SoftwareX

Article	Citations
GPFniCS: A generalised phase field method to model fracture	131
MetaCluster: An open-source Python library for metaheuristic-based clustering problems	125
Web-NDefA: Open-source and web-based online platform for 3-D deformation analysis of geodetic networks	97
Hybrid adaptive battery parameter estimation approach for equivalent circuit model toolbox	68
AKFruitYield: Modular benchmarking and video analysis software for Azure Kinect cameras for fruit size and fruit yield estimation in apple orchards	62
RankspeQ: An R package platform for genotype characterization and performance-ranking based on MultispeQ measurements	59
Daily Video: A tool for quality of experience (QoE) in long-term context research	58
MetricHunter: A software metric dataset generator utilizing SourceMonitor upon public GitHub repositories	51
KMstability: R tools to report the stability and precision of Kaplan–Meier estimates as well as measures of follow-up in time-to-event studies	51
In-Cognitive: A web-based Python application for fuzzy cognitive map design, simulation, and uncertainty analysis based on the Monte Carlo method	49
Blink: An educational software debugger for Scratch	46
MAWA: Enhancing mobile web browsing through web augmentation for improved user experience	43
PanNDE: A modular architecture for high-performance NDE simulation	42
mics-library: A Python package for reproducible studies on the Multiple Indicator Cluster Survey	42
SCSV_IPS: A software for the estimation of the shear coefficient of spin viscosity during the movement of a ferrofluid under the effect of an external rotating magnetic field	38
An open-source application software to determine the preconsolidation pressure of soils in incremental loading oedometer testing: pySigmaP	38
Executable HTML	34
McDAPS: A multi-channel physiological signals display and analysis system for clinical researchers	32
Open-source skull reconstruction with MONAI	30
JMetaBFOP: A tool for solving global optimization problems	28
Visualizing Abaqus output database in ParaView: A universal converter in Python and C++	27
Motion planning for triple-axis spectrometers	27
Stplanpy: A sustainable transportation planner for Python	26
GPR: A Python implementation of an extremely simple classifier based on fuzzy logic and gene expression programming	25
PyOPAsolver: A python based tool for ordinal priority approach operations and normalization	24

Editorial Board	24
Smyrida: A web application for process mining and interactive visualization	24
Update 2.0 to rheed++: A complex computer model for dynamical one-beam calculations of RHEED intensity oscillations	23
OpenIPDM: A probabilistic framework for estimating the deterioration and effect of interventions on bridges	23
The SiLA 2 Manager for rapid device integration and workflow automation	22
Morphogenesis of Isobenefit urbanism: Isobenefit-cities simulator	22
Multtestlib: A Python package for performing unit tests using multiprocessing	22
HISAPS: High-order smoothing spline with automatic parameter selection and shape constraints	21
EduGuard RetainX: An advanced analytical dashboard for predicting and improving student retention in tertiary education	21
NAVI Assistant: A tool to integrate chatbots into EUD Solutions	21
CombinatorixPy: Advancing mixture descriptors for computational chemistry	20
OpenVR: Teleoperation for manipulation	20
microStabilize: In-plane microstructure stabilization in optical microscopy via normalized correlation coefficient matching method	20
LOBEFIT: LEO satellite broadcast ephemeris fitting open-source software based on automatic differentiation technique	19
decideXpert: Collaborative system using AHP-TOPSIS and fuzzy techniques for multicriteria group decision-making	18
The IDL tool suite: Specifying and analyzing inter-parameter dependencies in web APIs	18
CacheSim: A cache simulation framework for evaluating caching algorithms on resource-constrained edge devices	18
PyDicer: An open-source python library for conversion and analysis of radiotherapy DICOM data	18
APOTHEOSIS: An efficient approximate similarity search system	17
WiN-GUI Version 2: A graphical tool for neuron-based encoding	17
GraphOptima: A graph layout optimization framework for visualizing large networks	17
PowerDynamics.jl—An experimentally validated open-source package for the dynamical analysis of power grids	16
