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\"If you're just learning how to program Julia is an excellent JIT-compiled, dynamically typed language with a clean syntax. This hands-on guide uses Julia 1.0 to walk you through programming one step at a time, beginning with basic programming concepts before moving on to more advanced capabilities, such as creating new types and multiple dispatch. Designed from the beginning for high performance, Julia is a general-purpose language ideal for not only numerical analysis and computational science but also web programming and scripting. Through exercises in each chapter, you'll try not programming concepts as you learn them. \"Think Julia\" is perfect for students at the high school or college level as well as self-learners and professionals who need to learn programing basics.\"-- Provided by publisher

The conservation field is experiencing a rapid increase in the amount, variety, and quality of spatial data that can help us understand species movement and landscape connectivity patterns. As interest grows in more dynamic representations of movement potential, modelers are often limited by the capacity of their analytic tools to handle these datasets. Technology developments in software and high-performance computing are rapidly emerging in many fields, but uptake within conservation may lag, as our tools or our choice of computing language can constrain our ability to keep pace. We recently updated Circuitscape, a widely used connectivity analysis tool developed by Brad McRae and Viral Shah, by implementing it in Julia, a high-performance computing language. In this initial re-code (Circuitscape 5.0) and later updates, we improved computational efficiency and parallelism, achieving major speed improvements, and enabling assessments across larger extents or with higher resolution data. Here, we reflect on the benefits to conservation of strengthening collaborations with computer scientists, and extract examples from a collection of 572 Circuitscape applications to illustrate how through a decade of repeated investment in the software, applications have been many, varied, and increasingly dynamic. Beyond empowering continued innovations in dynamic connectivity, we expect that faster run times will play an important role in facilitating co-production of connectivity assessments with stakeholders, increasing the likelihood that connectivity science will be incorporated in land use decisions.

In this paper we present the development of an energy and power system modelling, simulation, and analysis (ePowerSim.jl) package in Julia programming language. ePowerSim.jl is designed to present a uniform data interface for static, quasi-static, dynamic analysis, as well as network operation optimisation. It provides a co-simulation framework for the further development and experimentation of various types of models of electric power systems components or abstract entities that have mathematical formalism or data representation. ePowerSim.jl makes extensive use of cutting edge packages such as DifferentialEquations.jl, Dataframes.jl, NamedTupleTools.jl, Helics.jl, ForwardDiff.jl, JuMP.jl, and BifurcationKit just to mention a few in the Julia ecosystem. Models of synchronous generator, synchronous condenser, excitation systems, and governors developed in the package were used to model IEEE 9 bus and IEEE 14 bus test networks and subsequently validated by a real-time digital simulator of electric power systems (RTDS). The results obtains for static and dynamic models simulation in ePowerSim.jl show a close match with a simulation of the same system in RTDS. A maximum error of 0.00001 pu and 0.0001 pu were obtained for steady states and transient state respectively. Similarly, a maximum deviation of 0.0001 pu was obtained during validation for voltage magnitude during transient state at buses in the network.

As the dimensionality, throughput and complexity of cytometry data increases, so does the demand for user-friendly, interactive analysis tools that leverage high-performance machine learning frameworks. Here we introduce FlowAtlas: an interactive web application that enables dimensionality reduction of cytometry data without down-sampling and that is compatible with datasets stained with non-identical panels. FlowAtlas bridges the user-friendly environment of FlowJo and computational tools in Julia developed by the scientific machine learning community, eliminating the need for coding and bioinformatics expertise. New population discovery and detection of rare populations in FlowAtlas is intuitive and rapid. We demonstrate the capabilities of FlowAtlas using a human multi-tissue, multi-donor immune cell dataset, highlighting key immunological findings. FlowAtlas is available at https://github.com/gszep/FlowAtlas.jl.git .

