SoftwareX

Article	Citations
Open data from the first and second observing runs of Advanced LIGO and Advanced Virgo	303
ixpeobssim: A simulation and analysis framework for the imaging X-ray polarimetry explorer	100
2.0 - MOOSE: Enabling massively parallel multiphysics simulation	91
The Contiki-NG open source operating system for next generation IoT devices	68
PESummary: The code agnostic Parameter Estimation Summary page builder	51
GstLAL: A software framework for gravitational wave discovery	49
coherent WaveBurst, a pipeline for unmodeled gravitational-wave data analysis	48
EMPIRE: An open-source model based on multi-horizon programming for energy transition analyses	42
GWpy: A Python package for gravitational-wave astrophysics	41
life: A flexible, high performance library for the numerical solution of complex finite element problems	39
drtsans: The data reduction toolkit for small-angle neutron scattering at Oak Ridge National Laboratory	37
ECGdeli - An open source ECG delineation toolbox for MATLAB	36
SPARC: Simulation Package for Ab-initio Real-space Calculations	36
pymcdm—The universal library for solving multi-criteria decision-making problems	35
DynaProg: Deterministic Dynamic Programming solver for finite horizon multi-stage decision problems	33
pySuStaIn: A Python implementation of the Subtype and Stage Inference algorithm	32
TFMLAB: A MATLAB toolbox for 4D traction force microscopy	31
PADRES: Tool for PrivAcy, Data REgulation and Security	30
CLUMP: A Code Library to generate Universal Multi-sphere Particles	30
PyOMA and PyOMA_GUI: A Python module and software for Operational Modal Analysis	30
Fundamental clustering algorithms suite	29
WLDT: A general purpose library to build IoT digital twins	28
RCE: An Integration Environment for Engineering and Science	25
TSSEARCH: Time Series Subsequence Search Library	25
Handling decision-making in Intuitionistic Fuzzy environment: PyIFDM package	23

ennemi: Non-linear correlation detection with mutual information	22
sparse-ir: Optimal compression and sparse sampling of many-body propagators	22
Praznik: High performance information-based feature selection	20
Update 3.0 to “PuMA: The Porous Microstructure Analysis software”, (PII:S2352711018300281)	19
RegionTPMS — Region based triply periodic minimal surfaces (TPMS) for 3-D printed multiphase bone scaffolds with exact porosity values	19
ScaFi: A Scala DSL and Toolkit for Aggregate Programming	19
CIOA: Circle-Inspired Optimization Algorithm, an algorithm for engineering optimization	19
PowerSystems.jl — A power system data management package for large scale modeling	19
AMLBID: An auto-explained Automated Machine Learning tool for Big Industrial Data	18
MATVines: A vine copula package for MATLAB	17
genieclust: Fast and robust hierarchical clustering	17
IbIPP for topology optimization—An Image-based Initialization and Post-Processing code written in MATLAB	17
Crispyn—A Python library for determining criteria significance with objective weighting methods	17
Polyrun: A Java library for sampling from the bounded convex polytopes	17
histolab: A Python library for reproducible Digital Pathology preprocessing with automated testing	16
MATBOX: An Open-source Microstructure Analysis Toolbox for microstructure generation, segmentation, characterization, visualization, correlation, and meshing	15
Thermofeel: A python thermal comfort indices library	15
Spine Toolbox: A flexible open-source workflow management system with scenario and data management	15
RealPi2dDIC: A Low-cost and open-source approach to in situ 2D Digital Image Correlation (DIC) applications	15
A model for cost- and greenhouse gas optimal material and energy allocation of biomass and hydrogen	15
ag5Tools: An R package for downloading and extracting agrometeorological data from the AgERA5 database	15
An open-source camera system for experimental measurements	14
The SiLA 2 Manager for rapid device integration and workflow automation	14
Cluster permutation analysis for EEG series based on non-parametric Wilcoxon–Mann–Whitney statistical tests	14
PSPSO: A package for parameters selection using particle swarm optimization	14
