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Ai4EComponentLib.jl(Ai4EComponentLib) is a component-base model library based on Julia language, which relies on the differential equation solver DifferentialEquations.jl and the symbolic modeling tool Modelingtoolkit.jl. To handle problems…
With the advent of high-throughput sequencing (HTS) in molecular biology and medicine, the need for scalable statistical solutions for modeling complex biological systems has become of critical importance. The increasing number of platforms…
We present NEP-PACK a novel open-source library for the solution of nonlinear eigenvalue problems (NEPs). The package provides a framework to represent NEPs, as well as efficient implementations of many state-of-the-art algorithms. The…
Structural identifiability is the theoretical ability to uniquely recover model parameters from ideal, noise-free data and is a prerequisite for reliable parameter estimation in epidemic modeling. Despite its importance for calibration and…
AtomTwin$.$jl is an open-source Julia package for developing and simulating quantum protocols, hardware configurations and building digital twins for neutral-atom quantum processors and related atomic quantum devices. AtomTwin operates…
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the…
We present an open source computational framework geared towards the efficient numerical investigation of open quantum systems written in the Julia programming language. Built exclusively in Julia and based on standard quantum optics…
Agent based modelling is a computational approach that aims to understand the behaviour of complex systems through simplified interactions of programmable objects in computer memory called agents. Agent based models (ABMs) are predominantly…
The integration of converter-interfaced generation (CIG) from renewable energy sources poses challenges to the stability and transient behavior of electric power systems. Understanding the dynamic behavior of low-inertia power systems is…
We present MultiObjectiveAlgorithms.jl, an open-source Julia library for solving multi-objective optimization problems written in JuMP. MultiObjectiveAlgorithms.jl implements a number of different solution algorithms, which all rely on an…
OptControl.jl(OptControl) implements that modeling optimal control problems with symbolic algebra system based on Julia language, and generates the corresponding numerical optimization codes to solve them with packages from Julia.…
We introduce a representation of any atom in any chemical environment for the generation of efficient quantum machine learning (QML) models of common electronic ground-state properties. The representation is based on scaled distribution…
We present IncompressibleNavierStokes.jl, an open-source Julia package for solving the incompressible Navier--Stokes equations on staggered Cartesian grids. The package features matrix-free, hardware-agnostic kernels that are compiled from…
Score-driven models, also known as generalized autoregressive score models, represent a class of observation-driven time series models. They possess powerful properties, such as the ability to model different conditional distributions and…
SymBoltz is a new Julia package for solving the linear Einstein-Boltzmann equations in cosmology. It features a symbolic-numeric interface for specifying equations, is free of approximation switching schemes, and is compatible with…
We present TNRKit, an open-source Julia package for Tensor Network Renormalization (TNR) of two- and three-dimensional classical statistical models and Euclidean lattice field theories. Built on top of TensorKit, it provides a…
The MPSDynamics.jl package provides an easy to use interface for performing open quantum systems simulations at zero and finite temperatures. The package has been developed with the aim of studying non-Markovian open system dynamics using…
We present BKP, a user-friendly and extensible R package that implements the Beta Kernel Process (BKP) -- a fully nonparametric and computationally efficient framework for modeling spatially varying binomial probabilities. The BKP model…
In this paper we survey recent work on the use of statistical model checking techniques for biological applications. We begin with an overview of the basic modelling techniques for biochemical reactions and their corresponding stochastic…
We describe a molecule-oriented modelling approach based on a collection of Petri net models organized in the form of modules into a prototype database accessible through a web interface. The JAK/STAT signalling pathway with the extensive…