SoftwareX

Article	Citations
Open data from the first and second observing runs of Advanced LIGO and Advanced Virgo	265
CBE Thermal Comfort Tool: Online tool for thermal comfort calculations and visualizations	165
ADIOS 2: The Adaptable Input Output System. A framework for high-performance data management	99
Mutation++	77
ixpeobssim: A simulation and analysis framework for the imaging X-ray polarimetry explorer	77
Sherpa: Robust hyperparameter optimization for machine learning	75
pythermalcomfort: A Python package for thermal comfort research	72
sDNA: 3-d spatial network analysis for GIS, CAD, Command Line & Python	55
The Contiki-NG open source operating system for next generation IoT devices	50
Xcompact3D: An open-source framework for solving turbulence problems on a Cartesian mesh	48
2.0 - MOOSE: Enabling massively parallel multiphysics simulation	47
Omicron: A tool to characterize transient noise in gravitational-wave detectors	41
PESummary: The code agnostic Parameter Estimation Summary page builder	41
coherent WaveBurst, a pipeline for unmodeled gravitational-wave data analysis	37
MUSEN: An open-source framework for GPU-accelerated DEM simulations	36
GstLAL: A software framework for gravitational wave discovery	36
CemrgApp: An interactive medical imaging application with image processing, computer vision, and machine learning toolkits for cardiovascular research	34
drtsans: The data reduction toolkit for small-angle neutron scattering at Oak Ridge National Laboratory	32
GWpy: A Python package for gravitational-wave astrophysics	30
MOBOpt — multi-objective Bayesian optimization	30
ECGdeli - An open source ECG delineation toolbox for MATLAB	29
EMPIRE: An open-source model based on multi-horizon programming for energy transition analyses	29
life: A flexible, high performance library for the numerical solution of complex finite element problems	28
SPARC: Simulation Package for Ab-initio Real-space Calculations	27
PADRES: Tool for PrivAcy, Data REgulation and Security	27

DynaProg: Deterministic Dynamic Programming solver for finite horizon multi-stage decision problems	27
Mcfly: Automated deep learning on time series	26
“photosearcher” package in R: An accessible and reproducible method for harvesting large datasets from Flickr	26
TFMLAB: A MATLAB toolbox for 4D traction force microscopy	23
Fundamental clustering algorithms suite	23
TSSEARCH: Time Series Subsequence Search Library	21
RCE: An Integration Environment for Engineering and Science	21
Lethe: An open-source parallel high-order adaptative CFD solver for incompressible flows	20
SWIGLAL: Python and Octave interfaces to the LALSuite gravitational-wave data analysis libraries	20
2D-VSR-Sim: A simulation tool for the optimization of 2-D voxel-based soft robots	19
CIRN Quantitative Coastal Imaging Toolbox	19
Handling decision-making in Intuitionistic Fuzzy environment: PyIFDM package	18
pymcdm—The universal library for solving multi-criteria decision-making problems	18
ennemi: Non-linear correlation detection with mutual information	18
WLDT: A general purpose library to build IoT digital twins	18
OpenPIV-MATLAB — An open-source software for particle image velocimetry; test case: Birds’ aerodynamics	17
AMLBID: An auto-explained Automated Machine Learning tool for Big Industrial Data	17
PCAfold: Python software to generate, analyze and improve PCA-derived low-dimensional manifolds	17
Efficient WENO library for OpenFOAM	17
pySuStaIn: A Python implementation of the Subtype and Stage Inference algorithm	17
PyOMA and PyOMA_GUI: A Python module and software for Operational Modal Analysis	16
PowerSystems.jl — A power system data management package for large scale modeling	16
Clava: C/C++ source-to-source compilation using LARA	16
CLUMP: A Code Library to generate Universal Multi-sphere Particles	15
ESP3: An open-source software for the quantitative processing of hydro-acoustic data	15
Laserchicken—A tool for distributed feature calculation from massive LiDAR point cloud datasets	15
MULTIFRAC: An ImageJ plugin for multiscale characterization of 2D and 3D stack images	15
CUSTOMHyS: Customising Optimisation Metaheuristics via Hyper-heuristic Search	14
