SoftwareX

Papers
(The median citation count of SoftwareX is 1. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-09-01 to 2025-09-01.)
ArticleCitations
EvalNE: A framework for network embedding evaluation161
FMD: A parallel library for performing classical molecular dynamics simulations148
Update (3.0) to LyapXool: Quadratic programming118
Q-Facies: A tool for the quantitative interpretation of groundwater hydrochemical facies83
SACETraj: An AutoCAD Catmull-Rom Spline Trajectory Interpolator82
FS-Studio: An extensive and efficient feature selection experimentation tool for Weka Explorer62
Version [1.1]- [Handling decision-making in intuitionistic fuzzy environment: PyIFDM package]61
I-STL2MOOSE: From STL data to integrated volumetrical meshes for MOOSE59
STUDIO: A Python graphical tool for analyzing street user observations from video data57
McDAPS: A multi-channel physiological signals display and analysis system for clinical researchers42
MAWA: Enhancing mobile web browsing through web augmentation for improved user experience37
CNV-Z; a new tool for detecting copy number variation in next generation sequencing data37
Saihu: A common interface of worst-case delay analysis tools for time-sensitive networks32
An open-source application software to determine the preconsolidation pressure of soils in incremental loading oedometer testing: pySigmaP31
Web-based surface plasmon resonance signal processing system for fast analyte analysis31
BiometricIdentity dApp: Decentralized biometric authentication based on fuzzy commitment and blockchain31
IDOL: A web application for mixed integer linear multiobjective optimization30
BOXVIA: Bayesian optimization executable and visualizable application29
ReflectDetect: A software tool for AprilTag-guided in-flight radiometric calibration for UAV-mounted 2D snapshot multi-camera imagery28
CacheSim: A cache simulation framework for evaluating caching algorithms on resource-constrained edge devices28
juSPH: A Julia-based open-source package of parallel Smoothed Particle Hydrodynamics (SPH) for dam break problems27
HOST: Harmonic oscillator seasonal-trend model for analyzing the reoccurring nature of extreme events27
An open-source parallel topology optimization framework based on unstructured 3D FEA using PETSc and Eigen27
An application for solving minimization problems using the Harmony search algorithm27
Exploiting Simu5G for generating datasets for training and testing AI models for 5G/6G network applications25
The SiLA 2 Manager for rapid device integration and workflow automation25
TD-COF: A new method for detecting tandem duplications in next generation sequencing data25
SST v1.0.0 with C API: Pluggable security solution for the Internet of Things24
FIDWaC - Fast inverse distance weighting and compression23
ResoFox: A GUI-based tool for calculating resolution and relative intensity of neutron powder diffractometers23
Tab2KGWiz: Interactive assistant for mapping tabular data to knowledge graphs22
OpenIPDM: A probabilistic framework for estimating the deterioration and effect of interventions on bridges22
NCC: An R-package for analysis and simulation of platform trials with non-concurrent controls22
TROVA: TRansport Of water VApor21
TimeAwareBPMN-js: An editor and temporal verification tool for Time-Aware BPMN processes21
Version 2 — RPExpand: Software for Riesz projection expansion of resonance phenomena21
MFPP: Matrix-based flexible project planning20
WITio: A MATLAB data evaluation toolbox to script broader insights into big data from WITec microscopes20
CensSpatial: An R package for estimation and diagnostics in spatial censored regression models20
REFRAME–A software framework for managing reactive dependencies in object-oriented applications19
Flow-models 2.0: Elephant flows modeling and detection with machine learning19
ShakerMaker: A framework that simplifies the simulation of seismic ground-motions19
PNW-Cnet v4: Automated species identification for passive acoustic monitoring19
pyMechOpt: A Python toolbox for optimizing of reaction mechanisms18
BBR: An open-source standard workflow based on biophysical crop parameters for automatic Botrytis cinerea assessment in vineyards18
ScoreREM: A user-friendly Matlab-GUI for rapid eye movement (REM) sleep microstructure (Phasic/Tonic) annotation and quantification18
