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Formal modelling of Multi-Agent Systems (MAS) is a challenging task due to high complexity, interaction, parallelism and continuous change of roles and organisation between agents. In this paper we record our research experience on formal…
The prediction of the behavior of the disease, the level of affectation in a population and the ways to control it are the most important aspects studied by epidemiology using tools such as historical data and mathematical models. So, our…
We apply tools from topological data analysis to two mathematical models inspired by biological aggregations such as bird flocks, fish schools, and insect swarms. Our data consists of numerical simulation output from the models of Vicsek…
Stochastic modelling provides an indispensable tool for understanding how random events at the molecular level influence cellular functions. In practice, the common challenge is to calibrate a large number of model parameters against the…
Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown,…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
During development, highly ordered structures emerge as cells collectively coordinate with each other. While recent advances have clarified how individual cells process and respond to external signals, understanding collective cellular…
Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript…
This chapter reviews the purpose and use of models from the field of complex systems and, in particular, the implications of trying to use models to understand or make decisions within complex situations, such as policy makers usually face.…
The ability to represent intracellular biochemical dynamics via deterministic and stochastic modelling is one of the crucial components to move biological sciences in the observe-predict-control-design knowledge ladder. Compared to the…
Modeling biological processes is a highly demanding task because not all processes are fully understood. Mathematical models allow us to test hypotheses about possible mechanisms of biological processes. The mathematical mechanisms…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
Mathematical models are vital interpretive and predictive tools used to assist in the understanding of cell migration. There are typically two approaches to modelling cell migration: either micro-scale, discrete or macro-scale, continuum.…
In digital pathology, the spatial context of cells is important for cell classification, cancer diagnosis and prognosis. To model such complex cell context, however, is challenging. Cells form different mixtures, lineages, clusters and…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…
In an ecological context, panel data arise when time series measurements are made on a collection of ecological processes. Each process may correspond to a spatial location for field data, or to an experimental ecosystem in a designed…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
The absence of a conventional association between the cell-cell cohabitation and its emergent dynamics into cliques during development has hindered our understanding of how cell populations proliferate, differentiate, and compete, i.e. the…
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting cellular heterogeneity in reference tissues and in disease. This new wave of molecular data has highlighted the expected diversity of…