SoftwareX

Article	Citations
EvalNE: A framework for network embedding evaluation	161
FMD: A parallel library for performing classical molecular dynamics simulations	148
Update (3.0) to LyapXool: Quadratic programming	118
Q-Facies: A tool for the quantitative interpretation of groundwater hydrochemical facies	83
SACETraj: An AutoCAD Catmull-Rom Spline Trajectory Interpolator	82
FS-Studio: An extensive and efficient feature selection experimentation tool for Weka Explorer	62
Version [1.1]- [Handling decision-making in intuitionistic fuzzy environment: PyIFDM package]	61
I-STL2MOOSE: From STL data to integrated volumetrical meshes for MOOSE	59
STUDIO: A Python graphical tool for analyzing street user observations from video data	57
McDAPS: A multi-channel physiological signals display and analysis system for clinical researchers	42
CNV-Z; a new tool for detecting copy number variation in next generation sequencing data	37
MAWA: Enhancing mobile web browsing through web augmentation for improved user experience	37
Saihu: A common interface of worst-case delay analysis tools for time-sensitive networks	32
BiometricIdentity dApp: Decentralized biometric authentication based on fuzzy commitment and blockchain	31
An open-source application software to determine the preconsolidation pressure of soils in incremental loading oedometer testing: pySigmaP	31
Web-based surface plasmon resonance signal processing system for fast analyte analysis	31
IDOL: A web application for mixed integer linear multiobjective optimization	30
BOXVIA: Bayesian optimization executable and visualizable application	29
CacheSim: A cache simulation framework for evaluating caching algorithms on resource-constrained edge devices	28
ReflectDetect: A software tool for AprilTag-guided in-flight radiometric calibration for UAV-mounted 2D snapshot multi-camera imagery	28
An application for solving minimization problems using the Harmony search algorithm	27
juSPH: A Julia-based open-source package of parallel Smoothed Particle Hydrodynamics (SPH) for dam break problems	27
HOST: Harmonic oscillator seasonal-trend model for analyzing the reoccurring nature of extreme events	27
An open-source parallel topology optimization framework based on unstructured 3D FEA using PETSc and Eigen	27
TD-COF: A new method for detecting tandem duplications in next generation sequencing data	25

Exploiting Simu5G for generating datasets for training and testing AI models for 5G/6G network applications	25
The SiLA 2 Manager for rapid device integration and workflow automation	25
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	23
FIDWaC - Fast inverse distance weighting and compression	23
NCC: An R-package for analysis and simulation of platform trials with non-concurrent controls	22
Tab2KGWiz: Interactive assistant for mapping tabular data to knowledge graphs	22
OpenIPDM: A probabilistic framework for estimating the deterioration and effect of interventions on bridges	22
Version 2 — RPExpand: Software for Riesz projection expansion of resonance phenomena	21
TROVA: TRansport Of water VApor	21
TimeAwareBPMN-js: An editor and temporal verification tool for Time-Aware BPMN processes	21
MFPP: Matrix-based flexible project planning	20
WITio: A MATLAB data evaluation toolbox to script broader insights into big data from WITec microscopes	20
CensSpatial: An R package for estimation and diagnostics in spatial censored regression models	20
ShakerMaker: A framework that simplifies the simulation of seismic ground-motions	19
PNW-Cnet v4: Automated species identification for passive acoustic monitoring	19
REFRAME–A software framework for managing reactive dependencies in object-oriented applications	19
Flow-models 2.0: Elephant flows modeling and detection with machine learning	19
DFT-MF: Enhanced deepfake detection using mouth movement and transfer learning	18
pyMechOpt: A Python toolbox for optimizing of reaction mechanisms	18
BBR: An open-source standard workflow based on biophysical crop parameters for automatic Botrytis cinerea assessment in vineyards	18
ScoreREM: A user-friendly Matlab-GUI for rapid eye movement (REM) sleep microstructure (Phasic/Tonic) annotation and quantification	18
Kunai: A static analysis framework for Android apps	18
LitOrganizer: Automating the process of data extraction and organization for scientific literature reviews	17
Version [2.0] — [pyMCMA: Uniformly distributed Pareto-front representation]	17
Version 1.1.1 - TROVA: TRansport Of water VApor	17