EBSDPolygonizer: Enabling realistic microstructural modelling	16
pyRoCS: A Python package to evaluate the resilience of complex systems	16
CityZones: A geospatial multi-tier software tool to compute urban risk zones	16
Stop@: A framework for scalable and noise-resistant stop-move segmentation of large datasets of trajectories in outdoor and indoor spaces	16
LeXInt: GPU-accelerated exponential integrators package	16
SACETraj: An AutoCAD Catmull-Rom Spline Trajectory Interpolator	16
CNV-Z; a new tool for detecting copy number variation in next generation sequencing data	15
Adapting LIGO workflows to run in the Open Science Grid	15
SOUL: Scala Oversampling and Undersampling Library for imbalance classification	15
EvalNE: A framework for network embedding evaluation	14
ObiWan-Microbi: OMERO-based integrated workflow for annotating microbes in the cloud	14
The Forest Conservation Evaluation Tool: Accessible impact evaluation for Latin America	14
FS-Studio: An extensive and efficient feature selection experimentation tool for Weka Explorer	14
Hydrogen Permeation and Absorption Tool (HyPAT v2.0): An update to facilitate analyses of data from hydrogen absorption experiments	14
Open community platform for hearing aid algorithm research: open Master Hearing Aid (openMHA)	14
Beachmeter – a simple tool for semi-automatic beach morphodynamics measurement	14
MOOSE Optimization Module: Physics-constrained optimization	14
A Python-based tool for constructing observables from the DSN’s closed-loop archival tracking data files	13
CVIK: A Matlab-based cluster validity index toolbox for automatic data clustering	13
Numba-MPI v1.0: Enabling MPI communication within Numba/LLVM JIT-compiled Python code	13
LeXInt: Package for exponential integrators employing Leja interpolation	13
iBluff: An open-source R package for geomorphic analysis of coastal bluffs/cliffs	13
New, flexible and open-source fisheries self-reporting app: The Shiny4SelfReport	13
Input/Output Library for Higher-Order Computational Fluid Dynamics Data	13
Image2DEM: A geometrical digital twin generator for the detailed structural analysis of existing masonry infrastructure stock	13
OpenImpala: OPEN source IMage based PArallisable Linear Algebra solver	13
LEI2JSON: Schema-based validation and conversion of livestock event information	13
ELC: Software and tutorial for finite-element modeling of electrochemical desalination	13

Video quality metrics toolkit: An open source software to assess video quality	12
RegionTPMS — Region based triply periodic minimal surfaces (TPMS) for 3-D printed multiphase bone scaffolds with exact porosity values	12
GCPU_OpticalFlow: A GPU accelerated Python software for strain measurement	12
Q-Facies: A tool for the quantitative interpretation of groundwater hydrochemical facies	12
tx2_fcnn_node: An open-source ROS compatible tool for monocular depth reconstruction	12
TD-COF: A new method for detecting tandem duplications in next generation sequencing data	11
Update 3.1 to FonaDyn — a system for real-time analysis of the electroglottogram, over the voice range	11
rockphypy: An extensive Python library for rock physics modeling	11
juSPH: A Julia-based open-source package of parallel Smoothed Particle Hydrodynamics (SPH) for dam break problems	11
TermX: The semantic interoperability, knowledge management and sharing platform	11
STUDIO: A Python graphical tool for analyzing street user observations from video data	11
TreeSim: An object-oriented individual tree simulator and 3D visualization tool in Python	11
Dreamento: an open-source dream engineering toolbox for sleep EEG wearables	11
PND: Physics-informed neural-network software for molecular dynamics applications	11
HOST: Harmonic oscillator seasonal-trend model for analyzing the reoccurring nature of extreme events	11
SST v1.0.0 with C API: Pluggable security solution for the Internet of Things	11
Excursiona: A collaborative mobile application for excursions in nature	11
RPaSDT—Rumor Propagation and Source Detection Toolkit	11
CACPPAF, a COMSOL application to characterize polyelectrolyte properties of actin filaments	10
NCC: An R-package for analysis and simulation of platform trials with non-concurrent controls	10
MNEflow: Neural networks for EEG/MEG decoding and interpretation	10
