SoftwareX

Article	Citations
An open-source parallel topology optimization framework based on unstructured 3D FEA using PETSc and Eigen	195
FMD: A parallel library for performing classical molecular dynamics simulations	168
ReflectDetect: A software tool for AprilTag-guided in-flight radiometric calibration for UAV-mounted 2D snapshot multi-camera imagery	147
NCC: An R-package for analysis and simulation of platform trials with non-concurrent controls	145
FS-Studio: An extensive and efficient feature selection experimentation tool for Weka Explorer	115
TD-COF: A new method for detecting tandem duplications in next generation sequencing data	83
CNV-Z; a new tool for detecting copy number variation in next generation sequencing data	76
McDAPS: A multi-channel physiological signals display and analysis system for clinical researchers	58
MAWA: Enhancing mobile web browsing through web augmentation for improved user experience	46
Web-based surface plasmon resonance signal processing system for fast analyte analysis	44
HOST: Harmonic oscillator seasonal-trend model for analyzing the reoccurring nature of extreme events	41
Saihu: A common interface of worst-case delay analysis tools for time-sensitive networks	41
STUDIO: A Python graphical tool for analyzing street user observations from video data	41
CacheSim: A cache simulation framework for evaluating caching algorithms on resource-constrained edge devices	39
TROVA: TRansport Of water VApor	37
Q-Facies: A tool for the quantitative interpretation of groundwater hydrochemical facies	35
IDOL: A web application for mixed integer linear multiobjective optimization	34
Version [1.1]- [Handling decision-making in intuitionistic fuzzy environment: PyIFDM package]	32
OpenIPDM: A probabilistic framework for estimating the deterioration and effect of interventions on bridges	32
Update (3.0) to LyapXool: Quadratic programming	32
I-STL2MOOSE: From STL data to integrated volumetrical meshes for MOOSE	31
MyAphasia: A mobile application for the treatment of Aphasia in a hospital environment	30
ParetoInvest: Integrating real-time financial data and multi-objective meta-heuristics for portfolio optimization	30
Muscle fatigue monitoring and analysis system: Myosense	29
AURA: An Adaptive Utility Ranking Algorithm for Multi-Criteria Decision Making with Python-based decision support interface	28

juSPH: A Julia-based open-source package of parallel Smoothed Particle Hydrodynamics (SPH) for dam break problems	28
SACETraj: An AutoCAD Catmull-Rom Spline Trajectory Interpolator	28
UQpy Version 4.2: Uncertainty quantification with Python	28
Exploiting Simu5G for generating datasets for training and testing AI models for 5G/6G network applications	27
10StepsinExcelforWoS: Streamlining bibliometric analysis in web of science using Microsoft excel	27
BOXVIA: Bayesian optimization executable and visualizable application	27
Tab2KGWiz: Interactive assistant for mapping tabular data to knowledge graphs	26
Editorial Board	26
XR4MCR: Multiplayer collaborative robotics maintenance training platform in extended reality	25
An application for solving minimization problems using the Harmony search algorithm	24
FIDWaC - Fast inverse distance weighting and compression	24
SST v1.0.0 with C API: Pluggable security solution for the Internet of Things	24
ResoFox: A GUI-based tool for calculating resolution and relative intensity of neutron powder diffractometers	24
BiometricIdentity dApp: Decentralized biometric authentication based on fuzzy commitment and blockchain	24
XCompress: LLM assisted Python-based text compression toolkit	23
VEqMon2D—Equations of motion generation tool of 2D vehicles with Matlab	23
DSIPTS: A high productivity environment for time series forecasting models	23
Rcall: An R interface for MATLAB	23
clickR: Semi-automatic pre-processing of messy data with change tracking for integral dataset cleaning	23
CensSpatial: An R package for estimation and diagnostics in spatial censored regression models	22
T-Ridership: A web tool for reprogramming public transportation fleets to minimize COVID-19 transmission	22
EnMAP-Box: Imaging spectroscopy in QGIS	22
GetSensorData: An extensible Android-based application for multi-sensor data registration	22
Turn+: A MATLAB-based software for dynamic turning, chatter analysis, and surface roughness prediction	21
Version 1.1.1 - TROVA: TRansport Of water VApor	21
WITio: A MATLAB data evaluation toolbox to script broader insights into big data from WITec microscopes	21
The StaDyn programming language	20
