The eukaryotic endomembrane system is controlled by small GTPases of the Rab family,
which are activated at defined times and locations in a switch-like manner. While this switch …

Stochastic modeling has become an essential tool for studying biochemical reaction
networks. There is a growing need for user-friendly and feature-complete software for model …

Differential sensitivity analysis is indispensable in fitting parameters, understanding
uncertainty, and forecasting the results of both thought and lab experiments. Although there …

This paper presents an approach towards computationally efficient discrete-event-simulation
designed to take advantage of high-performance computing architecture. We demonstrate …

Modeling biochemical systems can provide insights into behaviors that are difficult to
observe or understand. It requires software, programming, and understanding of the system …

We present sismonr, an R package for an integral generation and simulation of in silico
biological systems. The package generates gene regulatory networks, which include protein …

We introduce Pathogen. jl for simulation and inference of transmission network individual
level models (TN-ILMs) of infectious disease spread in continuous time. TN-ILMs can be …

Interacting Particle Systems (IPSs) are used to model spatio-temporal stochastic systems in
many disparate areas of science. We design an algorithmic framework that reduces IPS …

This project investigated mathematical optimisation methods to improve open-pit mine
management, on a minute-to-minute scale. High-performance computer simulations were …

There exists a wide variety of stochastic simulators written in Julia for the purposes of
modeling natural, social, or economic phenomena [1–6]. However, these simulators are not …