SoftwareX

Article	Citations
EvalNE: A framework for network embedding evaluation	158
FMD: A parallel library for performing classical molecular dynamics simulations	147
Update (3.0) to LyapXool: Quadratic programming	112
Q-Facies: A tool for the quantitative interpretation of groundwater hydrochemical facies	79
FS-Studio: An extensive and efficient feature selection experimentation tool for Weka Explorer	75
Version [1.1]- [Handling decision-making in intuitionistic fuzzy environment: PyIFDM package]	61
BOXVIA: Bayesian optimization executable and visualizable application	59
SACETraj: An AutoCAD Catmull-Rom Spline Trajectory Interpolator	56
STUDIO: A Python graphical tool for analyzing street user observations from video data	55
McDAPS: A multi-channel physiological signals display and analysis system for clinical researchers	39
CNV-Z; a new tool for detecting copy number variation in next generation sequencing data	35
MAWA: Enhancing mobile web browsing through web augmentation for improved user experience	33
BiometricIdentity dApp: Decentralized biometric authentication based on fuzzy commitment and blockchain	31
Saihu: A common interface of worst-case delay analysis tools for time-sensitive networks	31
Web-based surface plasmon resonance signal processing system for fast analyte analysis	30
An open-source application software to determine the preconsolidation pressure of soils in incremental loading oedometer testing: pySigmaP	29
IDOL: A web application for mixed integer linear multiobjective optimization	28
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	27
TROVA: TRansport Of water VApor	27
An open-source parallel topology optimization framework based on unstructured 3D FEA using PETSc and Eigen	27
SST v1.0.0 with C API: Pluggable security solution for the Internet of Things	26
I-STL2MOOSE: From STL data to integrated volumetrical meshes for MOOSE	26
The SiLA 2 Manager for rapid device integration and workflow automation	25
juSPH: A Julia-based open-source package of parallel Smoothed Particle Hydrodynamics (SPH) for dam break problems	24

An application for solving minimization problems using the Harmony search algorithm	24
Exploiting Simu5G for generating datasets for training and testing AI models for 5G/6G network applications	23
HOST: Harmonic oscillator seasonal-trend model for analyzing the reoccurring nature of extreme events	23
TD-COF: A new method for detecting tandem duplications in next generation sequencing data	23
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	21
Version 2 — RPExpand: Software for Riesz projection expansion of resonance phenomena	21
TimeAwareBPMN-js: An editor and temporal verification tool for Time-Aware BPMN processes	20
PNW-Cnet v4: Automated species identification for passive acoustic monitoring	19
CensSpatial: An R package for estimation and diagnostics in spatial censored regression models	19
T-Ridership: A web tool for reprogramming public transportation fleets to minimize COVID-19 transmission	19
Flow-models 2.0: Elephant flows modeling and detection with machine learning	19
WITio: A MATLAB data evaluation toolbox to script broader insights into big data from WITec microscopes	19
ShakerMaker: A framework that simplifies the simulation of seismic ground-motions	18
DSIPTS: A high productivity environment for time series forecasting models	18
REFRAME–A software framework for managing reactive dependencies in object-oriented applications	18
A covariate software tool to guide test activity allocation	18
clickR: Semi-automatic pre-processing of messy data with change tracking for integral dataset cleaning	18
Kunai: A static analysis framework for Android apps	18
XCompress: LLM assisted Python-based text compression toolkit	18
Rcall: An R interface for MATLAB	17
VEqMon2D—Equations of motion generation tool of 2D vehicles with Matlab	17
QuITO: Numerical software for constrained nonlinear optimal control problems	17
MFPP: Matrix-based flexible project planning	17
The StaDyn programming language	17
GenSDF: An MPI-Fortran based signed-distance-field generator for computational fluid dynamics applications	16
Version 1.1.1 - TROVA: TRansport Of water VApor	16
LitOrganizer: Automating the process of data extraction and organization for scientific literature reviews	16
MALVADA: A framework for generating datasets of malware execution traces	16
pyMechOpt: A Python toolbox for optimizing of reaction mechanisms	16