GenSDF: An MPI-Fortran based signed-distance-field generator for computational fluid dynamics applications	17
XCompress: LLM assisted Python-based text compression toolkit	16
A covariate software tool to guide test activity allocation	16
clickR: Semi-automatic pre-processing of messy data with change tracking for integral dataset cleaning	16
MALVADA: A framework for generating datasets of malware execution traces	16
DSIPTS: A high productivity environment for time series forecasting models	16
EnMAP-Box: Imaging spectroscopy in QGIS	15
Rcall: An R interface for MATLAB	15
VEqMon2D—Equations of motion generation tool of 2D vehicles with Matlab	15
GetSensorData: An extensible Android-based application for multi-sensor data registration	15
QuITO: Numerical software for constrained nonlinear optimal control problems	15
BioEmoDetector: A flexible platform for detecting emotions from health narratives	15
The StaDyn programming language	15
SpinGlassPEPS.jl: Tensor-network package for Ising-like optimization on quasi-two-dimensional graphs	14
DataMetProcess: An open-source package and Shiny application for the acquisition and processing of meteorological data from INMET	14
DAUD: A data driven algorithm to find discrete approximations of unknown continuous distributions	14
T-Ridership: A web tool for reprogramming public transportation fleets to minimize COVID-19 transmission	14
Climatrix: Xarray accessor for climate data sampling and reconstruction	14
P2PFaaS: A framework for FaaS peer-to-peer scheduling and load balancing in Fog and Edge computing	13
SolarQGIS: A QGIS application for calculating solar radiation on 3D vector GIS data	13
PLATFORM: Parallel Linear Algebra Tool FOr Reduced Modeling	13
JGMP: Java bindings and wrappers for the GMP library	13
clusEvol: An R package for Cluster Evolution Analytics	13
MorphoGen: Topology optimization software for Extremely Modular Systems	13

E2	13
ShinyGAStool: A user-friendly tool for candidate gene association studies	13
A C++17 thread pool for high-performance scientific computing	13
pyBaram: Parallel compressible flow solver in high-performance Python for teaching and research	13
PATSMA: Parameter Auto-tuning for Shared Memory Algorithms	13
Pynblint: A quality assurance tool to improve the quality of Python Jupyter notebooks	13
Ordinalysis: Interpretability of multidimensional ordinal data	13
Masked-Piper: Masking personal identities in visual recordings while preserving multimodal information	13
Version [7.1] – [IV-PSNR: Software for immersive video objective quality evaluation]	12
Floodsar: Automatic mapping of river flooding extent from multitemporal SAR imagery	12
APLOSE: A web-based annotation platform for underwater passive acoustic monitoring	12
Version 2.0.0 - M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations	12
MobiScout: A scalable cloud-based driving and activity monitoring platform featuring an IOS app and a WatchOS extension	12
GenClass: A parallel tool for data classification based on Grammatical Evolution	12
ModelicaGridData: Massive power system simulation data generation and labeling tool using Modelica and Python	12
MitoSeg: Mitochondria segmentation tool	12
PyQBench: A Python library for benchmarking gate-based quantum computers	12
TeDDy: Templated decision diagram library	12
Diagnostic Expert Advisor: A platform for developing machine learning models on medical time-series data	12
QPPLab: A generally applicable software package for detecting, analyzing, and visualizing large-scale quasiperiodic spatiotemporal patterns (QPPs) of brain activity	12
xkl: A legacy software for detailed acoustic analysis of speech made modern	12
GraphXplore: Visual exploration and accessible preprocessing of medical data	11
Spectrally regularised LVMs: A spectral regularisation framework for latent variable models designed for single-channel applications	11
Causal ML: Python package for causal inference machine learning	11
IPv6CC: IPv6 covert channels for testing networks against stegomalware and data exfiltration	11
ZEN-garden: Optimizing energy transition pathways with user-oriented data handling	11
Phenoflow-ML: A next-generation phenotyping framework to capture ML-based phenotypes	11
PyCinemetrics: Computational film studies tool based on deep learning and PySide2	11
WireGuard-AES: Hardware based encryption to WireGuard for VPN gateways	11
Development of an ABAQUS™ plug-in for predicting composite plates stiffness with in-plane periodicity	11