A new software package for the Julia language, CountTimeSeries.jl, is under review, which provides likelihood based methods for integer-valued time series. The package’s functionalities are showcased in a simulation study on finite sample properties of Maximum Likelihood (ML) estimation and three real-life data applications. First, the number of newly infected COVID-19 patients is predicted. Then, previous findings on the need for overdispersion and zero inflation are reviewed in an application on animal submissions in New Zealand. Further, information criteria are used for model selection to investigate patterns in corporate insolvencies in Rhineland-Palatinate. Theoretical background and implementation details are described, and complete code for all applications is provided online. The CountTimeSeries package is available at the general Julia package registry.

The paper proposes finite element method algorithm implemented in Julia programming language. The main features of Julia programming language are described. The results of Kirsch problem solution are presented. Comparing obtained results with appropriate calculations with open-source finite element software Code Aster are also presented.

The open-source code PSSFSS for analysis and design of polarization selective surfaces (PSSs), and frequency selective surfaces (FSSs) is presented, beginning with an introduction to the Julia programming language in which the code is written. Analysis methods and algorithms used in PSSFSS are described, highlighting features of Julia that make it attractive for developing this type of application. Usage examples illustrate the code’s ease of use, speed, and accuracy.

The Anaerobic Digestion Model 1 is the quasi-industry standard for modelling anaerobic digestion, and it has seen several new implementations in recent years. It is assumed that these implementations would give the same results; however, a thorough comparison of these implementations has never been reported. This paper considers four different implementations of ADM1: one in Julia, one in Java, and two in Python. The Julia code is a de novo implementation of the ODE formulation of ADM1 that is reported here for the first time. The existing Java and Python codes implement the more common DAE formulation. Therefore, this paper also examines how DAE implementations compare to ODE implementations in terms of computational speed as well as solutions returned. As expected, the ODE and DAE forms both return comparable solutions. However, contrary to popular belief, the Julia ODE implementation is faster than the DAE implementations, namely by one to three orders of magnitude of compute time, depending on the simulation scenario and the reference implementation used for comparison.

Many scientific problems focus on observed patterns of change or on how to design a system to achieve particular dynamics. Those problems often require fitting differential equation models to target trajectories. Fitting such models can be difficult because each evaluation of the fit must calculate the distance between the model and target patterns at numerous points along a trajectory. The gradient of the fit with respect to the model parameters can be challenging to compute. Recent technical advances in automatic differentiation through numerical differential equation solvers potentially change the fitting process into a relatively easy problem, opening up new possibilities to study dynamics. However, application of the new tools to real data may fail to achieve a good fit. This article illustrates how to overcome a variety of common challenges, using the classic ecological data for oscillations in hare and lynx populations. Models include simple ordinary differential equations (ODEs) and neural ordinary differential equations (NODEs), which use artificial neural networks to estimate the derivatives of differential equation systems. Comparing the fits obtained with ODEs versus NODEs, representing small and large parameter spaces, and changing the number of variable dimensions provide insight into the geometry of the observed and model trajectories. To analyze the quality of the models for predicting future observations, a Bayesian‐inspired preconditioned stochastic gradient Langevin dynamics (pSGLD) calculation of the posterior distribution of predicted model trajectories clarifies the tendency for various models to underfit or overfit the data. Coupling fitted differential equation systems with pSGLD sampling provides a powerful way to study the properties of optimization surfaces, raising an analogy with mutation‐selection dynamics on fitness landscapes. New computational methods from machine learning and artificial neural networks, such as automatic differentiation, enhance computational approaches to the study of ecological dynamics. This article illustrates the power of these new methods by fitting differential equations to the classic hare‐lynx population fluctuations. This article also applies another technical computational innovation, preconditioned stochastic gradient Langevin dynamics, for the Bayesian analysis of parameter fits to the data.

Transcription factors (TFs) affect the production of mRNAs. In essence, the TFs form a large computational network that controls many aspects of cellular function. This article introduces a computational method to optimize TF networks. The method extends recent advances in artificial neural network optimization. In a simple example, computational optimization discovers a four-dimensional TF network that maintains a circadian rhythm over many days, successfully buffering strong stochastic perturbations in molecular dynamics and entraining to an external day–night signal that randomly turns on and off at intervals of several days. This work highlights the similar challenges in understanding how computational TF and neural networks gain information and improve performance.