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
MAWA: Enhancing mobile web browsing through web augmentation for improved user experience	37
CNV-Z; a new tool for detecting copy number variation in next generation sequencing data	37
Saihu: A common interface of worst-case delay analysis tools for time-sensitive networks	32
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
BiometricIdentity dApp: Decentralized biometric authentication based on fuzzy commitment and blockchain	31
IDOL: A web application for mixed integer linear multiobjective optimization	30
BOXVIA: Bayesian optimization executable and visualizable application	29
ReflectDetect: A software tool for AprilTag-guided in-flight radiometric calibration for UAV-mounted 2D snapshot multi-camera imagery	28
CacheSim: A cache simulation framework for evaluating caching algorithms on resource-constrained edge devices	28
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
An application for solving minimization problems using the Harmony search algorithm	27
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
TD-COF: A new method for detecting tandem duplications in next generation sequencing data	25
SST v1.0.0 with C API: Pluggable security solution for the Internet of Things	24
FIDWaC - Fast inverse distance weighting and compression	23
ResoFox: A GUI-based tool for calculating resolution and relative intensity of neutron powder diffractometers	23
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
NCC: An R-package for analysis and simulation of platform trials with non-concurrent controls	22
TROVA: TRansport Of water VApor	21
TimeAwareBPMN-js: An editor and temporal verification tool for Time-Aware BPMN processes	21
Version 2 — RPExpand: Software for Riesz projection expansion of resonance phenomena	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
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
ShakerMaker: A framework that simplifies the simulation of seismic ground-motions	19
PNW-Cnet v4: Automated species identification for passive acoustic monitoring	19
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
DFT-MF: Enhanced deepfake detection using mouth movement and transfer learning	18
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
LitOrganizer: Automating the process of data extraction and organization for scientific literature reviews	17
Version [2.0] — [pyMCMA: Uniformly distributed Pareto-front representation]	17
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
XCompress: LLM assisted Python-based text compression toolkit	16
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
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
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
SpinGlassPEPS.jl: Tensor-network package for Ising-like optimization on quasi-two-dimensional graphs	14
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
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
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
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
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
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
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
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
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
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
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
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
Hyperomet: An OpenSees interface for nonlinear analysis of unreinforced masonry buildings	7
End to end navigation stack for nuclear power plant inspection with mobile robot	7
ASSUME: An agent-based simulation framework for exploring electricity market dynamics with reinforcement learning	7
CtrlAer: Programmable real-time execution of scientific experiments using a domain specific language for the Raspberry Pi Pico/Pico 2	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
MicEMD: Open-source toolbox for electromagnetic modeling, inversion, and classification in underground metal target detection	7
refellips: A Python package for the analysis of variable angle spectroscopic ellipsometry data	7
Yekta: A low-code framework for automated test models generation	7
Corrigendum to “pyLAIS: A Python package for Layered Adaptive Importance Sampling” [SoftwareX 29 (2025), 101976]	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
PickShift: A user-friendly Python tool to assess the surficial uncertainties associated with polygons extracted from historical planimetric data	7
PCAfold 2.0—Novel tools and algorithms for low-dimensional manifold assessment and optimization	7
Leveraging OpenSimMPLS: A simulation platform for GoS/MPLS networks in research and education	7
RAVSim v2.0: Enhanced visualization and comparative analysis for neural network models	7
Version [2.0] - [VIC-Borg: Multiobjective automatic calibration toolkit for VIC model]	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
qNoise: A generator of non-Gaussian colored noise	7
VERONA: A python library for benchmarking deep learning in business process monitoring	7
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
OSLiFe-DiSC: Open source licenses discovering, selecting and comparing	6
Version [1.0]- HAT-VIS — A MATLAB-based hypergraph visualization tool	6
pymetamodels: A Python package for metamodeling and design automation	6
HistomicsTK: A Python toolkit for pathology image analysis algorithms	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
FCM-VSS: An AI powered secured fuzzy cognitive maps management toolkit for visualization, simulation and summarization	6
Hydrogen Permeation and Absorption Tool (HyPAT v2.0): An update to facilitate analyses of data from hydrogen absorption experiments	6
ENTIRETY — sEmanNTIc pRovisioning and govErning ioT devices in smart energY domain	6
A new approach for drone tracking with drone using Proximal Policy Optimization based distributed deep reinforcement learning	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
Enabling scientific machine learning in MOOSE using Libtorch	6
New, flexible and open-source fisheries self-reporting app: The Shiny4SelfReport	6
Trial Monitor: Scaffolding personalised Web dashboards for Human–Computer Interaction field trials	6
Rhizomer: Interactive semantic knowledge graphs exploration	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
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
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