PÉEK: A cloud-based application for automatic electrocardiogram pre-diagnosis	10
SimCES platform for modular simulation: Featuring platform independence, container ecosystem, and development toolkit	10
ADITU: A mesh-free formulation for the solution of Helmholtz equation in bounded and unbounded domains	10
SootLib: A soot model library for combustion simulation	10
GCBICT: Green Coffee Bean Identification Command-line Tool	10
Version [1.1]- [Handling decision-making in intuitionistic fuzzy environment: PyIFDM package]	10
Release 2.0 — NEMSIM-RT: A real-time distributed spiking neural network simulator	10
OptiGUI DataCollector: A graphical user interface for automating the data collecting process in optical and photonics labs	10
OpenFL-XAI: Federated learning of explainable artificial intelligence models in Python	10
VELCRO: A visual-based programming tool for effortless deep learning model construction	10
ACME (Agile Crop Model Ensemble): A package to generate and run large virtual experiments with ensembles of crop simulation models	10
PYCASO: Python module for calibration of cameras by Soloff’s method	10
Identifying safety–critical concerns in unmanned aerial vehicle software platforms with SALIENT	10
shinyHugePlot: An R package for displaying the features of data with a huge sample size	10
pyGNMF: A Python library for implementation of generalised non-negative matrix factorisation method	10
MultiFEBE: A multi-domain finite element–boundary element solver for linear mixed-dimensional mechanical problems	10
JaxSGMC: Modular stochastic gradient MCMC in JAX	10
MSCPDPLab: A MATLAB toolbox for transfer learning based multi-source cross-project defect prediction	10
IDOL: A web application for mixed integer linear multiobjective optimization	9
AMLBID: An auto-explained Automated Machine Learning tool for Big Industrial Data	9
Gym-preCICE: Reinforcement learning environments for active flow control	9
Toolbox to simulate and mitigate COVID-19 propagation	9
A modular LabVIEW application frame for Knudsen Effusion Mass Spectrometry instrument control	9
CyEnGNet—App: A new Cytoscape app for the reconstruction of large co-expression networks using an ensemble approach	9
LiveDewStream: A stream processing platform for running in-lab distributed deep learning inferences on smartphone clusters at the edge	9
MWSegEval—An image analysis toolbox for microwave breast images	9
Drop Project: An automatic assessment tool for programming assignments	9
ennemi: Non-linear correlation detection with mutual information	9
RCE: An Integration Environment for Engineering and Science	9
DockerChannel: A framework for evaluating information leakages of Docker containers	9
Roborueda: Python-based GUI to control a wheelchair and monitor user posture	9
OpenSeesPyView: Python programming-based visualization and post-processing tool for OpenSeesPy	9
CLUSplus: A decision tree-based framework for predicting structured outputs	9
pyGLLE: A Python toolkit for solving the generalized Lugiato–Lefever equation	9
Version 1.3-BANSHEE—A MATLAB toolbox for Non-Parametric Bayesian Networks	9
PPWSim: Privacy preserving wireless sensor network simulator	8
AquaGS: An integrated GUI pipeline for genomic selection in aquaculture breeding	8
A directed greybox fuzzing tool for continuous integration	8
genieclust: Fast and robust hierarchical clustering	8
FastRealBoostBins: An ensemble classifier for fast predictions implemented in Python via numba.jit and numba.cuda	8
Chaak: Urban Hydrological Impact modeling	8
HICA: A MATLAB-based hierarchical image clustering algorithm for classifying parts suitable for additive and traditional manufacturing technologies	8
DeepWealth: A generalizable open-source deep learning framework using satellite images for well-being estimation	8
Unidimensional forced convection generalized Graetz solutions	8
Dental loop SnP: Speech and phonetic pattern recognition	8
EmintWeb: Creation of embedded web applications in C++ for specific systems	8
Saihu: A common interface of worst-case delay analysis tools for time-sensitive networks	8
mango: A modular python-based agent simulation framework	8
JuBat: A Julia-based framework for battery modelling using finite element method	8
A Robot Operating System (ROS) package for mapping flow fields in rivers via Particle Image Velocimetry (PIV)	8
