SoftwareX

Article	Citations
FMD: A parallel library for performing classical molecular dynamics simulations	200
NCC: An R-package for analysis and simulation of platform trials with non-concurrent controls	169
FS-Studio: An extensive and efficient feature selection experimentation tool for Weka Explorer	152
TD-COF: A new method for detecting tandem duplications in next generation sequencing data	148
McDAPS: A multi-channel physiological signals display and analysis system for clinical researchers	118
MAWA: Enhancing mobile web browsing through web augmentation for improved user experience	83
Web-based surface plasmon resonance signal processing system for fast analyte analysis	79
HOST: Harmonic oscillator seasonal-trend model for analyzing the reoccurring nature of extreme events	58
STUDIO: A Python graphical tool for analyzing street user observations from video data	52
Saihu: A common interface of worst-case delay analysis tools for time-sensitive networks	46
CacheSim: A cache simulation framework for evaluating caching algorithms on resource-constrained edge devices	42
Q-Facies: A tool for the quantitative interpretation of groundwater hydrochemical facies	42
TROVA: TRansport Of water VApor	42
Version [1.1]- [Handling decision-making in intuitionistic fuzzy environment: PyIFDM package]	39
Update (3.0) to LyapXool: Quadratic programming	37
I-STL2MOOSE: From STL data to integrated volumetrical meshes for MOOSE	35
OpenIPDM: A probabilistic framework for estimating the deterioration and effect of interventions on bridges	35
ParetoInvest: Integrating real-time financial data and multi-objective meta-heuristics for portfolio optimization	34
BOXVIA: Bayesian optimization executable and visualizable application	32
MyAphasia: A mobile application for the treatment of Aphasia in a hospital environment	32
Editorial Board	31
10StepsinExcelforWoS: Streamlining bibliometric analysis in web of science using Microsoft excel	31
Tab2KGWiz: Interactive assistant for mapping tabular data to knowledge graphs	30
ResoFox: A GUI-based tool for calculating resolution and relative intensity of neutron powder diffractometers	29
XR4MCR: Multiplayer collaborative robotics maintenance training platform in extended reality	29

An application for solving minimization problems using the Harmony search algorithm	28
SST v1.0.0 with C API: Pluggable security solution for the Internet of Things	28
juSPH: A Julia-based open-source package of parallel Smoothed Particle Hydrodynamics (SPH) for dam break problems	28
BiometricIdentity dApp: Decentralized biometric authentication based on fuzzy commitment and blockchain	28
AURA: An Adaptive Utility Ranking Algorithm for Multi-Criteria Decision Making with Python-based decision support interface	28
UQpy Version 4.2: Uncertainty quantification with Python	28
SACETraj: An AutoCAD Catmull-Rom Spline Trajectory Interpolator	28
An open-source parallel topology optimization framework based on unstructured 3D FEA using PETSc and Eigen	27
FIDWaC - Fast inverse distance weighting and compression	26
ReflectDetect: A software tool for AprilTag-guided in-flight radiometric calibration for UAV-mounted 2D snapshot multi-camera imagery	26
Exploiting Simu5G for generating datasets for training and testing AI models for 5G/6G network applications	26
CNV-Z; a new tool for detecting copy number variation in next generation sequencing data	26
IDOL: A web application for mixed integer linear multiobjective optimization	26
Muscle fatigue monitoring and analysis system: Myosense	25
XCompress: LLM assisted Python-based text compression toolkit	24
GeoLoadST: An open-source Python package for spatiotemporal load-instability analysis in distribution power networks	24
DSIPTS: A high productivity environment for time series forecasting models	24
PyWSNSim: A Python-based component-oriented simulation framework for sinkhole attack analysis in large-scale WSNs	24
T-Ridership: A web tool for reprogramming public transportation fleets to minimize COVID-19 transmission	23
GetSensorData: An extensible Android-based application for multi-sensor data registration	23
VEqMon2D—Equations of motion generation tool of 2D vehicles with Matlab	23
Turn+: A MATLAB-based software for dynamic turning, chatter analysis, and surface roughness prediction	22
CensSpatial: An R package for estimation and diagnostics in spatial censored regression models	22
DFT-MF: Enhanced deepfake detection using mouth movement and transfer learning	21