TrAQ: A novel, versatile, semi-automated, two-dimensional motor behavioural tracking software	11
Emipy: An open-source Python-based tool to analyze industrial emissions in Europe	11
Modelling biocontrol of invasive insects using WaspSim: A MATLAB simulation model	10
Version [1.1]—[MSAT: Matrix stability analysis tool for shock-capturing schemes]	10
India Policy Insights: A geospatial and temporal data science and visualization platform and architecture	10
Compression of triangulated solids’ surfaces by Decimating Reconstructable Triangles	10
Scymol: A python-based software package for initializing and running molecular dynamics simulations using LAMMPS	10
FLAGR: A flexible high-performance library for rank aggregation	10
pyMeshFOAM: Automated meshing for CFD and fluid–structure simulations	10
Gdistns: R package for maximum goodness-of-fit estimates of the generalized G distributions	10
HITS: Hyperplanes intersection tabu search for maximum score estimation	10
DigiRhythm: An R package for evaluating circadian rhythmicity in animals using the degree of functional coupling	10
REMLA: An R package for robust expectation-maximization estimation for latent variable models	10
gosset: An R package for analysis and synthesis of ranking data in agricultural experimentation	10
pycity_scheduling—A Python framework for the development and assessment of optimisation-based power scheduling algorithms for multi-energy systems in city districts	10
STM: A software tool for predicting daily temperature in stored animal slurry	10
Atlantic cod growth model: Open source Python package for numerical growth experiments	10
Binary complex amplitude application: An all-in-one Matlab application for the advanced laser beam shaping with digital micromirror device	10
Corrigendum to “RAVSim v2.0: Enhanced visualization and comparative analysis for neural network models” [SoftwareX volume 29, February 2025 Article Number: 102006]	10
ScaFi: A Scala DSL and Toolkit for Aggregate Programming	10
Decidim.viz: A data dashboard prototype for a digital democracy platform	10
Power TAC: Software architecture for a competitive simulation of sustainable smart energy markets	9
SimilarityTS: Toolkit for the evaluation of similarity for multivariate time series	9
GSITK: A sentiment analysis framework for agile replication and development	9
TraClets: A trajectory representation and classification library	9
Simplify: A Python library for optimizing pruned neural networks	9
“dynmix”: An R package for the estimation of dynamic finite mixtures	9
DroneTimeline: Forensic timeline analysis for drones	9
ArcNLET-Py: An ArcGIS-based nitrogen load estimation toolbox developed using python for ArcGIS pro	9
Gideon Replay: A library to replay interactions in web-applications	9
OpenLSA: An open-source toolbox for computing full-field displacements from images of periodic patterns	9
3TM: Software for the 3-Tau Model	9
Docker Unified UIMA Interface: New perspectives for NLP on big data	8
Covira: A COVID-19 risk assessment, visualization and communication tool	8
Performing highly efficient Minima Hopping structure predictions using the Atomic Simulation Environment (ASE)	8
3.0 - MOOSE: Enabling massively parallel multiphysics simulations	8
MaSMaker: An open-source, portable software to create and integrate maze-like surfaces into arbitrary geometries	8
Version [1.1.0]- [DLDiagnosis: A mobile and web application for diseases classification using Deep Learning]	8
Editorial Board	8
CellRex: Software platform for managing biological cell data	8
SmarTS: A Java package for smart contract test suite generation and execution	8
Geospatial Analytics Extension for KNIME	8
Simplifying computational workflows with the Multiscale Atomic Zeolite Simulation Environment (MAZE)	8
TSSEARCH: Time Series Subsequence Search Library	8
Update 2.5 to “Takin: An open-source software for experiment planning, visualisation, and data analysis”, (PII: S2352711016300152)	8
BDEsize: An R package for efficient determination of sample size in a balanced design of experiments	8
HETOOL: A Half-Edge Topological Object-Oriented Library for generic 2-D geometric modeling	8
Streetscape morphometrics: Expanding momepy to analyze urban form from the street point of view	8
Cyberattack detection through GPML: Graph Processing for Machine Learning	8
libcommute/pycommute: A quantum operator algebra domain-specific language and exact diagonalization toolkit	8

FuzConvSteganalysis: Steganalysis via fuzzy logic and convolutional neural network	8