MicroStructPy: A statistical microstructure mesh generator in Python	14
Dyssol—An open-source flowsheet simulation framework for particulate materials	14
IbIPP for topology optimization—An Image-based Initialization and Post-Processing code written in MATLAB	13
sparse-ir: Optimal compression and sparse sampling of many-body propagators	13
RegionTPMS — Region based triply periodic minimal surfaces (TPMS) for 3-D printed multiphase bone scaffolds with exact porosity values	13
piv-image-generator: An image generating software package for planar PIV and Optical Flow benchmarking	13
Polyrun: A Java library for sampling from the bounded convex polytopes	13
SeMi: A SEmantic Modeling machIne to build Knowledge Graphs with graph neural networks	13
ParKVFinder: A thread-level parallel approach in biomolecular cavity detection	13
Praznik: High performance information-based feature selection	13
Thermofeel: A python thermal comfort indices library	13
genieclust: Fast and robust hierarchical clustering	12
AMBER: A real-time pipeline for the detection of single pulse astronomical transients	12
NANOPTICS: In-depth analysis of NANomaterials for OPTICal localized surface plasmon resonance Sensing	12
MATBOX: An Open-source Microstructure Analysis Toolbox for microstructure generation, segmentation, characterization, visualization, correlation, and meshing	12
RealPi2dDIC: A Low-cost and open-source approach to in situ 2D Digital Image Correlation (DIC) applications	12
CIOA: Circle-Inspired Optimization Algorithm, an algorithm for engineering optimization	12
Crispyn—A Python library for determining criteria significance with objective weighting methods	12
AnsibleMetrics: A Python library for measuring Infrastructure-as-Code blueprints in Ansible	11
BANSHEE–A MATLAB toolbox for Non-Parametric Bayesian Networks	11
Pykat: Python package for modelling precision optical interferometers	11
MATVines: A vine copula package for MATLAB	11

PSPSO: A package for parameters selection using particle swarm optimization	11
Spine Toolbox: A flexible open-source workflow management system with scenario and data management	11
GTO: A toolkit to unify pipelines in genomic and proteomic research	11
DIETERpy: A Python framework for the Dispatch and Investment Evaluation Tool with Endogenous Renewables	10
An open-source camera system for experimental measurements	10
MODULO: A software for Multiscale Proper Orthogonal Decomposition of data	10
A model for cost- and greenhouse gas optimal material and energy allocation of biomass and hydrogen	10
Automatic dataset builder for Machine Learning applications to satellite imagery	10
BuckinghamPy: A Python software for dimensional analysis	10
rethnicity: An R package for predicting ethnicity from names	10
Neper2CAE and PyCiGen: Scripts to generate polycrystals and interface elements in Abaqus	10
The SiLA 2 Manager for rapid device integration and workflow automation	10
Update 3.0 to “PuMA: The Porous Microstructure Analysis software”, (PII:S2352711018300281)	10
GOPY: A tool for building 2D graphene-based computational models	10
histolab: A Python library for reproducible Digital Pathology preprocessing with automated testing	10
SentinAir system software: A flexible tool for data acquisition from heterogeneous sensors and devices	9
ScaFi: A Scala DSL and Toolkit for Aggregate Programming	9
2P-Kt: A logic-based ecosystem for symbolic AI	9
PowerDynamics.jl—An experimentally validated open-source package for the dynamical analysis of power grids	9
X-Ray Calc: A software for the simulation of X-ray reflectivity	9
GSITK: A sentiment analysis framework for agile replication and development	9
Cloud2FEM: A finite element mesh generator based on point clouds of existing/historical structures	9
advligorts: The Advanced LIGO real-time digital control and data acquisition system	9
Explorer.py: Mapping the energy landscapes of complex materials	9
GridTools: A framework for portable weather and climate applications	9
eeglib: A Python module for EEG feature extraction	9
Open community platform for hearing aid algorithm research: open Master Hearing Aid (openMHA)	9
Boosting AI applications: Labeling format for complex datasets	8