REFRAME–A software framework for managing reactive dependencies in object-oriented applications	21
pyMechOpt: A Python toolbox for optimizing of reaction mechanisms	21
The StaDyn programming language	21
DataMetProcess: An open-source package and Shiny application for the acquisition and processing of meteorological data from INMET	20
clickR: Semi-automatic pre-processing of messy data with change tracking for integral dataset cleaning	20
Version [2.0] — [pyMCMA: Uniformly distributed Pareto-front representation]	20
PNW-Cnet v4: Automated species identification for passive acoustic monitoring	20
GenSDF: An MPI-Fortran based signed-distance-field generator for computational fluid dynamics applications	20
DAUD: A data driven algorithm to find discrete approximations of unknown continuous distributions	19
Version 2 — RPExpand: Software for Riesz projection expansion of resonance phenomena	19
SolarQGIS: A QGIS application for calculating solar radiation on 3D vector GIS data	19
BioEmoDetector: A flexible platform for detecting emotions from health narratives	19
Climatrix: Xarray accessor for climate data sampling and reconstruction	19
ScoreREM: A user-friendly Matlab-GUI for rapid eye movement (REM) sleep microstructure (Phasic/Tonic) annotation and quantification	18
geonuts: An R package for mapping geolocations to European NUTS regions	18
FL-DApp: Open-source decentralized application for reputation in O-RAN federated learning	18
BIM-CAP: A tool for assessing building information modelling capabilities of architecture, engineering, construction and facilities management processes	18
FishTank.jl: A model-driven approach to gamified scientific modeling and visualization in Julia	18
SGLC-Calc: A MATLAB tool for comprehensive bidirectional satellite-ground laser communication link performance analysis	18
Rcall: An R interface for MATLAB	17
MALVADA: A framework for generating datasets of malware execution traces	17
WITio: A MATLAB data evaluation toolbox to script broader insights into big data from WITec microscopes	17
Version 1.1.1 - TROVA: TRansport Of water VApor	16
EnMAP-Box: Imaging spectroscopy in QGIS	16
Kunai: A static analysis framework for Android apps	16
BBR: An open-source standard workflow based on biophysical crop parameters for automatic Botrytis cinerea assessment in vineyards	16

NUCLEUS – A Matlab-based graphical user interface for forward and inverse modelling of NMR relaxometry data	16
SpinGlassPEPS.jl: Tensor-network package for Ising-like optimization on quasi-two-dimensional graphs	16
HAMLET: A modular agent-based Python framework for energy markets and systems	16
QuITO: Numerical software for constrained nonlinear optimal control problems	16
pyRuleAnalyzer: A python package for enhancing decision rules in tree-based machine learning models	16
WicdPico: A modular CircuitPython framework for affordable, web-based instrumentation and control in scientific research	16
Flow-models 2.0: Elephant flows modeling and detection with machine learning	16
Version [7.1] – [IV-PSNR: Software for immersive video objective quality evaluation]	15
PLATFORM: Parallel Linear Algebra Tool FOr Reduced Modeling	15
LitOrganizer: Automating the process of data extraction and organization for scientific literature reviews	15
ModelicaGridData: Massive power system simulation data generation and labeling tool using Modelica and Python	15
TeDDy: Templated decision diagram library	15
ZEN-garden: Optimizing energy transition pathways with user-oriented data handling	15
E2	15
Development of an ABAQUS™ plug-in for predicting composite plates stiffness with in-plane periodicity	15
P2PFaaS: A framework for FaaS peer-to-peer scheduling and load balancing in Fog and Edge computing	15
MobiScout: A scalable cloud-based driving and activity monitoring platform featuring an IOS app and a WatchOS extension	15
AMBER: Algorithm for Multiplexing spectrometer Background Estimation with Rotation-independence	15
clusEvol: An R package for Cluster Evolution Analytics	15
pyBaram: Parallel compressible flow solver in high-performance Python for teaching and research	15
PATSMA: Parameter Auto-tuning for Shared Memory Algorithms	14
JGMP: Java bindings and wrappers for the GMP library	14
Spec2chat: A Python library for task-oriented dialogue generation from OpenAPI specifications	14
Floodsar: Automatic mapping of river flooding extent from multitemporal SAR imagery	14
ShinyGAStool: A user-friendly tool for candidate gene association studies	14