Kunai: A static analysis framework for Android apps18
DFT-MF: Enhanced deepfake detection using mouth movement and transfer learning18
Version 1.1.1 - TROVA: TRansport Of water VApor17
GenSDF: An MPI-Fortran based signed-distance-field generator for computational fluid dynamics applications17
LitOrganizer: Automating the process of data extraction and organization for scientific literature reviews17
Version [2.0] — [pyMCMA: Uniformly distributed Pareto-front representation]17
A covariate software tool to guide test activity allocation16
clickR: Semi-automatic pre-processing of messy data with change tracking for integral dataset cleaning16
MALVADA: A framework for generating datasets of malware execution traces16
DSIPTS: A high productivity environment for time series forecasting models16
XCompress: LLM assisted Python-based text compression toolkit16
GetSensorData: An extensible Android-based application for multi-sensor data registration15
QuITO: Numerical software for constrained nonlinear optimal control problems15
BioEmoDetector: A flexible platform for detecting emotions from health narratives15
The StaDyn programming language15
EnMAP-Box: Imaging spectroscopy in QGIS15
Rcall: An R interface for MATLAB15
VEqMon2D—Equations of motion generation tool of 2D vehicles with Matlab15
DataMetProcess: An open-source package and Shiny application for the acquisition and processing of meteorological data from INMET14
DAUD: A data driven algorithm to find discrete approximations of unknown continuous distributions14
T-Ridership: A web tool for reprogramming public transportation fleets to minimize COVID-19 transmission14
Climatrix: Xarray accessor for climate data sampling and reconstruction14
SpinGlassPEPS.jl: Tensor-network package for Ising-like optimization on quasi-two-dimensional graphs14
clusEvol: An R package for Cluster Evolution Analytics13
MorphoGen: Topology optimization software for Extremely Modular Systems13
E213
ShinyGAStool: A user-friendly tool for candidate gene association studies13
A C++17 thread pool for high-performance scientific computing13
pyBaram: Parallel compressible flow solver in high-performance Python for teaching and research13
PATSMA: Parameter Auto-tuning for Shared Memory Algorithms13
Pynblint: A quality assurance tool to improve the quality of Python Jupyter notebooks13
Ordinalysis: Interpretability of multidimensional ordinal data13
Masked-Piper: Masking personal identities in visual recordings while preserving multimodal information13
P2PFaaS: A framework for FaaS peer-to-peer scheduling and load balancing in Fog and Edge computing13
SolarQGIS: A QGIS application for calculating solar radiation on 3D vector GIS data13
PLATFORM: Parallel Linear Algebra Tool FOr Reduced Modeling13
JGMP: Java bindings and wrappers for the GMP library13
MitoSeg: Mitochondria segmentation tool12
PyQBench: A Python library for benchmarking gate-based quantum computers12
TeDDy: Templated decision diagram library12
Diagnostic Expert Advisor: A platform for developing machine learning models on medical time-series data12
QPPLab: A generally applicable software package for detecting, analyzing, and visualizing large-scale quasiperiodic spatiotemporal patterns (QPPs) of brain activity12
xkl: A legacy software for detailed acoustic analysis of speech made modern12
Version [7.1] – [IV-PSNR: Software for immersive video objective quality evaluation]12
Floodsar: Automatic mapping of river flooding extent from multitemporal SAR imagery12
APLOSE: A web-based annotation platform for underwater passive acoustic monitoring12
Version 2.0.0 - M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations12
MobiScout: A scalable cloud-based driving and activity monitoring platform featuring an IOS app and a WatchOS extension12
GenClass: A parallel tool for data classification based on Grammatical Evolution12
ModelicaGridData: Massive power system simulation data generation and labeling tool using Modelica and Python12
ZEN-garden: Optimizing energy transition pathways with user-oriented data handling11
Phenoflow-ML: A next-generation phenotyping framework to capture ML-based phenotypes11
PyCinemetrics: Computational film studies tool based on deep learning and PySide211