GWmodelS: A software for geographically weighted models	14
Automatic dataset builder for Machine Learning applications to satellite imagery	14
eeglib: A Python module for EEG feature extraction	13
Neper2CAE and PyCiGen: Scripts to generate polycrystals and interface elements in Abaqus	13
rethnicity: An R package for predicting ethnicity from names	13
pyrepo-mcda — Reference objects based MCDA software package	13
BuckinghamPy: A Python software for dimensional analysis	12
QuantImPy: Minkowski functionals and functions with Python	12
pyFDM: A Python library for uncertainty decision analysis methods	12
Digital government: Mobile applications and their impact on access to public information	12
Cloud2FEM: A finite element mesh generator based on point clouds of existing/historical structures	12
advligorts: The Advanced LIGO real-time digital control and data acquisition system	12
litstudy: A Python package for literature reviews	12
Cortado: A dedicated process mining tool for interactive process discovery	12
Open community platform for hearing aid algorithm research: open Master Hearing Aid (openMHA)	12
OpenTEPES: Open-source Transmission and Generation Expansion Planning	11
MaCySTe: A virtual testbed for maritime cybersecurity	11
2P-Kt: A logic-based ecosystem for symbolic AI	11
DIETERpy: A Python framework for the Dispatch and Investment Evaluation Tool with Endogenous Renewables	11
Version [OpenIPSL 2.0.0] - [iTesla Power Systems Library (iPSL): A Modelica library for phasor time-domain simulations]	11
GSITK: A sentiment analysis framework for agile replication and development	11
highRES-Europe: The high spatial and temporal Resolution Electricity System model for Europe	11
Flash-X: A multiphysics simulation software instrument	11
GNNkeras: A Keras-based library for Graph Neural Networks and homogeneous and heterogeneous graph processing	11
GridTools: A framework for portable weather and climate applications	11

AnyMOD.jl: A Julia package for creating energy system models	10
cashocs: A Computational, Adjoint-Based Shape Optimization and Optimal Control Software	10
DFT-MF: Enhanced deepfake detection using mouth movement and transfer learning	10
TROVA: TRansport Of water VApor	10
PowerDynamics.jl—An experimentally validated open-source package for the dynamical analysis of power grids	10
XAMG: A library for solving linear systems with multiple right-hand side vectors	10
Exasim: Generating discontinuous Galerkin codes for numerical solutions of partial differential equations on graphics processors	10
GenClass: A parallel tool for data classification based on Grammatical Evolution	10
FEniCS–preCICE: Coupling FEniCS to other simulation software	10
OpenSeesPyView: Python programming-based visualization and post-processing tool for OpenSeesPy	10
ttcrpy: A Python package for traveltime computation and raytracing	10
MPLBM-UT: Multiphase LBM library for permeable media analysis	10
EnMAP-Box: Imaging spectroscopy in QGIS	10
PND: Physics-informed neural-network software for molecular dynamics applications	10
iCorrVision-2D: An integrated python-based open-source Digital Image Correlation software for in-plane measurements (Part 1)	10
pyEIA: A Python-based framework for data analysis of electrochemical methods for immunoassays	10
StrutSurf: A tool for analysis of strut morphology and surface roughness in additively manufactured lattices	10
Meander Statistics Toolbox (MStaT): A toolbox for geometry characterization of bends in large meandering channels	9
The soiltestcorr R package: An accessible framework for reproducible correlation analysis of crop yield and soil test data	9
Explorer.py: Mapping the energy landscapes of complex materials	9
RuleXAI—A package for rule-based explanations of machine learning model	9
Boosting AI applications: Labeling format for complex datasets	9
pyfao56: FAO-56 evapotranspiration in Python	9
refellips: A Python package for the analysis of variable angle spectroscopic ellipsometry data	9
EZFF: Python library for multi-objective parameterization and uncertainty quantification of interatomic forcefields for molecular dynamics	9