Pynblint: A quality assurance tool to improve the quality of Python Jupyter notebooks	14
MorphoGen: Topology optimization software for Extremely Modular Systems	14
APLOSE: A web-based annotation platform for underwater passive acoustic monitoring	13
OnlineNeuro: Active online learning for effective exploration of neural simulation parameters	13
TrAQ: A novel, versatile, semi-automated, two-dimensional motor behavioural tracking software	13
NER-FAM: Named entity recognition with faceted aggregation for multimedia web search engines	13
A C++17 thread pool for high-performance scientific computing	13
EBAT: Evaluation of Behavioural Authentication Toolbox	13
Enyxe: A modular framework for the elastoplastic analysis of polycrystalline materials in damask	13
fluxfixer: An R package for producing thermal dissipation sap flow data with high quality control	13
FMUiL: An open-source package for in-the-loop simulations with functional mock-up units	13
HIT: A fully automated mosaicking software for corneal confocal microscopy	13
ArUco Nano: a simpler, faster, and more reliable fiducial marker detector	13
py4dgeo: Open-source scientific software for topographic change analysis in 3D/4D geographic point clouds	13
Version v2.0.0 — Reinforced-lib: Rapid prototyping of reinforcement learning solutions	13
Version 2.0.0 - M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations	13
Version [2.0]-[NeoCoMM: Neocortical neuro-inspired computational model for realistic microscale simulations]	12
Causal ML: Python package for causal inference machine learning	12
WireGuard-AES: Hardware based encryption to WireGuard for VPN gateways	12
Diagnostic Expert Advisor: A platform for developing machine learning models on medical time-series data	12
MitoSeg: Mitochondria segmentation tool	12
PyQBench: A Python library for benchmarking gate-based quantum computers	12
Phenoflow-ML: A next-generation phenotyping framework to capture ML-based phenotypes	12
QPPLab: A generally applicable software package for detecting, analyzing, and visualizing large-scale quasiperiodic spatiotemporal patterns (QPPs) of brain activity	12
GraphXplore: Visual exploration and accessible preprocessing of medical data	12
Ecological macroeconomics with Philia 1.0	12
PyCinemetrics: Computational film studies tool based on deep learning and PySide2	12
Spectrally regularised LVMs: A spectral regularisation framework for latent variable models designed for single-channel applications	12
Masked-Piper: Masking personal identities in visual recordings while preserving multimodal information	12
xkl: A legacy software for detailed acoustic analysis of speech made modern	12
rDSM—A robust Downhill Simplex Method software package for high-dimensional optimization problems	11
Binary complex amplitude application: An all-in-one Matlab application for the advanced laser beam shaping with digital micromirror device	11
FuzConvSteganalysis: Steganalysis via fuzzy logic and convolutional neural network	11
Emipy: An open-source Python-based tool to analyze industrial emissions in Europe	11
An open-source toolbox for curvature capture in porous media	11
Modelling biocontrol of invasive insects using WaspSim: A MATLAB simulation model	11
pyMeshFOAM: Automated meshing for CFD and fluid–structure simulations	11
Ordinalysis: Interpretability of multidimensional ordinal data	11
Decidim.viz: A data dashboard prototype for a digital democracy platform	11
CIDS-Sim: Simulator for collaborative intrusion detection system based on federated learning	11
STM: A software tool for predicting daily temperature in stored animal slurry	11
TSSEARCH: Time Series Subsequence Search Library	11
SimViz: Interactive visualizations to analyze similarity measures	11
Version [1.1]—[MSAT: Matrix stability analysis tool for shock-capturing schemes]	11
Atlantic cod growth model: Open source Python package for numerical growth experiments	10
TaBSA – A framework for training and benchmarking algorithms for scheduling tasks for mobile robots working in dynamic environments	10
ArcNLET-Py: An ArcGIS-based nitrogen load estimation toolbox developed using python for ArcGIS pro	10
gosset: An R package for analysis and synthesis of ranking data in agricultural experimentation	10
CellRex: Software platform for managing biological cell data	10
SimilarityTS: Toolkit for the evaluation of similarity for multivariate time series	10
REMLA: An R package for robust expectation-maximization estimation for latent variable models	10