WireGuard-AES: Hardware based encryption to WireGuard for VPN gateways11
Development of an ABAQUS™ plug-in for predicting composite plates stiffness with in-plane periodicity11
TrAQ: A novel, versatile, semi-automated, two-dimensional motor behavioural tracking software11
Emipy: An open-source Python-based tool to analyze industrial emissions in Europe11
GraphXplore: Visual exploration and accessible preprocessing of medical data11
Spectrally regularised LVMs: A spectral regularisation framework for latent variable models designed for single-channel applications11
Causal ML: Python package for causal inference machine learning11
IPv6CC: IPv6 covert channels for testing networks against stegomalware and data exfiltration11
DigiRhythm: An R package for evaluating circadian rhythmicity in animals using the degree of functional coupling10
REMLA: An R package for robust expectation-maximization estimation for latent variable models10
gosset: An R package for analysis and synthesis of ranking data in agricultural experimentation10
pycity_scheduling—A Python framework for the development and assessment of optimisation-based power scheduling algorithms for multi-energy systems in city districts10
STM: A software tool for predicting daily temperature in stored animal slurry10
Atlantic cod growth model: Open source Python package for numerical growth experiments10
Binary complex amplitude application: An all-in-one Matlab application for the advanced laser beam shaping with digital micromirror device10
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 Programming10
Decidim.viz: A data dashboard prototype for a digital democracy platform10
Modelling biocontrol of invasive insects using WaspSim: A MATLAB simulation model10
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 architecture10
Compression of triangulated solids’ surfaces by Decimating Reconstructable Triangles10
Scymol: A python-based software package for initializing and running molecular dynamics simulations using LAMMPS10
FLAGR: A flexible high-performance library for rank aggregation10
pyMeshFOAM: Automated meshing for CFD and fluid–structure simulations10
Gdistns: R package for maximum goodness-of-fit estimates of the generalized G distributions10
HITS: Hyperplanes intersection tabu search for maximum score estimation10
Simplify: A Python library for optimizing pruned neural networks9
“dynmix”: An R package for the estimation of dynamic finite mixtures9
DroneTimeline: Forensic timeline analysis for drones9
ArcNLET-Py: An ArcGIS-based nitrogen load estimation toolbox developed using python for ArcGIS pro9
Gideon Replay: A library to replay interactions in web-applications9
OpenLSA: An open-source toolbox for computing full-field displacements from images of periodic patterns9
3TM: Software for the 3-Tau Model9
Power TAC: Software architecture for a competitive simulation of sustainable smart energy markets9
SimilarityTS: Toolkit for the evaluation of similarity for multivariate time series9
GSITK: A sentiment analysis framework for agile replication and development9
TraClets: A trajectory representation and classification library9
TSSEARCH: Time Series Subsequence Search Library8
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 experiments8
HETOOL: A Half-Edge Topological Object-Oriented Library for generic 2-D geometric modeling8
Streetscape morphometrics: Expanding momepy to analyze urban form from the street point of view8
Cyberattack detection through GPML: Graph Processing for Machine Learning8
libcommute/pycommute: A quantum operator algebra domain-specific language and exact diagonalization toolkit8
FuzConvSteganalysis: Steganalysis via fuzzy logic and convolutional neural network8
SWANe: Standardized workflow for advanced neuroimaging in epilepsy8
Version [1.18
TremorSoft: An decision support application for differential diagnosis between Parkinson’s disease and essential tremor8
PlatformCommander — An open source software for an easy integration of motion platforms in research laboratories8
RIPN: A tool for implementing cyber-physical systems by using interpreted Petri Nets and teleo-reactive programs8
Docker Unified UIMA Interface: New perspectives for NLP on big data8
Covira: A COVID-19 risk assessment, visualization and communication tool8