ImbTreeAUC: An R package for building classification trees using the area under the ROC curve (AUC) on imbalanced datasets	9
Drop Project: An automatic assessment tool for programming assignments	9
RPExpand: Software for Riesz projection expansion of resonance phenomena	9
DQSEGDB: A time-interval database for storing gravitational wave observatory metadata	9
FeView: Finite element model (FEM) visualization and post-processing tool for OpenSees	9
laserbeamFoam: Laser ray-tracing and thermally induced state transition simulation toolkit	9
GPUCorrel: A GPU accelerated Digital Image Correlation software written in Python	8
OpenPLC61850: An IEC 61850 MMS compatible open source PLC for smart grid research	8
GSGP-CUDA — A CUDA framework for Geometric Semantic Genetic Programming	8
Simplify: A Python library for optimizing pruned neural networks	8
PTRAIL — A python package for parallel trajectory data preprocessing	8
Benopt-Heat: An economic optimization model to identify robust bioenergy technologies for the German heat transition	8
tsrobprep — an R package for robust preprocessing of time series data	8
3.0 - MOOSE: Enabling massively parallel multiphysics simulations	8
CLoTH: A Lightning Network Simulator	8
BOXVIA: Bayesian optimization executable and visualizable application	8
A framework for benchmarking clustering algorithms	8
PyBanshee version (1.0): A Python implementation of the MATLAB toolbox BANSHEE for Non-Parametric Bayesian Networks with updated features	8
oreo: An R package for large amplitude oscillatory analysis	8
Symbolic DNN-Tuner: A Python and ProbLog-based system for optimizing Deep Neural Networks hyperparameters	8
SiTree: A framework to implement single-tree simulators	8
CityZones: A geospatial multi-tier software tool to compute urban risk zones	8
TextCL: A Python package for NLP preprocessing tasks	7
Update 2.70 to “GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids”	7
DroneTimeline: Forensic timeline analysis for drones	7
Gxsview: Geometry and cross section viewer for calculating radiation transport	7
Causal ML: Python package for causal inference machine learning	7
tsflex: Flexible time series processing & feature extraction	7
VEqMon2D—Equations of motion generation tool of 2D vehicles with Matlab	7
MOOSE Navier–Stokes module	7
KrakN: Transfer Learning framework and dataset for infrastructure thin crack detection	7
ALIIAS: Anonymization/Pseudonymization with LimeSurvey integration and II-factor Authentication for Scientific research	7
j-Wave: An open-source differentiable wave simulator	7
ASVtorch toolkit: Speaker verification with deep neural networks	7
MFPP: Matrix-based flexible project planning	7
UGUCA: A spectral-boundary-integral method for modeling fracture and friction	7
gosset: An R package for analysis and synthesis of ranking data in agricultural experimentation	7
NL4Py: Agent-based modeling in Python with parallelizable NetLogo workspaces	7
SfM Flow: A comprehensive toolset for the evaluation of 3D reconstruction pipelines	7
TreeTool: A tool for detecting trees and estimating their DBH using forest point clouds	7
hdData360r: A high-dimensional panel data compiler for governance, trade, and competitiveness indicators of World Bank Group platforms	7
P2PFaaS: A framework for FaaS peer-to-peer scheduling and load balancing in Fog and Edge computing	6
GetSensorData: An extensible Android-based application for multi-sensor data registration	6
ORTiS solver codegen: C++ code generation tools for high performance, FPGA-based, real-time simulation of power electronic systems	6
CoFly: An automated, AI-based open-source platform for UAV precision agriculture applications	6
LEGO: The open-source Low-carbon Expansion Generation Optimization model	6
MultiGlobAl: Global alignment of multilayer networks	6
Flame Tracker: An image analysis program to measure flame characteristics	6
Update 2.0 to “Takin: An open-source software for experiment planning, visualisation, and data analysis”, (PII: S2352711016300152)	6
GANG-MAM: GAN based enGine for Modifying Android Malware	6