baskexact: An R package for analytical calculation of basket trial operating characteristics	8
Update (3.0) to LyapXool: Quadratic programming	7
cmaRs: A powerful predictive data mining package in R	7
histolab: A Python library for reproducible Digital Pathology preprocessing with automated testing	7
Web-based surface plasmon resonance signal processing system for fast analyte analysis	7
2BarG—A program to process split Hopkinson (Kolsky) bar test results	7
Version [1.2]- [pyrepo-mcda - Reference Objects based MCDA Software Package]	7
Version [1.1]- [Crispyn — A Python library for determining criteria significance with objective weighting methods]	7
FMD: A parallel library for performing classical molecular dynamics simulations	7

Taming the Panda with Python: A powerful duo for seamless robotics programming and integration	7
Applying positivity constraints to q-space trajectory imaging: The QTI+ implementation	7
An application for solving minimization problems using the Harmony search algorithm	7
Version 0.2 - CrackDect: Detecting crack densities in images of fiber-reinforced polymers	7
“Version 1.3.0 pyfao56: FAO-56 evapotranspiration in Python”	7
IMCP: A Python package for imbalanced and multiclass data classifier performance comparison	7
GeoWeightedModel : An R-Shiny package for Geographically Weighted Models	7
CoFly: An automated, AI-based open-source platform for UAV precision agriculture applications	7
I-STL2MOOSE: From STL data to integrated volumetrical meshes for MOOSE	7
Corrigendum to “BioNES: A plug-and-play MATLAB-based tool to use NES games for multimodal biofeedback” [SoftwareX 19 (2022) 101184]	7
Exploiting Simu5G for generating datasets for training and testing AI models for 5G/6G network applications	6
schlably: A Python framework for deep reinforcement learning based scheduling experiments	6
irs-partition: An Intrusion Response System utilizing Deep Q-Networks and system partitions	6
COMBEAMS: A numerical tool for the structural verification of steel-concrete composite beams	6
Automatic dataset builder for Machine Learning applications to satellite imagery	6
EcgScorer: An open source MATLAB toolbox for ECG signal quality assessment	6
TROVA: TRansport Of water VApor	6
PACU: Precision agriculture computational utilities	6
BOXVIA: Bayesian optimization executable and visualizable application	6
LayerFold: A Python library to reduce the depth of neural networks	6
PyECOM: A Python tool for analyzing and simulating Energy Communities	6
LIC: An R package for optimal subset selection for distributed data	6
BiometricIdentity dApp: Decentralized biometric authentication based on fuzzy commitment and blockchain	6
Discrete Element Simulations of particles interacting via capillary forces using MercuryDPM	6
pyMechOpt: A Python toolbox for optimizing of reaction mechanisms	6
Subgroups: A Python library for Subgroup Discovery	6
DynaProg: Deterministic Dynamic Programming solver for finite horizon multi-stage decision problems	6
Thermofeel: A python thermal comfort indices library	6
SPARC: Simulation Package for Ab-initio Real-space Calculations	6
pySuStaIn: A Python implementation of the Subtype and Stage Inference algorithm	6
AllInOne Pre-processing: A comprehensive preprocessing framework in plant field phenotyping	6
IFC2BCM: A Tool for Generating IndoorGML and Building Configuration Model from IFC	6
iCorrVision-2D: An integrated python-based open-source Digital Image Correlation software for in-plane measurements (Part 1)	6
Corrigendum to “CDB-AP: An application for coincidence Doppler broadening spectroscopy analysis” [SoftwareX 23 (2023) 101475]	6
pyFIRI — A free and open source Python software package of the non-auroral Earth’s lower ionosphere	6
FRESA.CAD::ILAA: Estimating the exploratory residualization transform	6
WACline: A Software Product Line to harness heterogeneity in Web Annotation	6
PyWindAM: A Python software for wind field analysis and cloud-based data management	6
pyFDM: A Python library for uncertainty decision analysis methods	6
AISLE: A matchmaking tool for pairing SMEs with digital solutions	6
life: A flexible, high performance library for the numerical solution of complex finite element problems	6
direpack: A Python 3 package for state-of-the-art statistical dimensionality reduction methods	6
Latent-dry: Solar drying with latent heat storage in Python, Fortran and TRNSYS	6