HITS: Hyperplanes intersection tabu search for maximum score estimation	10
“dynmix”: An R package for the estimation of dynamic finite mixtures	10
Streetscape morphometrics: Expanding momepy to analyze urban form from the street point of view	10
Scymol: A python-based software package for initializing and running molecular dynamics simulations using LAMMPS	10

SmarTS: A Java package for smart contract test suite generation and execution	10
Geospatial Analytics Extension for KNIME	10
Corrigendum to “RAVSim v2.0: Enhanced visualization and comparative analysis for neural network models” [SoftwareX volume 29, February 2025 Article Number: 102006]	10
Cyberattack detection through GPML: Graph Processing for Machine Learning	10
FLAGR: A flexible high-performance library for rank aggregation	10
EMDLAB: An open-source finite element package for electromagnetic analysis of electrical machines	10
HuReTEx: From deep learning models to explainable information flow models	10
Power TAC: Software architecture for a competitive simulation of sustainable smart energy markets	10
RIPN: A tool for implementing cyber-physical systems by using interpreted Petri Nets and teleo-reactive programs	10
DigiRhythm: An R package for evaluating circadian rhythmicity in animals using the degree of functional coupling	10
SPARS: A reinforcement learning-enabled simulator for power management in HPC job scheduling	9
Multi-agent home energy management assistant (HEMA)	9
PickShift: A user-friendly Python tool to assess the surficial uncertainties associated with polygons extracted from historical planimetric data	9
Compression of triangulated solids’ surfaces by Decimating Reconstructable Triangles	9
tsdownsample: High-performance time series downsampling for scalable visualization	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
Update 2.5 to “Takin: An open-source software for experiment planning, visualisation, and data analysis”, (PII: S2352711016300152)	9
Version [1.1.0]- [DLDiagnosis: A mobile and web application for diseases classification using Deep Learning]	9
MemProfiler: A tracing and analysis system for memory fragmentation	9
Gdistns: R package for maximum goodness-of-fit estimates of the generalized G distributions	9
Expand: An ad-hoc file system for parallel and distributed environments	9
TraClets: A trajectory representation and classification library	9
FD-REST: A lightweight RESTful platform for real-time fault detection and diagnosis in industrial systems	9
Performing highly efficient Minima Hopping structure predictions using the Atomic Simulation Environment (ASE)	9
Version [	9
SOLDIER: SOLution for Dam behavior Interpretation and safety Evaluation with boosted Regression trees	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
DroneTimeline: Forensic timeline analysis for drones	9
Docker Unified UIMA Interface: New perspectives for NLP on big data	9
India Policy Insights: A geospatial and temporal data science and visualization platform and architecture	9
OpenLSA: An open-source toolbox for computing full-field displacements from images of periodic patterns	9
MicEMD: Open-source toolbox for electromagnetic modeling, inversion, and classification in underground metal target detection	9
Scythe: A Python toolkit for orchestrating embarrassingly parallel experiments via distributed queues	9
qNoise: A generator of non-Gaussian colored noise	9
Hyperomet: An OpenSees interface for nonlinear analysis of unreinforced masonry buildings	9
RAVSim v2.0: Enhanced visualization and comparative analysis for neural network models	9
ScaFi: A Scala DSL and Toolkit for Aggregate Programming	9
TremorSoft: An decision support application for differential diagnosis between Parkinson’s disease and essential tremor	8
svds-C: A multi-thread C code for computing truncated singular value decomposition	8
SWANe: Standardized workflow for advanced neuroimaging in epilepsy	8
ASSUME: An agent-based simulation framework for exploring electricity market dynamics with reinforcement learning	8
RINEXAV: GNSS global network selection open-source software based on qualitative analysis of RINEX files	8
APScavenge: Centralized WPA-Enterprise network security assessment tool	8
duet-tools: A python package for interacting with the DUET program	8
AIoTU: An open-source IoT and machine learning platform for smart agriculture and yield prediction	8
Climaticpark-py - A python framework for the climatic simulation of vehicular parking lots	8