Exasim: Generating discontinuous Galerkin codes for numerical solutions of partial differential equations on graphics processors	8
Deep-water framework: The Swiss army knife of humans working with machine learning models	8
refellips: A Python package for the analysis of variable angle spectroscopic ellipsometry data	8
DfAnalyzer: Runtime dataflow analysis tool for Computational Science and Engineering applications	8
SoccER: Computer graphics meets sports analytics for soccer event recognition	8
OpenSeesPyView: Python programming-based visualization and post-processing tool for OpenSeesPy	8
SurfRCaT: A tool for remote calibration of pre-existing coastal cameras to enable their use as quantitative coastal monitoring tools	8
GNNkeras: A Keras-based library for Graph Neural Networks and homogeneous and heterogeneous graph processing	8
pyEIA: A Python-based framework for data analysis of electrochemical methods for immunoassays	8
XAMG: A library for solving linear systems with multiple right-hand side vectors	8
FEniCS–preCICE: Coupling FEniCS to other simulation software	8
TROVA: TRansport Of water VApor	8
StrutSurf: A tool for analysis of strut morphology and surface roughness in additively manufactured lattices	8
A discrete event simulation procedure for validating programs of requirements: The case of hospital space planning	8
MVTS-Data Toolkit: A Python package for preprocessing multivariate time series data	8
FeView: Finite element model (FEM) visualization and post-processing tool for OpenSees	8
Nebula: Monte Carlo simulator of electron–matter interaction	8
pyrepo-mcda — Reference objects based MCDA software package	7
DQSEGDB: A time-interval database for storing gravitational wave observatory metadata	7
OpenPLC61850: An IEC 61850 MMS compatible open source PLC for smart grid research	7
ttcrpy: A Python package for traveltime computation and raytracing	7
A MATLAB package for automatic extraction of flow index in OCT-A images by intelligent vessel manipulation	7
SiTree: A framework to implement single-tree simulators	7
Meander Statistics Toolbox (MStaT): A toolbox for geometry characterization of bends in large meandering channels	7
Cortado: A dedicated process mining tool for interactive process discovery	7
UGUCA: A spectral-boundary-integral method for modeling fracture and friction	7
DroneTimeline: Forensic timeline analysis for drones	7
torcpy: Supporting task parallelism in Python	7
ImbTreeAUC: An R package for building classification trees using the area under the ROC curve (AUC) on imbalanced datasets	7
ag5Tools: An R package for downloading and extracting agrometeorological data from the AgERA5 database	7
SHEMAT-Suite: An open-source code for simulating flow, heat and species transport in porous media	7
litstudy: A Python package for literature reviews	7
OpenTEPES: Open-source Transmission and Generation Expansion Planning	7
UnBlo	7
Update (1.2) to ANDURIL and ANDURYL: Performance improvements and a graphical user interface	7
MaCySTe: A virtual testbed for maritime cybersecurity	7
rust-code-analysis: A Rust library to analyze and extract maintainability information from source codes	7
Flash-X: A multiphysics simulation software instrument	7
OONIS — Object-Oriented Network Infection Simulator	6
OpenArch: An open-source package for determining the minimum-thickness of arches under seismic loads	6
The soiltestcorr R package: An accessible framework for reproducible correlation analysis of crop yield and soil test data	6
cashocs: A Computational, Adjoint-Based Shape Optimization and Optimal Control Software	6
NL4Py: Agent-based modeling in Python with parallelizable NetLogo workspaces	6
OSCAR: A MATLAB based package to simulate realistic optical cavities	6
highRES-Europe: The high spatial and temporal Resolution Electricity System model for Europe	6
iCorrVision-2D: An integrated python-based open-source Digital Image Correlation software for in-plane measurements (Part 1)	6
Benopt-Heat: An economic optimization model to identify robust bioenergy technologies for the German heat transition	6
MPLBM-UT: Multiphase LBM library for permeable media analysis	6
GWmodelS: A software for geographically weighted models	6