BioEmoDetector: A flexible platform for detecting emotions from health narratives	15
ScoreREM: A user-friendly Matlab-GUI for rapid eye movement (REM) sleep microstructure (Phasic/Tonic) annotation and quantification	15
GetSensorData: An extensible Android-based application for multi-sensor data registration	15
Version [2.0] — [pyMCMA: Uniformly distributed Pareto-front representation]	15
BBR: An open-source standard workflow based on biophysical crop parameters for automatic Botrytis cinerea assessment in vineyards	15
DataMetProcess: An open-source package and Shiny application for the acquisition and processing of meteorological data from INMET	15
DFT-MF: Enhanced deepfake detection using mouth movement and transfer learning	14
Development of an ABAQUS™ plug-in for predicting composite plates stiffness with in-plane periodicity	14
EnMAP-Box: Imaging spectroscopy in QGIS	14
PyCinemetrics: Computational film studies tool based on deep learning and PySide2	14
A C++17 thread pool for high-performance scientific computing	14
JGMP: Java bindings and wrappers for the GMP library	13
MorphoGen: Topology optimization software for Extremely Modular Systems	13
clusEvol: An R package for Cluster Evolution Analytics	13
Ordinalysis: Interpretability of multidimensional ordinal data	13
MobiScout: A scalable cloud-based driving and activity monitoring platform featuring an IOS app and a WatchOS extension	13
pyBaram: Parallel compressible flow solver in high-performance Python for teaching and research	13
PATSMA: Parameter Auto-tuning for Shared Memory Algorithms	13
E2	13
ShinyGAStool: A user-friendly tool for candidate gene association studies	13

PyQBench: A Python library for benchmarking gate-based quantum computers	13
P2PFaaS: A framework for FaaS peer-to-peer scheduling and load balancing in Fog and Edge computing	13
Pynblint: A quality assurance tool to improve the quality of Python Jupyter notebooks	13
PLATFORM: Parallel Linear Algebra Tool FOr Reduced Modeling	13
xkl: A legacy software for detailed acoustic analysis of speech made modern	13
ModelicaGridData: Massive power system simulation data generation and labeling tool using Modelica and Python	13
MitoSeg: Mitochondria segmentation tool	12
ZEN-garden: Optimizing energy transition pathways with user-oriented data handling	12
TeDDy: Templated decision diagram library	12
QPPLab: A generally applicable software package for detecting, analyzing, and visualizing large-scale quasiperiodic spatiotemporal patterns (QPPs) of brain activity	12
APLOSE: A web-based annotation platform for underwater passive acoustic monitoring	12
Version [7.1] – [IV-PSNR: Software for immersive video objective quality evaluation]	12
TrAQ: A novel, versatile, semi-automated, two-dimensional motor behavioural tracking software	12
Floodsar: Automatic mapping of river flooding extent from multitemporal SAR imagery	12
GenClass: A parallel tool for data classification based on Grammatical Evolution	12
Version [1.1]—[MSAT: Matrix stability analysis tool for shock-capturing schemes]	11
GraphXplore: Visual exploration and accessible preprocessing of medical data	11
Masked-Piper: Masking personal identities in visual recordings while preserving multimodal information	11
pycity_scheduling—A Python framework for the development and assessment of optimisation-based power scheduling algorithms for multi-energy systems in city districts	11
Docker Unified UIMA Interface: New perspectives for NLP on big data	11
Performing highly efficient Minima Hopping structure predictions using the Atomic Simulation Environment (ASE)	11
Diagnostic Expert Advisor: A platform for developing machine learning models on medical time-series data	11
Emipy: An open-source Python-based tool to analyze industrial emissions in Europe	11
pyMeshFOAM: Automated meshing for CFD and fluid–structure simulations	11
SmarTS: A Java package for smart contract test suite generation and execution	11
Modelling biocontrol of invasive insects using WaspSim: A MATLAB simulation model	11
Version 2.0.0 - M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations	11
Causal ML: Python package for causal inference machine learning	11
IPv6CC: IPv6 covert channels for testing networks against stegomalware and data exfiltration	11
STM: A software tool for predicting daily temperature in stored animal slurry	11