REFRAME–A software framework for managing reactive dependencies in object-oriented applications	20
Kunai: A static analysis framework for Android apps	20
pyMechOpt: A Python toolbox for optimizing of reaction mechanisms	20
GenSDF: An MPI-Fortran based signed-distance-field generator for computational fluid dynamics applications	19
BioEmoDetector: A flexible platform for detecting emotions from health narratives	19
BBR: An open-source standard workflow based on biophysical crop parameters for automatic Botrytis cinerea assessment in vineyards	19
ScoreREM: A user-friendly Matlab-GUI for rapid eye movement (REM) sleep microstructure (Phasic/Tonic) annotation and quantification	19
Version [2.0] — [pyMCMA: Uniformly distributed Pareto-front representation]	18
DataMetProcess: An open-source package and Shiny application for the acquisition and processing of meteorological data from INMET	18
Flow-models 2.0: Elephant flows modeling and detection with machine learning	18
NUCLEUS – A Matlab-based graphical user interface for forward and inverse modelling of NMR relaxometry data	18
QuITO: Numerical software for constrained nonlinear optimal control problems	17
LitOrganizer: Automating the process of data extraction and organization for scientific literature reviews	17
MALVADA: A framework for generating datasets of malware execution traces	17
pyRuleAnalyzer: A python package for enhancing decision rules in tree-based machine learning models	17
HAMLET: A modular agent-based Python framework for energy markets and systems	17
DFT-MF: Enhanced deepfake detection using mouth movement and transfer learning	16
DAUD: A data driven algorithm to find discrete approximations of unknown continuous distributions	16
SolarQGIS: A QGIS application for calculating solar radiation on 3D vector GIS data	16
PNW-Cnet v4: Automated species identification for passive acoustic monitoring	16
SpinGlassPEPS.jl: Tensor-network package for Ising-like optimization on quasi-two-dimensional graphs	16
Climatrix: Xarray accessor for climate data sampling and reconstruction	16
Version 2 — RPExpand: Software for Riesz projection expansion of resonance phenomena	16

AMBER: Algorithm for Multiplexing spectrometer Background Estimation with Rotation-independence	16
GraphXplore: Visual exploration and accessible preprocessing of medical data	15
ShinyGAStool: A user-friendly tool for candidate gene association studies	15
PATSMA: Parameter Auto-tuning for Shared Memory Algorithms	15
PLATFORM: Parallel Linear Algebra Tool FOr Reduced Modeling	15
E2	15
Diagnostic Expert Advisor: A platform for developing machine learning models on medical time-series data	15
Ordinalysis: Interpretability of multidimensional ordinal data	15
clusEvol: An R package for Cluster Evolution Analytics	15
MobiScout: A scalable cloud-based driving and activity monitoring platform featuring an IOS app and a WatchOS extension	15
xkl: A legacy software for detailed acoustic analysis of speech made modern	15
JGMP: Java bindings and wrappers for the GMP library	15
PyQBench: A Python library for benchmarking gate-based quantum computers	14
MorphoGen: Topology optimization software for Extremely Modular Systems	14
MitoSeg: Mitochondria segmentation tool	14
TeDDy: Templated decision diagram library	14
Version [2.0]-[NeoCoMM: Neocortical neuro-inspired computational model for realistic microscale simulations]	14
Floodsar: Automatic mapping of river flooding extent from multitemporal SAR imagery	14
ModelicaGridData: Massive power system simulation data generation and labeling tool using Modelica and Python	14
Pynblint: A quality assurance tool to improve the quality of Python Jupyter notebooks	14
Ecological macroeconomics with Philia 1.0	14
Version [7.1] – [IV-PSNR: Software for immersive video objective quality evaluation]	14
QPPLab: A generally applicable software package for detecting, analyzing, and visualizing large-scale quasiperiodic spatiotemporal patterns (QPPs) of brain activity	13
Version 2.0.0 - M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations	13
A C++17 thread pool for high-performance scientific computing	13
Spec2chat: A Python library for task-oriented dialogue generation from OpenAPI specifications	13
pyBaram: Parallel compressible flow solver in high-performance Python for teaching and research	13
EBAT: Evaluation of Behavioural Authentication Toolbox	13
Version v2.0.0 — Reinforced-lib: Rapid prototyping of reinforcement learning solutions	13