AnyMOD.jl: A Julia package for creating energy system models	6
One-dimensional turbulence (ODT): Computationally efficient modeling and simulation of turbulent flows	6
tsflex: Flexible time series processing & feature extraction	6

ASVtorch toolkit: Speaker verification with deep neural networks	6
ORTiS solver codegen: C++ code generation tools for high performance, FPGA-based, real-time simulation of power electronic systems	6
MJOLNIR: A software package for multiplexing neutron spectrometers	6
TextCL: A Python package for NLP preprocessing tasks	6
oreo: An R package for large amplitude oscillatory analysis	6
GSGP-CUDA — A CUDA framework for Geometric Semantic Genetic Programming	6
EZFF: Python library for multi-objective parameterization and uncertainty quantification of interatomic forcefields for molecular dynamics	6
QBMMlib: A library of quadrature-based moment methods	6
Rcall: An R interface for MATLAB	6
pyFDM: A Python library for uncertainty decision analysis methods	6
VEqMon2D—Equations of motion generation tool of 2D vehicles with Matlab	5
PND: Physics-informed neural-network software for molecular dynamics applications	5
Cluster permutation analysis for EEG series based on non-parametric Wilcoxon–Mann–Whitney statistical tests	5
PyBanshee version (1.0): A Python implementation of the MATLAB toolbox BANSHEE for Non-Parametric Bayesian Networks with updated features	5
A Python interface to the Dutch Atmospheric Large-Eddy Simulation	5
Covira: A COVID-19 risk assessment, visualization and communication tool	5
Simplify: A Python library for optimizing pruned neural networks	5
eadf: Representation of far-field antenna responses in Python	5
GenClass: A parallel tool for data classification based on Grammatical Evolution	5
DFT-MF: Enhanced deepfake detection using mouth movement and transfer learning	5
TumorDecon: A digital cytometry software	5
Update 2.70 to “GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids”	5
KrakN: Transfer Learning framework and dataset for infrastructure thin crack detection	5
Gxsview: Geometry and cross section viewer for calculating radiation transport	5
YAWL: An open source Business Process Management System from science for science	5
Symbolic DNN-Tuner: A Python and ProbLog-based system for optimizing Deep Neural Networks hyperparameters	5
EQP - A 2D/3D library for integration of polynomials times step function	5
laserbeamFoam: Laser ray-tracing and thermally induced state transition simulation toolkit	5
TraCurate: Efficiently curating cell tracks	5
Digital government: Mobile applications and their impact on access to public information	5
RPExpand: Software for Riesz projection expansion of resonance phenomena	5
SfM Flow: A comprehensive toolset for the evaluation of 3D reconstruction pipelines	5
QuantImPy: Minkowski functionals and functions with Python	5
Historical geocoding assistant	5
Update 2.0 to “Takin: An open-source software for experiment planning, visualisation, and data analysis”, (PII: S2352711016300152)	5
CSTNU Tool: A Java library for checking temporal networks	5
PTRAIL — A python package for parallel trajectory data preprocessing	4
beamWeldFoam: Numerical simulation of high energy density fusion and vapourisation-inducing processes	4
NSDPY: A python package to download DNA sequences from NCBI	4
pksensi: An R package to apply global sensitivity analysis in physiologically based kinetic modeling	4
CityZones: A geospatial multi-tier software tool to compute urban risk zones	4
tsrobprep — an R package for robust preprocessing of time series data	4
PCAfold 2.0—Novel tools and algorithms for low-dimensional manifold assessment and optimization	4
Applying positivity constraints to q-space trajectory imaging: The QTI+ implementation	4
MOOSE Stochastic Tools: A module for performing parallel, memory-efficient in situ stochastic simulations	4
RuleXAI—A package for rule-based explanations of machine learning model	4
Flame Tracker: An image analysis program to measure flame characteristics	4
AniLength: GUI-based automatic worm length measurement software using image processing and deep neural network	4
Rehab-Immersive: A framework to support the development of virtual reality applications in upper limb rehabilitation	4