Rehab-Immersive: A framework to support the development of virtual reality applications in upper limb rehabilitation	6
Dental Loop FLT: Facial landmark tracking	6
NSDPY: A python package to download DNA sequences from NCBI	6
irs-partition: An Intrusion Response System utilizing Deep Q-Networks and system partitions	6
ELC: Software and tutorial for finite-element modeling of electrochemical desalination	6

EC-KitY: Evolutionary computation tool kit in Python with seamless machine learning integration	6
OpenArch: An open-source package for determining the minimum-thickness of arches under seismic loads	6
Niimpy: A toolbox for behavioral data analysis	6
Historical geocoding assistant	6
Seismo-VLAB: An open-source finite element software for seismic meso-scale simulations	6
SEDBYS: A python-based SED Builder for Young Stars	6
secml: Secure and explainable machine learning in Python	6
TAFFO: The compiler-based precision tuner	6
Rcall: An R interface for MATLAB	6
A covariate software tool to guide test activity allocation	6
TraCurate: Efficiently curating cell tracks	6
OONIS — Object-Oriented Network Infection Simulator	6
High performance Savu software for fast 3D model-based iterative reconstruction of large data at Diamond Light Source	6
One-dimensional turbulence (ODT): Computationally efficient modeling and simulation of turbulent flows	6
MOOSE Stochastic Tools: A module for performing parallel, memory-efficient in situ stochastic simulations	6
MATLAB tool for probability density assessment and nonparametric estimation	6
CSTNU Tool: A Java library for checking temporal networks	6
BASEveg: A python package to model riparian vegetation dynamics coupled with river morphodynamics	5
A new approach for drone tracking with drone using Proximal Policy Optimization based distributed deep reinforcement learning	5
PCAfold 2.0—Novel tools and algorithms for low-dimensional manifold assessment and optimization	5
Dental loop SnP: Speech and phonetic pattern recognition	5
watex: machine learning research in water exploration	5
AllInOne Pre-processing: A comprehensive preprocessing framework in plant field phenotyping	5
MultiVehicle Simulator (MVSim): Lightweight dynamics simulator for multiagents and mobile robotics research	5
IPv6CC: IPv6 covert channels for testing networks against stegomalware and data exfiltration	5
PyTME (Python Template Matching Engine): A fast, flexible, and multi-purpose template matching library for cryogenic electron microscopy data	5
Fast-DENSER: Fast Deep Evolutionary Network Structured Representation	5
dcor: Distance correlation and energy statistics in Python	5
UQpy v4.1: Uncertainty quantification with Python	5
BBR: An open-source standard workflow based on biophysical crop parameters for automatic Botrytis cinerea assessment in vineyards	5
GTOPX space mission benchmarks	5
PyLESA: A Python modelling tool for planning-level Local, integrated, and smart Energy Systems Analysis	5
DATTES: Data analysis tools for tests on energy storage	5
TumorDecon: A digital cytometry software	5
RPaSDT—Rumor Propagation and Source Detection Toolkit	5
PocketFinderGNN: A manufacturing feature recognition software based on Graph Neural Networks (GNNs) using PyTorch Geometric and NetworkX	5
TTB-2D: Train–Track–Bridge interaction simulation tool for Matlab	5
Covira: A COVID-19 risk assessment, visualization and communication tool	5
Face recognition algorithm based on particle swarm optimization and image feature compensation	5
FM-2D - open-source platform for the 2-dimensional numerical modeling and seismic analysis of buildings	5
An open-source framework for publishing/subscribing IEC 61850 R-GOOSE and R-SV	5
AMED: Aggregated multimedia exploratory and discovery search software	5
TFInterpy: A high-performance spatial interpolation Python package	5
AKFruitData: A dual software application for Azure Kinect cameras to acquire and extract informative data in yield tests performed in fruit orchard environments	5
Power Market Tool (POMATO) for the analysis of zonal electricity markets	5
beamWeldFoam: Numerical simulation of high energy density fusion and vapourisation-inducing processes	5