Binary complex amplitude application: An all-in-one Matlab application for the advanced laser beam shaping with digital micromirror device	10
FuzConvSteganalysis: Steganalysis via fuzzy logic and convolutional neural network	10
Power TAC: Software architecture for a competitive simulation of sustainable smart energy markets	10
Gideon Replay: A library to replay interactions in web-applications	10
“dynmix”: An R package for the estimation of dynamic finite mixtures	10
gosset: An R package for analysis and synthesis of ranking data in agricultural experimentation	10
3TM: Software for the 3-Tau Model	10
TraClets: A trajectory representation and classification library	10
Simplify: A Python library for optimizing pruned neural networks	10
SimilarityTS: Toolkit for the evaluation of similarity for multivariate time series	10
TSSEARCH: Time Series Subsequence Search Library	10
libcommute/pycommute: A quantum operator algebra domain-specific language and exact diagonalization toolkit	10
Covira: A COVID-19 risk assessment, visualization and communication tool	10
Decidim.viz: A data dashboard prototype for a digital democracy platform	10
Gdistns: R package for maximum goodness-of-fit estimates of the generalized G distributions	10
ArcNLET-Py: An ArcGIS-based nitrogen load estimation toolbox developed using python for ArcGIS pro	10
FLAGR: A flexible high-performance library for rank aggregation	10
OpenLSA: An open-source toolbox for computing full-field displacements from images of periodic patterns	9
India Policy Insights: A geospatial and temporal data science and visualization platform and architecture	9
REMLA: An R package for robust expectation-maximization estimation for latent variable models	9
GSITK: A sentiment analysis framework for agile replication and development	9
HITS: Hyperplanes intersection tabu search for maximum score estimation	9
Compression of triangulated solids’ surfaces by Decimating Reconstructable Triangles	9
Corrigendum to “RAVSim v2.0: Enhanced visualization and comparative analysis for neural network models” [SoftwareX volume 29, February 2025 Article Number: 102006]	9
DigiRhythm: An R package for evaluating circadian rhythmicity in animals using the degree of functional coupling	9
Simplifying computational workflows with the Multiscale Atomic Zeolite Simulation Environment (MAZE)	9
Atlantic cod growth model: Open source Python package for numerical growth experiments	9
ScaFi: A Scala DSL and Toolkit for Aggregate Programming	8
3.0 - MOOSE: Enabling massively parallel multiphysics simulations	8
PlatformCommander — An open source software for an easy integration of motion platforms in research laboratories	8
OpenPLC61850: An IEC 61850 MMS compatible open source PLC for smart grid research	8
SWANe: Standardized workflow for advanced neuroimaging in epilepsy	8
CtrlAer: Programmable real-time execution of scientific experiments using a domain specific language for the Raspberry Pi Pico/Pico 2	8
Traffic weaver: Semi-synthetic time-varying traffic generator based on averaged time series	8
Scymol: A python-based software package for initializing and running molecular dynamics simulations using LAMMPS	8
Geospatial Analytics Extension for KNIME	8
BDEsize: An R package for efficient determination of sample size in a balanced design of experiments	8
Update 2.5 to “Takin: An open-source software for experiment planning, visualisation, and data analysis”, (PII: S2352711016300152)	8
A computerized tool for the kinematic limit analysis of 2D masonry structures failing on a tilting table	8
〈qo|	8
HETOOL: A Half-Edge Topological Object-Oriented Library for generic 2-D geometric modeling	8
DroneTimeline: Forensic timeline analysis for drones	8
Editorial Board	8
TremorSoft: An decision support application for differential diagnosis between Parkinson’s disease and essential tremor	8
OpenTEPES: Open-source Transmission and Generation Expansion Planning	8
MaSMaker: An open-source, portable software to create and integrate maze-like surfaces into arbitrary geometries	8
tsdownsample: High-performance time series downsampling for scalable visualization	8
qNoise: A generator of non-Gaussian colored noise	7
RINEXAV: GNSS global network selection open-source software based on qualitative analysis of RINEX files	7
Hyperomet: An OpenSees interface for nonlinear analysis of unreinforced masonry buildings	7

Leveraging OpenSimMPLS: A simulation platform for GoS/MPLS networks in research and education	7
