Related papers: The Community Simulator: A Python package for micr…
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…
The analysis of the evolutionary dynamics of a population with many polymorphic loci is challenging since a large number of possible genotypes needs to be tracked. In the absence of analytical solutions, forward computer simulations are an…
We present a detailed model of collaboration in communities of practice and we examine its dynamical consequences for the group as a whole. We establish the existence of a novel mechanism that allows the community to naturally adapt to…
Ecosystems are among the most interesting and well-studied examples of self-organized complex systems. Community ecology, the study of how species interact with each other and the environment, has a rich tradition. Over the last few years,…
Community structure is pervasive in various real-world networks, portraying the strong local clustering of nodes. Unveiling the community structure of a network is deemed to a crucial step towards understanding the dynamics on the network.…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
A novel mathematical framework is proposed to describe the ecological and evolutionary consequences of consumer--resource interactions. Both the consumer and resource are assumed to consist of several (sub)species, which interact between…
We discuss the relevance of studying ecology within the framework of Complexity Science from a statistical mechanics approach. Ecology is concerned with understanding how systems level properties emerge out of the multitude of interactions…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
Algorithmic fairness has received considerable attention due to the failures of various predictive AI systems that have been found to be unfairly biased against subgroups of the population. Many approaches have been proposed to mitigate…
Simulation of population dynamics is a central research theme in computational biology, which contributes to understanding the interactions between predators and preys. Conventional mathematical tools of this theme, however, are incapable…
The use of third-party packages is becoming increasingly popular and has led to the emergence of large software package ecosystems with a maze of inter-dependencies. Since the reliance on these ecosystems enables developers to reduce…
Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering, and other research fields.…
In recent years, there has been growing interest in studying evolutionary games with environmental feedback. Previous studies exclusively focus on two-player games. However, extension to multi-player game is needed to study problems such as…
This document is due to appear as a chapter of the forthcoming Handbook of Approximate Bayesian Computation (ABC) by S. Sisson, L. Fan, and M. Beaumont. Here we describe some of the circumstances under which statistical ecologists might…
Many socio-economical critical domains (such as sustainability, public health, and disasters) are characterized by highly complex and dynamic systems, requiring data and model-driven simulations to support decision-making. Due to a large…
We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve…
Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities…
The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact not only with each other but indirectly through environmental effects, however…
Ecological systems can be seen as networks of interactions between individual, species, or habitat patches. A key feature of many ecological networks is their organization into modules, which are subsets of elements that are more connected…