Performing highly efficient Minima Hopping structure predictions using the Atomic Simulation Environment (ASE)8
3.0 - MOOSE: Enabling massively parallel multiphysics simulations8
MaSMaker: An open-source, portable software to create and integrate maze-like surfaces into arbitrary geometries8
Version [1.1.0]- [DLDiagnosis: A mobile and web application for diseases classification using Deep Learning]8
Editorial Board8
CellRex: Software platform for managing biological cell data8
SmarTS: A Java package for smart contract test suite generation and execution8
Geospatial Analytics Extension for KNIME8
Simplifying computational workflows with the Multiscale Atomic Zeolite Simulation Environment (MAZE)8
Hyperomet: An OpenSees interface for nonlinear analysis of unreinforced masonry buildings7
End to end navigation stack for nuclear power plant inspection with mobile robot7
ASSUME: An agent-based simulation framework for exploring electricity market dynamics with reinforcement learning7
CtrlAer: Programmable real-time execution of scientific experiments using a domain specific language for the Raspberry Pi Pico/Pico 27
OpenPLC61850: An IEC 61850 MMS compatible open source PLC for smart grid research7
Traffic weaver: Semi-synthetic time-varying traffic generator based on averaged time series7
svds-C: A multi-thread C code for computing truncated singular value decomposition7
MicEMD: Open-source toolbox for electromagnetic modeling, inversion, and classification in underground metal target detection7
refellips: A Python package for the analysis of variable angle spectroscopic ellipsometry data7
Yekta: A low-code framework for automated test models generation7
Corrigendum to “pyLAIS: A Python package for Layered Adaptive Importance Sampling” [SoftwareX 29 (2025), 101976]7
tsdownsample: High-performance time series downsampling for scalable visualization7
OpenTEPES: Open-source Transmission and Generation Expansion Planning7
quicR: An R library for streamlined data handling of real-time quaking induced conversion assays7
PickShift: A user-friendly Python tool to assess the surficial uncertainties associated with polygons extracted from historical planimetric data7
PCAfold 2.0—Novel tools and algorithms for low-dimensional manifold assessment and optimization7
Leveraging OpenSimMPLS: A simulation platform for GoS/MPLS networks in research and education7
RAVSim v2.0: Enhanced visualization and comparative analysis for neural network models7
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 trees7
PyBanshee version (1.0): A Python implementation of the MATLAB toolbox BANSHEE for Non-Parametric Bayesian Networks with updated features7
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 noise7
VERONA: A python library for benchmarking deep learning in business process monitoring7
In-Cognitive: A web-based Python application for fuzzy cognitive map design, simulation, and uncertainty analysis based on the Monte Carlo method6
LeXInt: GPU-accelerated exponential integrators package6
CityZones: A geospatial multi-tier software tool to compute urban risk zones6
OSLiFe-DiSC: Open source licenses discovering, selecting and comparing6
Version [1.0]- HAT-VIS — A MATLAB-based hypergraph visualization tool6
pymetamodels: A Python package for metamodeling and design automation6
HistomicsTK: A Python toolkit for pathology image analysis algorithms6
Digital ecosystem for FAIR time series data management in environmental system science6
A WebExtension framework for experimentation and evaluation of webpage segmentation methods6
Computing Continuum Simulator: A comprehensive framework for continuum architecture evaluation6
TrustML: A Python package for computing the trustworthiness of ML models6
CoCoStyle: Mixed initiative co-creative system to support creative process of fashion design6
robustDEA: A Java library for robust efficiency analysis6
A computerized tool for the kinematic limit analysis of 2D masonry structures failing on a tilting table6
Population potential on catchment area (PPCA): A Python-based tool for worldwide geospatial population analysis6
Robustimizer: A graphical user interface application for efficient uncertainty quantification, robust optimization, and reliability-based optimization of processes and designs6