Version [2.0] - [VIC-Borg: Multiobjective automatic calibration toolkit for VIC model]	8
MaSMaker: An open-source, portable software to create and integrate maze-like surfaces into arbitrary geometries	8
VERONA: A python library for benchmarking deep learning in business process monitoring	8
Yekta: A low-code framework for automated test models generation	8
Leveraging OpenSimMPLS: A simulation platform for GoS/MPLS networks in research and education	8
PyBanshee version (1.0): A Python implementation of the MATLAB toolbox BANSHEE for Non-Parametric Bayesian Networks with updated features	8
mailcom: Pseudonymization tool for textual data	8
Spectral Imaging Deep Learning Mapper - SpecDeepMap: An open-source EnMAP-Box semantic segmentation application for hyper- and multispectral mapping	8
refellips: A Python package for the analysis of variable angle spectroscopic ellipsometry data	8
quicR: An R library for streamlined data handling of real-time quaking induced conversion assays	8
Neutrostat: An R package for neutrosophic statistical models	8
Observer: An open-source framework for automating spectator for Real-time Strategy game of StarCraft	8
Traffic weaver: Semi-synthetic time-varying traffic generator based on averaged time series	8
〈	8
HETOOL: A Half-Edge Topological Object-Oriented Library for generic 2-D geometric modeling	8
End to end navigation stack for nuclear power plant inspection with mobile robot	8
EmuCast: A python package for generating time series forecasts with tunable error in model predictive control design and testing	8
Version 0.2.0 – TreeEyed: A QGIS plugin for tree monitoring in silvopastoral systems using state of the art AI models	8
Population potential on catchment area (PPCA): A Python-based tool for worldwide geospatial population analysis	8
Bilancio: An instrument-level balance-sheet simulator for monetary economics	8
A computerized tool for the kinematic limit analysis of 2D masonry structures failing on a tilting table	8
PCAfold 2.0—Novel tools and algorithms for low-dimensional manifold assessment and optimization	7
Version [1.0]- HAT-VIS — A MATLAB-based hypergraph visualization tool	7
Enabling scientific machine learning in MOOSE using Libtorch	7
AMED: Aggregated multimedia exploratory and discovery search software	7
TIQA-PSI: Toolbox for perceptual Image Quality Assessment of Pan-Sharpened Images	7
Computing Continuum Simulator: A comprehensive framework for continuum architecture evaluation	7
HistomicsTK: A Python toolkit for pathology image analysis algorithms	7
3DRSP: Matlab-based random sphere packing code in three dimensions	7
Open sensing: An interactive online tool for environmental data collection, monitoring, analysis, and modelling for custom environmental sensor devices	7
Smart Factory: A real-time predictive maintenance platform based on microservices architecture and deep learning	7
FishTally: Automated fish detection and counting tool	7
Think inside the (mk)box—A tool for creating and deploying application-specific Linux images utilized in a SiLA software development process	7
DataAiPrep: A comprehensive machine learning data quality assessment tool for training dataset optimization	7
TrustML: A Python package for computing the trustworthiness of ML models	7
Data4Land: How to enrich land-use/land-cover with historical vector(s)	7
Digital ecosystem for FAIR time series data management in environmental system science	7
Matlatzinca: A PyBANSHEE-based graphical user interface for elicitation of non-parametric Bayesian networks from experts	7
CoCoStyle: Mixed initiative co-creative system to support creative process of fashion design	7
CtrlAer: Programmable real-time execution of scientific experiments using a domain specific language for the Raspberry Pi Pico/Pico 2	7
DATTES: Data analysis tools for tests on energy storage	7
A WebExtension framework for experimentation and evaluation of webpage segmentation methods	7
Robustimizer: A graphical user interface application for efficient uncertainty quantification, robust optimization, and reliability-based optimization of processes and designs	7
pymetamodels: A Python package for metamodeling and design automation	7
Flow gym: A framework for the development, benchmarking, training, and deployment of flow-field quantification methods	7
A new approach for drone tracking with drone using Proximal Policy Optimization based distributed deep reinforcement learning	7
ExactPack: A python library of exact analytic solutions	7