Version [1.1.0]- [DLDiagnosis: A mobile and web application for diseases classification using Deep Learning]	7
MicEMD: Open-source toolbox for electromagnetic modeling, inversion, and classification in underground metal target detection	7
Growth Data—An automatic solution for seedling growth analysis via RGB-Depth imaging sensors	7
SOLDIER: SOLution for Dam behavior Interpretation and safety Evaluation with boosted Regression trees	7
End to end navigation stack for nuclear power plant inspection with mobile robot	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
Version [1.1	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
Corrigendum to “pyLAIS: A Python package for Layered Adaptive Importance Sampling” [SoftwareX 29 (2025), 101976]	7
1DCSEMQWE: 1D Controlled Source Electromagnetic Method in Geophysics Using Quadrature With Extrapolation	7
PyBanshee version (1.0): A Python implementation of the MATLAB toolbox BANSHEE for Non-Parametric Bayesian Networks with updated features	7
svds-C: A multi-thread C code for computing truncated singular value decomposition	7
VERONA: A python library for benchmarking deep learning in business process monitoring	7
Corrigendum to “LFG: An easy-to-use realistic synthetic LandFill Generator” [Software X Volume 28, December 2024, 101936]	7
Version [2.0] - [VIC-Borg: Multiobjective automatic calibration toolkit for VIC model]	7
ASSUME: An agent-based simulation framework for exploring electricity market dynamics with reinforcement learning	7
PickShift: A user-friendly Python tool to assess the surficial uncertainties associated with polygons extracted from historical planimetric data	7
Fast parallel calculation of modified Bessel function of the second kind and its derivatives	7
Think inside the (mk)box—A tool for creating and deploying application-specific Linux images utilized in a SiLA software development process	6
3DRSP: Matlab-based random sphere packing code in three dimensions	6
pyGRETA, pyCLARA, pyPRIMA: A pre-processing suite to generate flexible model regions for energy system models	6
TIQA-PSI: Toolbox for perceptual Image Quality Assessment of Pan-Sharpened Images	6
AKFruitYield: Modular benchmarking and video analysis software for Azure Kinect cameras for fruit size and fruit yield estimation in apple orchards	6
Identifying safety–critical concerns in unmanned aerial vehicle software platforms with SALIENT	6
Version [1.0]- HAT-VIS — A MATLAB-based hypergraph visualization tool	6
CityZones: A geospatial multi-tier software tool to compute urban risk zones	6
TrustML: A Python package for computing the trustworthiness of ML models	6
Version 0.2 - CrackDect: Detecting crack densities in images of fiber-reinforced polymers	6
ExactPack: A python library of exact analytic solutions	6
New, flexible and open-source fisheries self-reporting app: The Shiny4SelfReport	6
OSLiFe-DiSC: Open source licenses discovering, selecting and comparing	6
DATTES: Data analysis tools for tests on energy storage	6
pyJSON Schema Loader and JSON Editor: A tool for file-based metadata management	6
Version [1.2]- [pyrepo-mcda - Reference Objects based MCDA Software Package]	6
robustDEA: A Java library for robust efficiency analysis	6
AMED: Aggregated multimedia exploratory and discovery search software	6
Robustimizer: A graphical user interface application for efficient uncertainty quantification, robust optimization, and reliability-based optimization of processes and designs	6
cmaRs: A powerful predictive data mining package in R	6
TermX: The semantic interoperability, knowledge management and sharing platform	6
PYCASO: Python module for calibration of cameras by Soloff’s method	6
Benopt-Heat: An economic optimization model to identify robust bioenergy technologies for the German heat transition	6
Drop Project: An automatic assessment tool for programming assignments	6
A WebExtension framework for experimentation and evaluation of webpage segmentation methods	6
WACline: A Software Product Line to harness heterogeneity in Web Annotation	6
2D-xtDCR-LTBEM: A Fortran code for numerical solutions to the unsteady anisotropic-DCR equation of spatio-temporal coefficients	6
CoCoStyle: Mixed initiative co-creative system to support creative process of fashion design	6
Trial Monitor: Scaffolding personalised Web dashboards for Human–Computer Interaction field trials	6