SWANe: Standardized workflow for advanced neuroimaging in epilepsy	8
Version [1.1	8
TremorSoft: An decision support application for differential diagnosis between Parkinson’s disease and essential tremor	8
PlatformCommander — An open source software for an easy integration of motion platforms in research laboratories	8
RIPN: A tool for implementing cyber-physical systems by using interpreted Petri Nets and teleo-reactive programs	8
PickShift: A user-friendly Python tool to assess the surficial uncertainties associated with polygons extracted from historical planimetric data	7
RAVSim v2.0: Enhanced visualization and comparative analysis for neural network models	7
PCAfold 2.0—Novel tools and algorithms for low-dimensional manifold assessment and optimization	7
Version [2.0] - [VIC-Borg: Multiobjective automatic calibration toolkit for VIC model]	7
Leveraging OpenSimMPLS: A simulation platform for GoS/MPLS networks in research and education	7
SOLDIER: SOLution for Dam behavior Interpretation and safety Evaluation with boosted Regression trees	7
PyBanshee version (1.0): A Python implementation of the MATLAB toolbox BANSHEE for Non-Parametric Bayesian Networks with updated features	7
Corrigendum to “LFG: An easy-to-use realistic synthetic LandFill Generator” [Software X Volume 28, December 2024, 101936]	7
End to end navigation stack for nuclear power plant inspection with mobile robot	7
qNoise: A generator of non-Gaussian colored noise	7
ASSUME: An agent-based simulation framework for exploring electricity market dynamics with reinforcement learning	7
VERONA: A python library for benchmarking deep learning in business process monitoring	7
CtrlAer: Programmable real-time execution of scientific experiments using a domain specific language for the Raspberry Pi Pico/Pico 2	7
Hyperomet: An OpenSees interface for nonlinear analysis of unreinforced masonry buildings	7
OpenPLC61850: An IEC 61850 MMS compatible open source PLC for smart grid research	7
Traffic weaver: Semi-synthetic time-varying traffic generator based on averaged time series	7
svds-C: A multi-thread C code for computing truncated singular value decomposition	7
Yekta: A low-code framework for automated test models generation	7
MicEMD: Open-source toolbox for electromagnetic modeling, inversion, and classification in underground metal target detection	7
Corrigendum to “pyLAIS: A Python package for Layered Adaptive Importance Sampling” [SoftwareX 29 (2025), 101976]	7
refellips: A Python package for the analysis of variable angle spectroscopic ellipsometry data	7
tsdownsample: High-performance time series downsampling for scalable visualization	7
OpenTEPES: Open-source Transmission and Generation Expansion Planning	7
quicR: An R library for streamlined data handling of real-time quaking induced conversion assays	7
A new approach for drone tracking with drone using Proximal Policy Optimization based distributed deep reinforcement learning	6
ENTIRETY — sEmanNTIc pRovisioning and govErning ioT devices in smart energY domain	6
hyperbox-brain: A Python toolbox for hyperbox-based machine learning algorithms	6
WACline: A Software Product Line to harness heterogeneity in Web Annotation	6
Think inside the (mk)box—A tool for creating and deploying application-specific Linux images utilized in a SiLA software development process	6
KneeBones3Dify: Open-source software for segmentation and 3D reconstruction of knee bones from MRI data	6
1DCSEMQWE: 1D Controlled Source Electromagnetic Method in Geophysics Using Quadrature With Extrapolation	6
2D-xtDCR-LTBEM: A Fortran code for numerical solutions to the unsteady anisotropic-DCR equation of spatio-temporal coefficients	6
Growth Data—An automatic solution for seedling growth analysis via RGB-Depth imaging sensors	6
Data4Land: How to enrich land-use/land-cover with historical vector(s)	6
RINEXAV: GNSS global network selection open-source software based on qualitative analysis of RINEX files	6
Climaticpark-py - A python framework for the climatic simulation of vehicular parking lots	6
pyJSON Schema Loader and JSON Editor: A tool for file-based metadata management	6
AMED: Aggregated multimedia exploratory and discovery search software	6
Wave-DNA: A software tool for simulating nonlinear acoustic waves emitted by moving boundaries	6
New, flexible and open-source fisheries self-reporting app: The Shiny4SelfReport	6
Enabling scientific machine learning in MOOSE using Libtorch	6
Rhizomer: Interactive semantic knowledge graphs exploration	6
