alho ◽  
B.K. Bhavathrathan ◽  
Monique Stinson ◽  
Raja Gopalakrishnan ◽  
Diem-Trinh Le ◽  
...  
Keyword(s):  
Agent Based ◽  
Urban Freight ◽  
Agent Based Modelling ◽  
Multi Scale ◽  
Modelling Framework

scholarly journals The FLAME-accelerated Signalling Tool (FaST): A tool for facile parallelisation of flexible agent-based models of cell signalling

2019 ◽  
Author(s):  
Gavin Fullstone ◽  
Cristiano Guttà ◽  
Amatus Beyer ◽  
Markus Rehm
Keyword(s):  
Cell Signalling ◽  
Parallel Applications ◽  
Spatial Effects ◽  
Agent Based Models ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Central Processing ◽  
Innovative Tool ◽  
Graphical Processing ◽  
Complex Features

AbstractAgent-based modelling is particularly adept at modelling complex features of cell signalling pathways, where heterogeneity, stochastic and spatial effects are important, thus increasing our understanding of decision processes in biology in such scenarios. However, agent-based modelling often is computationally prohibitive to implement. Parallel computing, either on central processing units (CPUs) or graphical processing units (GPUs), can provide a means to improve computational feasibility of agent-based applications but generally requires specialist coding knowledge and extensive optimisation. In this paper, we address these challenges through the development and implementation of the FLAME-accelerated signalling tool (FaST), a software that permits easy creation and parallelisation of agent-based models of cell signalling, on CPUs or GPUs. FaST incorporates validated new agent-based methods, for accurate modelling of reaction kinetics and, as proof of concept, successfully converted an ordinary differential equation (ODE) model of apoptosis execution into an agent-based model. We finally parallelised this model through FaST on CPUs and GPUs resulting in an increase in performance of 5.8× (16 CPUs) and 53.9× respectively. The FaST takes advantage of the communicating X-machine approach used by FLAME and FLAME GPU to allow easy alteration or addition of functionality to parallel applications, but still includes inherent parallelisation optimisation. The FaST, therefore, represents a new and innovative tool to easily create and parallelise bespoke, robust, agent-based models of cell signalling.

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 New Therapeutic Opportunities for the Treatment of Squamous Cell Carcinomas: A Focus on Novel Driver Kinases

2021 ◽  
Vol 22 (6) ◽  
pp. 2831
Author(s):  
Ryan Bensen ◽  
John Brognard
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Cell Fate ◽  
Squamous Cell ◽  
Copy Number Gain ◽  
Genetic Alterations ◽  
Distal Portion ◽  
Squamous Cell Carcinomas ◽  
Cell Fate Decisions ◽  
Genetic Landscape

Squamous cell carcinomas of the lung, head and neck, esophagus, and cervix account for more than two million cases of cancer per year worldwide with very few targetable therapies available and minimal clinical improvement in the past three decades. Although these carcinomas are differentiated anatomically, their genetic landscape shares numerous common genetic alterations. Amplification of the third chromosome’s distal portion (3q) is a distinguishing genetic alteration in most of these carcinomas and leads to copy-number gain and amplification of numerous oncogenic proteins. This area of the chromosome harbors known oncogenes involved in squamous cell fate decisions and differentiation, including TP63, SOX2, ECT2, and PIK3CA. Furthermore, novel targetable oncogenic kinases within this amplicon include PRKCI, PAK2, MAP3K13, and TNIK. TCGA analysis of these genes identified amplification in more than 20% of clinical squamous cell carcinoma samples, correlating with a significant decrease in overall patient survival. Alteration of these genes frequently co-occurs and is dependent on 3q-chromosome amplification. The dependency of cancer cells on these amplified kinases provides a route toward personalized medicine in squamous cell carcinoma patients through development of small-molecules targeting these kinases.

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 An Interactive WebGIS Framework for Coastal Erosion Risk Management

2021 ◽  
Vol 9 (6) ◽  
pp. 567
Author(s):  
Alessandra Capolupo ◽  
Cristina Monterisi ◽  
Alessandra Saponieri ◽  
Fabio Addona ◽  
Leonardo Damiani ◽  
...  
Keyword(s):  
Open Source ◽  
3D Visualization ◽  
Erosion Risk ◽  
Innovative Strategies ◽  
Web Mapping ◽  
Natural Processes ◽  
Multi Scale ◽  
Interactive Interface ◽  
Multi Temporal ◽  
User Friendly

The Italian coastline stretches over about 8350 km, with 3600 km of beaches, representing a significant resource for the country. Natural processes and anthropic interventions keep threatening its morphology, moulding its shape and triggering soil erosion phenomena. Thus, many scholars have been focusing their work on investigating and monitoring shoreline instability. Outcomes of such activities can be largely widespread and shared with expert and non-expert users through Web mapping. This paper describes the performances of a WebGIS prototype designed to disseminate the results of the Italian project Innovative Strategies for the Monitoring and Analysis of Erosion Risk, known as the STIMARE project. While aiming to include the entire national coastline, three study areas along the regional coasts of Puglia and Emilia Romagna have already been implemented as pilot cases. This WebGIS was generated using Free and Open-Source Software for Geographic information systems (FOSS4G). The platform was designed by combining Apache http server, Geoserver, as open-source server and PostgreSQL (with PostGIS extension) as database. Pure javascript libraries OpenLayers and Cesium were implemented to obtain a hybrid 2D and 3D visualization. A user-friendly interactive interface was programmed to help users visualize and download geospatial data in several formats (pdf, kml and shp), in accordance with the European INSPIRE directives, satisfying both multi-temporal and multi-scale perspectives.

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.

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