MATLAB tool for probability density assessment and nonparametric estimation	4
StatMechGlass: Python based software for composition–structure prediction in oxide glasses using statistical mechanics	4
edgar: An R package for the U.S. SEC EDGAR retrieval and parsing of corporate filings	4
PyLESA: A Python modelling tool for planning-level Local, integrated, and smart Energy Systems Analysis	4
Update 1.1 to “pysimm: A python package for simulation of molecular systems”, (PII: S2352711016300395)	4
AKFruitData: A dual software application for Azure Kinect cameras to acquire and extract informative data in yield tests performed in fruit orchard environments	4
TimeAwareBPMN-js: An editor and temporal verification tool for Time-Aware BPMN processes	4
LEGO: The open-source Low-carbon Expansion Generation Optimization model	4
watex: machine learning research in water exploration	4
BOXVIA: Bayesian optimization executable and visualizable application	4
CrackDect: Detecting crack densities in images of fiber-reinforced polymers	4
Drop Project: An automatic assessment tool for programming assignments	4
j-Wave: An open-source differentiable wave simulator	4
PhySim-11p: Simulation model for IEEE 802.11p physical layer in MATLAB	4
PySTPrism: Tools for voxel-based space–time prisms	4
P2PFaaS: A framework for FaaS peer-to-peer scheduling and load balancing in Fog and Edge computing	4
SEDBYS: A python-based SED Builder for Young Stars	4
GetSensorData: An extensible Android-based application for multi-sensor data registration	4
FleCSPH: The next generation FleCSIble parallel computational infrastructure for smoothed particle hydrodynamics	4
CLoTH: A Lightning Network Simulator	4
GPUCorrel: A GPU accelerated Digital Image Correlation software written in Python	4
hdData360r: A high-dimensional panel data compiler for governance, trade, and competitiveness indicators of World Bank Group platforms	4
Graphical interface for automated management of motion artifact within fMRI acquisitions: INFOBAR	4
ELC: Software and tutorial for finite-element modeling of electrochemical desalination	4
DATTES: Data analysis tools for tests on energy storage	4
GSimPy: A Python package for measuring group similarity	4
AllInOne Pre-processing: A comprehensive preprocessing framework in plant field phenotyping	4
takos: An R package for thermal analysis calculations	4
OpenImpala: OPEN source IMage based PArallisable Linear Algebra solver	4
pycity_scheduling—A Python framework for the development and assessment of optimisation-based power scheduling algorithms for multi-energy systems in city districts	4
OptiMic: A tool to generate optimized polycrystalline microstructures for materials simulations	4
secml: Secure and explainable machine learning in Python	4
RandPro- A practical implementation of random projection-based feature extraction for high dimensional multivariate data analysis in R	4
Seismo-VLAB: An open-source finite element software for seismic meso-scale simulations	4
Power Market Tool (POMATO) for the analysis of zonal electricity markets	4
MaMiCo 2.0: An enhanced open-source framework for high-performance molecular-continuum flow simulation	4
Geo-MST: A geographical minimum spanning tree plugin for QGIS	4
Analysing the resilience of agricultural production systems with ResiPy, the Python production resilience estimation package	3
HiTIME: An efficient model-selection approach for the detection of unknown drug metabolites in LC-MS data	3
PPWSim: Privacy preserving wireless sensor network simulator	3
A covariate software tool to guide test activity allocation	3
Sas-temper: Software for fitting small-angle scattering data that provides automated reproducibility characterization	3
SimCES platform for modular simulation: Featuring platform independence, container ecosystem, and development toolkit	3
XDrift—An R package to simulate spatially explicit pesticide spray-drift exposure of non-target-species habitats at landscape scales	3
EasyEIS: A software tool to perform electrochemical impedance spectroscopy using a source measure unit	3
RPaSDT—Rumor Propagation and Source Detection Toolkit	3