3DRSP: Matlab-based random sphere packing code in three dimensions6
APOTHEOSIS: An efficient approximate similarity search system6
FCM-VSS: An AI powered secured fuzzy cognitive maps management toolkit for visualization, simulation and summarization6
Hydrogen Permeation and Absorption Tool (HyPAT v2.0): An update to facilitate analyses of data from hydrogen absorption experiments6
ENTIRETY — sEmanNTIc pRovisioning and govErning ioT devices in smart energY domain6
A new approach for drone tracking with drone using Proximal Policy Optimization based distributed deep reinforcement learning6
hyperbox-brain: A Python toolbox for hyperbox-based machine learning algorithms6
WACline: A Software Product Line to harness heterogeneity in Web Annotation6
Think inside the (mk)box—A tool for creating and deploying application-specific Linux images utilized in a SiLA software development process6
KneeBones3Dify: Open-source software for segmentation and 3D reconstruction of knee bones from MRI data6
1DCSEMQWE: 1D Controlled Source Electromagnetic Method in Geophysics Using Quadrature With Extrapolation6
2D-xtDCR-LTBEM: A Fortran code for numerical solutions to the unsteady anisotropic-DCR equation of spatio-temporal coefficients6
Growth Data—An automatic solution for seedling growth analysis via RGB-Depth imaging sensors6
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 files6
Climaticpark-py - A python framework for the climatic simulation of vehicular parking lots6
pyJSON Schema Loader and JSON Editor: A tool for file-based metadata management6
AMED: Aggregated multimedia exploratory and discovery search software6
Wave-DNA: A software tool for simulating nonlinear acoustic waves emitted by moving boundaries6
Enabling scientific machine learning in MOOSE using Libtorch6
New, flexible and open-source fisheries self-reporting app: The Shiny4SelfReport6
Trial Monitor: Scaffolding personalised Web dashboards for Human–Computer Interaction field trials6
Rhizomer: Interactive semantic knowledge graphs exploration6
ExactPack: A python library of exact analytic solutions6
The Contiki-NG open source operating system for next generation IoT devices6
pyGRETA, pyCLARA, pyPRIMA: A pre-processing suite to generate flexible model regions for energy system models6
DATTES: Data analysis tools for tests on energy storage6
IST-ROS: A flexible object segmentation and tracking framework for robotics applications6
TIQA-PSI: Toolbox for perceptual Image Quality Assessment of Pan-Sharpened Images6
Fast parallel calculation of modified Bessel function of the second kind and its derivatives6
Matlatzinca: A PyBANSHEE-based graphical user interface for elicitation of non-parametric Bayesian networks from experts6
qo|6
Benopt-Heat: An economic optimization model to identify robust bioenergy technologies for the German heat transition6
HICA: A MATLAB-based hierarchical image clustering algorithm for classifying parts suitable for additive and traditional manufacturing technologies5
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 Applications5
ChargEVal — A multi-user framework for simulating and analysing charging station deployment scenarios using agent-based modelling5
CPR Algorithm—A new interpolation methodology and QGIS plugin for Colour Pattern Regression between aerial images and raster maps5
tx2_fcnn_node: An open-source ROS compatible tool for monocular depth reconstruction5
topoEEG: An Python-framework for analyzing EEG data in neurodegeneratives disease through Topological Deep Learning5
pyFIRI — A free and open source Python software package of the non-auroral Earth’s lower ionosphere5
Star-XP: A simulation framework for Polar-2/ low energy X-ray polarization detector5
MicroVIP: Microscopy image simulation on the Virtual Imaging Platform5
RegionTPMS — Region based triply periodic minimal surfaces (TPMS) for 3-D printed multiphase bone scaffolds with exact porosity values5
An NLP-driven face recognition system to improve Alzheimer’s patient engagement and care [MEMORY LANE]5
TechMiner: Analysis of bibliographic datasets using Python5
Hyper-Data: A Matlab based optimization software for data-driven hyperelasticity5
OpenIMDML: Open Instance Multi-Domain Motor Library utilizing the Modelica modeling language5
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