Trial Monitor: Scaffolding personalised Web dashboards for Human–Computer Interaction field trials	6
ExactPack: A python library of exact analytic solutions	6
The Contiki-NG open source operating system for next generation IoT devices	6
pyGRETA, pyCLARA, pyPRIMA: A pre-processing suite to generate flexible model regions for energy system models	6
DATTES: Data analysis tools for tests on energy storage	6
IST-ROS: A flexible object segmentation and tracking framework for robotics applications	6
TIQA-PSI: Toolbox for perceptual Image Quality Assessment of Pan-Sharpened Images	6
Fast parallel calculation of modified Bessel function of the second kind and its derivatives	6
Matlatzinca: A PyBANSHEE-based graphical user interface for elicitation of non-parametric Bayesian networks from experts	6
〈qo|	6
Benopt-Heat: An economic optimization model to identify robust bioenergy technologies for the German heat transition	6
In-Cognitive: A web-based Python application for fuzzy cognitive map design, simulation, and uncertainty analysis based on the Monte Carlo method	6
LeXInt: GPU-accelerated exponential integrators package	6
CityZones: A geospatial multi-tier software tool to compute urban risk zones	6
Version [1.0]- HAT-VIS — A MATLAB-based hypergraph visualization tool	6
OSLiFe-DiSC: Open source licenses discovering, selecting and comparing	6
HistomicsTK: A Python toolkit for pathology image analysis algorithms	6
pymetamodels: A Python package for metamodeling and design automation	6
Digital ecosystem for FAIR time series data management in environmental system science	6
A WebExtension framework for experimentation and evaluation of webpage segmentation methods	6
Computing Continuum Simulator: A comprehensive framework for continuum architecture evaluation	6
TrustML: A Python package for computing the trustworthiness of ML models	6
CoCoStyle: Mixed initiative co-creative system to support creative process of fashion design	6
robustDEA: A Java library for robust efficiency analysis	6
A computerized tool for the kinematic limit analysis of 2D masonry structures failing on a tilting table	6
Population potential on catchment area (PPCA): A Python-based tool for worldwide geospatial population analysis	6
Robustimizer: A graphical user interface application for efficient uncertainty quantification, robust optimization, and reliability-based optimization of processes and designs	6
3DRSP: Matlab-based random sphere packing code in three dimensions	6
APOTHEOSIS: An efficient approximate similarity search system	6
Hydrogen Permeation and Absorption Tool (HyPAT v2.0): An update to facilitate analyses of data from hydrogen absorption experiments	6
FCM-VSS: An AI powered secured fuzzy cognitive maps management toolkit for visualization, simulation and summarization	6
pyFIRI — A free and open source Python software package of the non-auroral Earth’s lower ionosphere	5
Star-XP: A simulation framework for Polar-2/ low energy X-ray polarization detector	5
MicroVIP: Microscopy image simulation on the Virtual Imaging Platform	5
RegionTPMS — Region based triply periodic minimal surfaces (TPMS) for 3-D printed multiphase bone scaffolds with exact porosity values	5
An NLP-driven face recognition system to improve Alzheimer’s patient engagement and care [MEMORY LANE]	5
TechMiner: Analysis of bibliographic datasets using Python	5
Hyper-Data: A Matlab based optimization software for data-driven hyperelasticity	5
OpenIMDML: Open Instance Multi-Domain Motor Library utilizing the Modelica modeling language	5
HICA: A MATLAB-based hierarchical image clustering algorithm for classifying parts suitable for additive and traditional manufacturing technologies	5
iCorrVision-2D: An integrated python-based open-source Digital Image Correlation software for in-plane measurements (Part 1)	5
Corrigendum to `Gdistns: R package for maximum goodness-of-fit estimates of the generalized G distributions' [SoftwareX 27 (2024) 101886]	5
NEFBDAA — .NET Environment for Building Dynamic Angular Applications	5
ChargEVal — A multi-user framework for simulating and analysing charging station deployment scenarios using agent-based modelling	5
CPR Algorithm—A new interpolation methodology and QGIS plugin for Colour Pattern Regression between aerial images and raster maps	5
tx2_fcnn_node: An open-source ROS compatible tool for monocular depth reconstruction	5
topoEEG: An Python-framework for analyzing EEG data in neurodegeneratives disease through Topological Deep Learning	5