Related papers: The Community Simulator: A Python package for micr…
The far-reaching consequences of ecological interactions in the dynamics of biological communities remain an intriguing subject. For decades, competition has been a cornerstone in ecological processes, but mounting evidence shows that…
In a complex community, species continuously adapt to each other. On rare occasions, the adaptation of a species can lead to the extinction of others, and even its own. "Adaptive dynamics" is the standard mathematical framework to describe…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
We study a dynamical model of a population of cooperators and defectors whose actions have long-term consequences on environmental "commons" - what we term the "resource". Cooperators contribute to restoring the resource whereas defectors…
Real-world optimisation problems are often dynamic. Previously good solutions must be updated or replaced due to changes in objectives and constraints. It is often claimed that evolutionary algorithms are particularly suitable for dynamic…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
The potential effects of conservation actions on threatened species can be predicted using ensemble ecosystem models by forecasting populations with and without intervention. These model ensembles commonly assume stable coexistence of…
The Python ecosystem represents a global, data rich, technology-enabled network. By analyzing Python's dependency network, its top 14 most imported libraries and cPython (or core Python) libraries, this research finds clear evidence the…
Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…
Traditional models of climate change use complex systems of coupled equations to simulate physical processes across the Earth system. These simulations are highly computationally expensive, limiting our predictions of climate change and…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
Shared resources enhance productivity yet at the same time provide channels for biological and digital contamination, turning physical or digital hygiene into a cooperation dilemma prone to free-riding. Here we introduce a game of…
Many algorithms have been proposed in the last ten years for the discovery of dynamic communities. However, these methods are seldom compared between themselves. In this article, we propose a generator of dynamic graphs with planted…
Integrating population genetics into community ecology theory is a major goal in ecology and evolution, but analyzing the resulting models is computationally daunting. Here we describe sPEGG ($\underline{\textrm{s}}\textrm{imulating}$…
This article describes lcpy, an open-source python package that allows for advanced parametric Life Cycle Assessment (LCA) and Life Cycle Costing (LCC) analysis. The package is designed to allow the user to model a process with a flexible,…
Urbanism is no longer planned on paper thanks to powerful models and 3D simulation platforms. However, current work is not open to the public and lacks an optimisation agent that could help in decision making. This paper describes the…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based simulations are used widely to compute a number of individual…
In computer experiments, a mathematical model implemented on a computer is used to represent complex physical phenomena. These models, known as computer simulators, enable experimental study of a virtual representation of the complex…