PC-TAS: A design environment for phase-change and classical thermoacoustic systems	5
OpenFL-XAI: Federated learning of explainable artificial intelligence models in Python	5
PmlBeta: A PyMOL extension for building β-amino acid insertions and <	5
OptiMic: A tool to generate optimized polycrystalline microstructures for materials simulations	5
Version 1.1.0—pyfao56: FAO-56 evapotranspiration in Python	5
Acme: A small 3D geometry library	5
Version 2.0.0 - M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations	5
Nancy: An efficient parallel Network Calculus library	5
ChatbotSQL: Conversational agent to support relational database query language learning	5
Simplifying computational workflows with the Multiscale Atomic Zeolite Simulation Environment (MAZE)	4
pyTEP: A Python package for interactive simulations of the Tennessee Eastman process	4
ZigBee enabled IoT based intelligent lane control system for autonomous agricultural electric vehicle application	4
HeNDS: A program for calculating average Helium NanoDroplet Sizes	4
High-throughput analysis of contact angle goniometry data using DropPy	4
NESIM-RT: A real-time distributed spiking neural network simulator	4
edgar: An R package for the U.S. SEC EDGAR retrieval and parsing of corporate filings	4
Quail: A lightweight open-source discontinuous Galerkin code in Python for teaching and prototyping	4
Image2DEM: A geometrical digital twin generator for the detailed structural analysis of existing masonry infrastructure stock	4
A multiscale Eulerian–Lagrangian cavitating flow solver in OpenFOAM	4
CLUSplus: A decision tree-based framework for predicting structured outputs	4
STL_Process: A .STL-based preprocessor for robot path planning in manufacturing and quality control processes	4
PyFWI: A Python package for full-waveform inversion and reservoir monitoring	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
Conducting eye-tracking studies on large and interactive process models using EyeMind	4
GIN: A web-application for constructing synthetic datasets of interconnected networks in bioinformatics	4
MISTIQS: An open-source software for performing quantum dynamics simulations on quantum computers	4
MaMiCo 2.0: An enhanced open-source framework for high-performance molecular-continuum flow simulation	4
TimeAwareBPMN-js: An editor and temporal verification tool for Time-Aware BPMN processes	4
BufferCapacity3 an interactive GUI program for modelling food ingredient buffering and pH	4
2BarG—A program to process split Hopkinson (Kolsky) bar test results	4
PRETUS: A plug-in based platform for real-time ultrasound imaging research	4
PPWSim: Privacy preserving wireless sensor network simulator	4
Reticula: A temporal network and hypergraph analysis software package	4
I-STL2MOOSE: From STL data to integrated volumetrical meshes for MOOSE	4
IRB-draft-generator: A generative AI tool to streamline the creation of institutional review board applications	4
CESSIPy: A Python open-source module for stochastic system identification in civil engineering	4
MartMi-BCI: A matlab-based real-time motor imagery brain-computer interface platform	4
PPGISr: An R package for Public Participatory GIS	4
uFTIR: An R package to process hyperspectral images of environmental samples captured with	4
AniLength: GUI-based automatic worm length measurement software using image processing and deep neural network	4
Update 1.1 to “pysimm: A python package for simulation of molecular systems”, (PII: S2352711016300395)	4
Fast shallow water-wave solver for plane inclined beaches	4
Open source vector field topology	4
MWSegEval—An image analysis toolbox for microwave breast images	4
CrackDect: Detecting crack densities in images of fiber-reinforced polymers	4
MNEflow: Neural networks for EEG/MEG decoding and interpretation	4
OpenImpala: OPEN source IMage based PArallisable Linear Algebra solver	4
SerialTrack: ScalE and rotation invariant augmented Lagrangian particle tracking	4
iCorrVision-3D: An integrated python-based open-source Digital Image Correlation Software for in-plane and out-of-plane measurements (Part 2)	4