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Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often…
Combustion kinetic modeling is an integral part of combustion simulation, and extensive studies have been devoted to developing both high fidelity and computationally affordable models. Despite these efforts, modeling combustion kinetics is…
Simulation of non-adiabatic dynamics of a quantum system coupled to dissipative environments poses significant challenges. New sophisticated methods are regularly being developed with an eye towards moving to larger systems and more…
Agent based modelling is a simulation method in which autonomous agents interact with their environment and one another, given a predefined set of rules. It is an integral method for modelling and simulating complex systems, such as…
Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise…
HarmonicBalance.jl is a publicly available Julia package designed to simplify and solve systems of periodic time-dependent nonlinear ordinary differential equations. Time dependence of the system parameters is treated with the harmonic…
In this paper we present GridapTopOpt, an extendable framework for level set-based topology optimisation that can be readily distributed across a personal computer or high-performance computing cluster. The package is written in Julia and…
Proprietary closed-source software is still the norm in advanced process control. Transparency and reproducibility are key aspects of scientific research. Free and open-source toolkit can contribute to the development, sharing and…
TypedMatrices.jl is a Julia package to organize test matrices. By default, the package comes with a number of built-in matrices and interfaces to help users select test cases based on their properties. The package is designed to be…
Gaussian processes are a class of flexible nonparametric Bayesian tools that are widely used across the sciences, and in industry, to model complex data sources. Key to applying Gaussian process models is the availability of well-developed…
The importance of computers is continually increasing in radiotherapy. Efficient algorithms, implementations and the ability to leverage advancements in computer science are crucial to improve cancer care even further and deliver the best…
BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these…
This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models \ expressed using Systems Biology Markup Language (SBML). SBML is the most widely…
Increasing emphasis on data and quantitative methods in the biomedical sciences is making biological research more computational. Collecting, curating, processing, and analysing large genomic and imaging data sets poses major computational…
MacroEnergy.jl (aka Macro) is an open-source framework for multi-sector capacity expansion modeling and analysis of macro-energy systems. It is written in Julia and uses the JuMP package to interface with a wide range of mathematical…
Predicting the degradation processes of molecules over long timescales is a key aspect of industrial materials design. However, it is made computationally challenging by the need to construct large networks of chemical reactions that are…
We present the Julia package HomotopyContinuation.jl, which provides an algorithmic framework for solving polynomial systems by numerical homotopy continuation. We introduce the basic capabilities of the package and demonstrate the software…
SpiDy.jl solves the non-Markovian stochastic dynamics of interacting classical spin vectors and harmonic oscillator networks in contact with a dissipative environment. The methods implemented allow the user to include arbitrary memory…
As astronomical data grows in volume and complexity, the scalability of analysis software becomes increasingly important. At the same time, astrophysics analysis software relies heavily on open-source contributions, so languages and tools…
Agent-based models (ABMs) offer a powerful framework for understanding complex systems. However, their computational demands often become a significant barrier as the number of agents and complexity of the simulation increase. Traditional…