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The study of reaction times and their underlying cognitive processes is an important field in Psychology. Reaction times are usually modeled through the ex-Gaussian distribution, because it provides a good fit to multiple empirical data.…

We present mechanoChemML, a machine learning software library for computational materials physics. mechanoChemML is designed to function as an interface between platforms that are widely used for machine learning on one hand, and others for…

Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST ``digital northern'', are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these…

Whole Slide Image (WSI) analysis plays a crucial role in modern digital pathology, enabling large-scale feature extraction from tissue samples. However, traditional feature extraction pipelines based on tools like CellProfiler often involve…

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…

TensorX is a Python library for prototyping, design, and deployment of complex neural network models in TensorFlow. A special emphasis is put on ease of use, performance, and API consistency. It aims to make available high-level components…

We present here the first release of the open-source python package ExoTETHyS, which aims to provide a stand-alone set of tools for modeling spectro-photometric observations of the transiting exoplanets. In particular, we describe: (1) a…

Computational meshes, as a way to partition space, form the basis of much of PDE simulation technology, for instance for the finite element and finite volume discretization methods. In complex simulations, we are often driven to modify an…

This document summarizes the main concepts of the finite element (FE) theory and constitutive relations as implemented in the open-source code phase-field multiphysics materials simulator PHIMATS https://github.com/ahcomat/PHIMATS. PHIMATS…

AI automation tools need machine-readable hyperparameter schemas to define their search spaces. At the same time, AI libraries often come with good human-readable documentation. While such documentation contains most of the necessary…

We present DeepAL, a Python library that implements several common strategies for active learning, with a particular emphasis on deep active learning. DeepAL provides a simple and unified framework based on PyTorch that allows users to…

Normalizing flows model probability distributions through an expressive tractable density. They transform a simple base distribution, such as a Gaussian, through a sequence of invertible functions, which are referred to as layers. These…

FluidDyn is a project to foster open-science and open-source in the fluid dynamics community. It is thought of as a research project to channel open-source dynamics, methods and tools to do science. We propose a set of Python packages…

Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and Nextflow enable users to automate the…

Advances in high-throughput simulation (HTS) software enabled computational databases and big data to become common resources in materials science. However, while computational power is increasingly larger, software packages orchestrating…

TorchOptics is an open-source Python library for differentiable Fourier optics simulations, developed using PyTorch to enable GPU-accelerated tensor computations and automatic differentiation. It provides a comprehensive framework for…

This paper summarizes the development of mVEM, a MATLAB software package containing efficient and easy-following codes for various virtual element methods (VEMs) published in the literature. We explain in detail the numerical implementation…

PyKOALA is an innovative Python-based library designed to provide a robust and flexible framework for Integral Field Spectroscopy (IFS) data reduction. By addressing the complexities of transforming raw measurements into scientifically…

Parsl is a parallel programming library for Python that aims to make it easy to specify parallelism in programs and to realize that parallelism on arbitrary parallel and distributed computing systems. Parsl relies on developers annotating…

This manual describes a set of utilities developed for Lattice QCD computations. They are collectively called QCDUtils. They comprise a set of Python programs each of them with a specific function: download gauge ensembles from the public…