rDSM—A robust Downhill Simplex Method software package for high-dimensional optimization problems	13
ZEN-garden: Optimizing energy transition pathways with user-oriented data handling	13
Development of an ABAQUS™ plug-in for predicting composite plates stiffness with in-plane periodicity	13
Masked-Piper: Masking personal identities in visual recordings while preserving multimodal information	13
NER-FAM: Named entity recognition with faceted aggregation for multimedia web search engines	13
P2PFaaS: A framework for FaaS peer-to-peer scheduling and load balancing in Fog and Edge computing	13
APLOSE: A web-based annotation platform for underwater passive acoustic monitoring	13
WireGuard-AES: Hardware based encryption to WireGuard for VPN gateways	12
PyCinemetrics: Computational film studies tool based on deep learning and PySide2	12
DigiRhythm: An R package for evaluating circadian rhythmicity in animals using the degree of functional coupling	12
Atlantic cod growth model: Open source Python package for numerical growth experiments	12
Spectrally regularised LVMs: A spectral regularisation framework for latent variable models designed for single-channel applications	12
HITS: Hyperplanes intersection tabu search for maximum score estimation	12
REMLA: An R package for robust expectation-maximization estimation for latent variable models	12
Compression of triangulated solids’ surfaces by Decimating Reconstructable Triangles	12
Phenoflow-ML: A next-generation phenotyping framework to capture ML-based phenotypes	12
Causal ML: Python package for causal inference machine learning	12
TrAQ: A novel, versatile, semi-automated, two-dimensional motor behavioural tracking software	12
Binary complex amplitude application: An all-in-one Matlab application for the advanced laser beam shaping with digital micromirror device	12
Scymol: A python-based software package for initializing and running molecular dynamics simulations using LAMMPS	11
pyMeshFOAM: Automated meshing for CFD and fluid–structure simulations	11
Corrigendum to “RAVSim v2.0: Enhanced visualization and comparative analysis for neural network models” [SoftwareX volume 29, February 2025 Article Number: 102006]	11
OpenLSA: An open-source toolbox for computing full-field displacements from images of periodic patterns	11
India Policy Insights: A geospatial and temporal data science and visualization platform and architecture	11
“dynmix”: An R package for the estimation of dynamic finite mixtures	11
Version [1.1]—[MSAT: Matrix stability analysis tool for shock-capturing schemes]	11
Modelling biocontrol of invasive insects using WaspSim: A MATLAB simulation model	11
SimViz: Interactive visualizations to analyze similarity measures	11
Emipy: An open-source Python-based tool to analyze industrial emissions in Europe	11
STM: A software tool for predicting daily temperature in stored animal slurry	11
Gdistns: R package for maximum goodness-of-fit estimates of the generalized G distributions	11
Decidim.viz: A data dashboard prototype for a digital democracy platform	11
TaBSA – A framework for training and benchmarking algorithms for scheduling tasks for mobile robots working in dynamic environments	11
TraClets: A trajectory representation and classification library	10
gosset: An R package for analysis and synthesis of ranking data in agricultural experimentation	10
An open-source toolbox for curvature capture in porous media	10
FLAGR: A flexible high-performance library for rank aggregation	10
SmarTS: A Java package for smart contract test suite generation and execution	10
CellRex: Software platform for managing biological cell data	10
ScaFi: A Scala DSL and Toolkit for Aggregate Programming	10
TSSEARCH: Time Series Subsequence Search Library	10
Docker Unified UIMA Interface: New perspectives for NLP on big data	10
EMDLAB: An open-source finite element package for electromagnetic analysis of electrical machines	10
Power TAC: Software architecture for a competitive simulation of sustainable smart energy markets	10
Performing highly efficient Minima Hopping structure predictions using the Atomic Simulation Environment (ASE)	10
Cyberattack detection through GPML: Graph Processing for Machine Learning	10
CIDS-Sim: Simulator for collaborative intrusion detection system based on federated learning	10
Geospatial Analytics Extension for KNIME	10
FuzConvSteganalysis: Steganalysis via fuzzy logic and convolutional neural network	10
HuReTEx: From deep learning models to explainable information flow models	10
DroneTimeline: Forensic timeline analysis for drones	10