Ignis: A one-dimensional laminar flame code	5
XCompress: LLM assisted Python-based text compression toolkit	5
Toward efficient data science: A comprehensive MLOps template for collaborative code development and automation	5
LFG: An easy-to-use realistic synthetic LandFill Generator	5
action-rules: GPU-accelerated Python package for counterfactual explanations and recommendations	5
highRES-Europe: The high spatial and temporal Resolution Electricity System model for Europe	5
CensSpatial: An R package for estimation and diagnostics in spatial censored regression models	5
Update 2.0 to “ViroCon: A software to compute multivariate extremes using the environmental contour method”	5
Federated Learning with Swift: An Extension of Flower and Performance Evaluation	5
EdgeCloud Mon: A lightweight monitoring stack for K3s clusters	5
Ranflood: A mitigation tool based on the principles of data flooding against ransomware	5
ShakerMaker: A framework that simplifies the simulation of seismic ground-motions	5
Raman Selection Rules Calculator: A simplified selection rules calculator for Raman spectroscopy experiment	5
DSAIL-TreeVision: A software tool for extracting tree biophysical parameters from stereoscopic images	5
ProADV: A toolkit for enhancing water dynamics research using acoustic doppler velocimeter devices	5
Gintegrator: Enhancing biological sequences data integration with real-time identifier translation	5
ShopiRound: An Android application-based e-commerce system to find products nearby using travelling salesman problem	5
ScoreREM: A user-friendly Matlab-GUI for rapid eye movement (REM) sleep microstructure (Phasic/Tonic) annotation and quantification	5
BioEmoDetector: A flexible platform for detecting emotions from health narratives	5
NEFBDAA — .NET Environment for Building Dynamic Angular Applications	5
Version 2.0 - pyFIRI — A free and open source Python software package of the non-auroral Earth’s lower ionosphere	5
NESIM-RT: A real-time distributed spiking neural network simulator	5
MPAT: Modular Petri Net Assembly Toolkit	5
gnss_lib_py: Analyzing GNSS data with Python	5
GradeStat: An R package for grade correspondence analysis	5
Version [1.1]–[pyrepo-mcda — Reference Objects based MCDA Software Package]	5
TDF: A compact file format plugin for FEniCS	5
Federated learning secure model: A framework for malicious clients detection	5
onlineBcp: An R package for online change point detection using a Bayesian approach	5
PSGpower: A MATLAB toolbox for analyzing sleep EEG data	5
WebRISC-V: A 32/64-bit RISC-V pipeline simulation tool	5
Scilab-RL: A software framework for efficient reinforcement learning and cognitive modeling research	5
LiPTool: A tool for learning-based autonomous index placement in databases	5
GγSANDnet: A neural network tool for prediction of shear stiffness (G) shear strain (γ) relationship for sands	5
DynExp—Highly flexible laboratory automation for dynamically changing classical and quantum experiments	5
WordListsAnalytics: An R package for multiple data analysis of Property Listing Tasks	5
CitySolution: A complaining task distributive mobile application for smart city corporation using deep learning	5
YADPF: A reusable deterministic dynamic programming implementation in MATLAB	5
PNW-Cnet v4: Automated species identification for passive acoustic monitoring	4
PowerSystems.jl — A power system data management package for large scale modeling	4
Kernel Tuning Toolkit	4
MatHH: A Matlab-based Hyper-Heuristic framework	4
SMART-TeleLoad: A new graphic user interface to generate affective loads for teleoperation	4
Davos: A Python package “smuggler” for constructing lightweight reproducible notebooks	4
FEniCS–preCICE: Coupling FEniCS to other simulation software	4
omicR: A tool to facilitate BLASTn alignments for sequence data	4
QuantuMoonLight: A low-code platform to experiment with quantum machine learning	4
IV-PSNR: Software for immersive video objective quality evaluation	4
Version [1.1]- [pyFDM: A python library for uncertainty decision analysis methods]	4
Star-XP: A simulation framework for Polar-2/ low energy X-ray polarization detector	4
WITio: A MATLAB data evaluation toolbox to script broader insights into big data from WITec microscopes	4
MarineEpi: A GUI-based Matlab toolbox to simulate marine pathogen transmission	4