A new approach for drone tracking with drone using Proximal Policy Optimization based distributed deep reinforcement learning	6
Enabling scientific machine learning in MOOSE using Libtorch	6
Matlatzinca: A PyBANSHEE-based graphical user interface for elicitation of non-parametric Bayesian networks from experts	6
FCM-VSS: An AI powered secured fuzzy cognitive maps management toolkit for visualization, simulation and summarization	6
Digital ecosystem for FAIR time series data management in environmental system science	6
Hybrid adaptive battery parameter estimation approach for equivalent circuit model toolbox	6
Computing Continuum Simulator: A comprehensive framework for continuum architecture evaluation	6
pymetamodels: A Python package for metamodeling and design automation	6
JaxSGMC: Modular stochastic gradient MCMC in JAX	6
IST-ROS: A flexible object segmentation and tracking framework for robotics applications	6
Beachmeter – a simple tool for semi-automatic beach morphodynamics measurement	6
KneeBones3Dify: Open-source software for segmentation and 3D reconstruction of knee bones from MRI data	6
Hydrogen Permeation and Absorption Tool (HyPAT v2.0): An update to facilitate analyses of data from hydrogen absorption experiments	6
hyperbox-brain: A Python toolbox for hyperbox-based machine learning algorithms	6
The Contiki-NG open source operating system for next generation IoT devices	6
ENTIRETY — sEmanNTIc pRovisioning and govErning ioT devices in smart energY domain	6
Rhizomer: Interactive semantic knowledge graphs exploration	6
NEFBDAA — .NET Environment for Building Dynamic Angular Applications	5
pyFIRI — A free and open source Python software package of the non-auroral Earth’s lower ionosphere	5
BrickLLM: A Python library for generating Brick-compliant RDF graphs using LLMs	5
EasyEIS: A software tool to perform electrochemical impedance spectroscopy using a source measure unit	5
Georges: A modular Python library for seamless beam dynamics simulations and optimization	5
An interactive R-Shiny app for quickly visualizing a tidy, long dataset with multiple dimensions with an application in clinical trial simulations for platform trials	5
CPR Algorithm—A new interpolation methodology and QGIS plugin for Colour Pattern Regression between aerial images and raster maps	5
Image2DEM: A geometrical digital twin generator for the detailed structural analysis of existing masonry infrastructure stock	5
ICOBA: A highly customizable iterative imagej macro for optimization of image co-localization batch analysis	5
CACP: Classification Algorithms Comparison Pipeline	5
MaMiCo 2.0: An enhanced open-source framework for high-performance molecular-continuum flow simulation	5
Hyper-Data: A Matlab based optimization software for data-driven hyperelasticity	5
DeepMTP: A Python-based deep learning framework for multi-target prediction	5
SMS-Builder: An adaptive software tool for building systematic mapping studies	5
IngredientDB: A GUI-based Matlab database program for estimating the pH of acid or acidified food formulations from buffer capacity models	5
Corrigendum to `Gdistns: R package for maximum goodness-of-fit estimates of the generalized G distributions' [SoftwareX 27 (2024) 101886]	5
iCorrVision-2D: An integrated python-based open-source Digital Image Correlation software for in-plane measurements (Part 1)	5
DynExp—Highly flexible laboratory automation for dynamically changing classical and quantum experiments	5
ShopiRound: An Android application-based e-commerce system to find products nearby using travelling salesman problem	5
ag5Tools: An R package for downloading and extracting agrometeorological data from the AgERA5 database	5
Nancy: An efficient parallel Network Calculus library	5
PKgui: A GUI software for Polubarinova-Kochina’s solutions of steady unconfined groundwater flow	5
ChargEVal — A multi-user framework for simulating and analysing charging station deployment scenarios using agent-based modelling	5
Imaging framework: An interoperable and extendable connector for image-related Java frameworks	5
PyfastSPM: A Python package to convert 1D FastSPM data streams into publication quality movies	5
OpenIMDML: Open Instance Multi-Domain Motor Library utilizing the Modelica modeling language	5
Star-XP: A simulation framework for Polar-2/ low energy X-ray polarization detector	5
OpenMechanochem: A Python module for mechanochemical simulations	5