ArcNLET-Py: An ArcGIS-based nitrogen load estimation toolbox developed using python for ArcGIS pro	10
Streetscape morphometrics: Expanding momepy to analyze urban form from the street point of view	10
RIPN: A tool for implementing cyber-physical systems by using interpreted Petri Nets and teleo-reactive programs	10
HETOOL: A Half-Edge Topological Object-Oriented Library for generic 2-D geometric modeling	9
Update 2.5 to “Takin: An open-source software for experiment planning, visualisation, and data analysis”, (PII: S2352711016300152)	9
3.0 - MOOSE: Enabling massively parallel multiphysics simulations	9
Corrigendum to “pyLAIS: A Python package for Layered Adaptive Importance Sampling” [SoftwareX 29 (2025), 101976]	9
PickShift: A user-friendly Python tool to assess the surficial uncertainties associated with polygons extracted from historical planimetric data	9
qNoise: A generator of non-Gaussian colored noise	9
SWANe: Standardized workflow for advanced neuroimaging in epilepsy	9
OpenTEPES: Open-source Transmission and Generation Expansion Planning	9
〈	9
Version [	9
SOLDIER: SOLution for Dam behavior Interpretation and safety Evaluation with boosted Regression trees	9
RAVSim v2.0: Enhanced visualization and comparative analysis for neural network models	9
Version [2.0] - [VIC-Borg: Multiobjective automatic calibration toolkit for VIC model]	9
tsdownsample: High-performance time series downsampling for scalable visualization	9
Traffic weaver: Semi-synthetic time-varying traffic generator based on averaged time series	9
Yekta: A low-code framework for automated test models generation	9
MaSMaker: An open-source, portable software to create and integrate maze-like surfaces into arbitrary geometries	9
SimilarityTS: Toolkit for the evaluation of similarity for multivariate time series	9
Version [1.1.0]- [DLDiagnosis: A mobile and web application for diseases classification using Deep Learning]	9
Corrigendum to “LFG: An easy-to-use realistic synthetic LandFill Generator” [Software X Volume 28, December 2024, 101936]	9
Grain2mesh: A Python and cubit mesh generator from unprocessed mesoscale images	9
Hyperomet: An OpenSees interface for nonlinear analysis of unreinforced masonry buildings	9
VERONA: A python library for benchmarking deep learning in business process monitoring	9
PyBanshee version (1.0): A Python implementation of the MATLAB toolbox BANSHEE for Non-Parametric Bayesian Networks with updated features	8
KneeBones3Dify: Open-source software for segmentation and 3D reconstruction of knee bones from MRI data	8
1DCSEMQWE: 1D Controlled Source Electromagnetic Method in Geophysics Using Quadrature With Extrapolation	8
Growth Data—An automatic solution for seedling growth analysis via RGB-Depth imaging sensors	8
TrustML: A Python package for computing the trustworthiness of ML models	8
OSLiFe-DiSC: Open source licenses discovering, selecting and comparing	8
RINEXAV: GNSS global network selection open-source software based on qualitative analysis of RINEX files	8
TremorSoft: An decision support application for differential diagnosis between Parkinson’s disease and essential tremor	8
CtrlAer: Programmable real-time execution of scientific experiments using a domain specific language for the Raspberry Pi Pico/Pico 2	8
Spectral Imaging Deep Learning Mapper - SpecDeepMap: An open-source EnMAP-Box semantic segmentation application for hyper- and multispectral mapping	8
Observer: An open-source framework for automating spectator for Real-time Strategy game of StarCraft	8
PCAfold 2.0—Novel tools and algorithms for low-dimensional manifold assessment and optimization	8
DATTES: Data analysis tools for tests on energy storage	8
hyperbox-brain: A Python toolbox for hyperbox-based machine learning algorithms	8
IST-ROS: A flexible object segmentation and tracking framework for robotics applications	8
pyJSON Schema Loader and JSON Editor: A tool for file-based metadata management	8
End to end navigation stack for nuclear power plant inspection with mobile robot	8
refellips: A Python package for the analysis of variable angle spectroscopic ellipsometry data	8
svds-C: A multi-thread C code for computing truncated singular value decomposition	8
Leveraging OpenSimMPLS: A simulation platform for GoS/MPLS networks in research and education	8
FD-REST: A lightweight RESTful platform for real-time fault detection and diagnosis in industrial systems	8
Climaticpark-py - A python framework for the climatic simulation of vehicular parking lots	8
Population potential on catchment area (PPCA): A Python-based tool for worldwide geospatial population analysis	8
TIQA-PSI: Toolbox for perceptual Image Quality Assessment of Pan-Sharpened Images	8
Version [1.0]- HAT-VIS — A MATLAB-based hypergraph visualization tool	8
Robustimizer: A graphical user interface application for efficient uncertainty quantification, robust optimization, and reliability-based optimization of processes and designs	8
robustDEA: A Java library for robust efficiency analysis	8
A computerized tool for the kinematic limit analysis of 2D masonry structures failing on a tilting table	8
Neutrostat: An R package for neutrosophic statistical models	8
quicR: An R library for streamlined data handling of real-time quaking induced conversion assays	8
ASSUME: An agent-based simulation framework for exploring electricity market dynamics with reinforcement learning	8
MicEMD: Open-source toolbox for electromagnetic modeling, inversion, and classification in underground metal target detection	8
Digital ecosystem for FAIR time series data management in environmental system science	7
HICA: A MATLAB-based hierarchical image clustering algorithm for classifying parts suitable for additive and traditional manufacturing technologies	7
Version [1.1]- [Crispyn — A Python library for determining criteria significance with objective weighting methods]	7
Wave-DNA: A software tool for simulating nonlinear acoustic waves emitted by moving boundaries	7
A WebExtension framework for experimentation and evaluation of webpage segmentation methods	7
LeXInt: GPU-accelerated exponential integrators package	7
UrbanHeatOpt: A software framework for supporting municipal heat transition planning	7
3DRSP: Matlab-based random sphere packing code in three dimensions	7
GeoEPIC: A comprehensive python package for spatial implementation of EPIC crop simulation model	7
Enabling scientific machine learning in MOOSE using Libtorch	7
Rhizomer: Interactive semantic knowledge graphs exploration	7
Matlatzinca: A PyBANSHEE-based graphical user interface for elicitation of non-parametric Bayesian networks from experts	7
CLIMB: Framework for CLIMate data bias-adjustment and downscaling	7
PyDicer: An open-source python library for conversion and analysis of radiotherapy DICOM data	7
In-Cognitive: A web-based Python application for fuzzy cognitive map design, simulation, and uncertainty analysis based on the Monte Carlo method	7
Subgroups: A Python library for Subgroup Discovery	7
Data4Land: How to enrich land-use/land-cover with historical vector(s)	7
FCM-VSS: An AI powered secured fuzzy cognitive maps management toolkit for visualization, simulation and summarization	7
HistomicsTK: A Python toolkit for pathology image analysis algorithms	7
PhishingWebCollector: Async python library for automated phishing feed collection	7
ExactPack: A python library of exact analytic solutions	7
ENTIRETY — sEmanNTIc pRovisioning and govErning ioT devices in smart energY domain	7
pymetamodels: A Python package for metamodeling and design automation	7
AMED: Aggregated multimedia exploratory and discovery search software	7
Think inside the (mk)box—A tool for creating and deploying application-specific Linux images utilized in a SiLA software development process	7
DeepWealth: A generalizable open-source deep learning framework using satellite images for well-being estimation	7
Version [1.2]- [pyrepo-mcda - Reference Objects based MCDA Software Package]	7
Identifying safety–critical concerns in unmanned aerial vehicle software platforms with SALIENT	7
The Contiki-NG open source operating system for next generation IoT devices	7
Benopt-Heat: An economic optimization model to identify robust bioenergy technologies for the German heat transition	7
CoCoStyle: Mixed initiative co-creative system to support creative process of fashion design	7
Computing Continuum Simulator: A comprehensive framework for continuum architecture evaluation	7
VaSP: Vascular Fluid–Structure Interaction Pipeline	7
2D-xtDCR-LTBEM: A Fortran code for numerical solutions to the unsteady anisotropic-DCR equation of spatio-temporal coefficients	7
Open sensing: An interactive online tool for environmental data collection, monitoring, analysis, and modelling for custom environmental sensor devices	7
A new approach for drone tracking with drone using Proximal Policy Optimization based distributed deep reinforcement learning	7
DynExp—Highly flexible laboratory automation for dynamically changing classical and quantum experiments	6