BrainGlobe Atlas API: a common interface for neuroanatomical atlases
BrainGlobe Atlas API: a common interface for neuroanatomical atlases - Published in JOSS (2020)
bwsample: Processing Best-Worst Scaling data
bwsample: Processing Best-Worst Scaling data - Published in JOSS (2021)
Kinetics Toolkit: An Open-Source Python Package to Facilitate Research in Biomechanics
Kinetics Toolkit: An Open-Source Python Package to Facilitate Research in Biomechanics - Published in JOSS (2021)
RivGraph: Automatic extraction and analysis of river and delta channel network topology
RivGraph: Automatic extraction and analysis of river and delta channel network topology - Published in JOSS (2021)
PolSAR tools: A QGIS plugin for generating SAR descriptors
PolSAR tools: A QGIS plugin for generating SAR descriptors - Published in JOSS (2021)
Makie.jl: Flexible high-performance data visualization for Julia
Makie.jl: Flexible high-performance data visualization for Julia - Published in JOSS (2021)
flowTorch - a Python library for analysis and reduced-order modeling of fluid flows
flowTorch - a Python library for analysis and reduced-order modeling of fluid flows - Published in JOSS (2021)
HOODESolver.jl: A Julia package for highly oscillatory problems
HOODESolver.jl: A Julia package for highly oscillatory problems - Published in JOSS (2021)
GRChombo: An adaptable numerical relativity code for fundamental physics
GRChombo: An adaptable numerical relativity code for fundamental physics - Published in JOSS (2021)
minimo: a linked data and metadata storage system for small labs
minimo: a linked data and metadata storage system for small labs - Published in JOSS (2021)
PopMedNet: A scalable and extensible open-source informatics platform designed to facilitate the implementation and operation of distributed health data networks
PopMedNet: A scalable and extensible open-source informatics platform designed to facilitate the implementation and operation of distributed health data networks - Published in JOSS (2022)
portalcasting: Supporting automated forecasting of rodent populations
portalcasting: Supporting automated forecasting of rodent populations - Published in JOSS (2022)
pyscreener: A Python Wrapper for Computational Docking Software
pyscreener: A Python Wrapper for Computational Docking Software - Published in JOSS (2022)
VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data
VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data - Published in JOSS (2022)
beamshapes: a Python package to generate directivity patterns for various sound source models
beamshapes: a Python package to generate directivity patterns for various sound source models - Published in JOSS (2022)
mctreesearch4j: A Monte Carlo Tree Search Implementation for the JVM
mctreesearch4j: A Monte Carlo Tree Search Implementation for the JVM - Published in JOSS (2022)
nsink: An R package for flow path nitrogen removal estimation
nsink: An R package for flow path nitrogen removal estimation - Published in JOSS (2022)
islatu: A Python package for the reduction of reflectometry data
islatu: A Python package for the reduction of reflectometry data - Published in JOSS (2022)
PyBioPAX: biological pathway exchange in Python
PyBioPAX: biological pathway exchange in Python - Published in JOSS (2022)
3D Line Radiative Transfer & Synthetic Observations with Magritte
3D Line Radiative Transfer & Synthetic Observations with Magritte - Published in JOSS (2022)
GSAreport: Easy to Use Global Sensitivity Reporting
GSAreport: Easy to Use Global Sensitivity Reporting - Published in JOSS (2022)
Kinematics-vis: A Visualization Tool for the Mathematics of Human Motion
Kinematics-vis: A Visualization Tool for the Mathematics of Human Motion - Published in JOSS (2021)
TorchMetrics - Measuring Reproducibility in PyTorch
TorchMetrics - Measuring Reproducibility in PyTorch - Published in JOSS (2022)
radioactivedecay: A Python package for radioactive decay calculations
radioactivedecay: A Python package for radioactive decay calculations - Published in JOSS (2022)
SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations
SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations - Published in JOSS (2022)
SwiftVISA: Controlling Instrumentation with a Swift-based Implementation of the VISA Communication Protocol
SwiftVISA: Controlling Instrumentation with a Swift-based Implementation of the VISA Communication Protocol - Published in JOSS (2023)
Qiskit Experiments: A Python package to characterize and calibrate quantum computers
Qiskit Experiments: A Python package to characterize and calibrate quantum computers - Published in JOSS (2023)
PySDM v1: particle-based cloud modeling package for warm-rain microphysics and aqueous chemistry
PySDM v1: particle-based cloud modeling package for warm-rain microphysics and aqueous chemistry - Published in JOSS (2022)
PyMPDATA v1: Numba-accelerated implementation of MPDATA with examples in Python, Julia and Matlab
PyMPDATA v1: Numba-accelerated implementation of MPDATA with examples in Python, Julia and Matlab - Published in JOSS (2022)
GasChromatographySimulator.jl
GasChromatographySimulator.jl - Published in JOSS (2022)
WoT-Server: Combining the Web-Of-Things and SensorThings standards to build an IoT platform
WoT-Server: Combining the Web-Of-Things and SensorThings standards to build an IoT platform - Published in JOSS (2026)
CAZy-parser a way to extract information from the Carbohydrate-Active enZYmes Database
CAZy-parser a way to extract information from the Carbohydrate-Active enZYmes Database - Published in JOSS (2016)
Effective-Quadratures (EQ): Polynomials for Computational Engineering Studies
Effective-Quadratures (EQ): Polynomials for Computational Engineering Studies - Published in JOSS (2017)
Frackit
Frackit: a framework for stochastic fracture network generation and analysis - Published in JOSS (2020)
crystract: A Crystallography Package in R for .cif Data Processing
crystract: A Crystallography Package in R for .cif Data Processing - Published in JOSS (2026)
Fetpype: An Open-Source Pipeline for Reproducible Fetal Brain MRI Analysis
Fetpype: An Open-Source Pipeline for Reproducible Fetal Brain MRI Analysis - Published in JOSS (2026)
scpviz: A Python bioinformatics toolkit for Single-cell Proteomics and multi-omics analysis
scpviz: A Python bioinformatics toolkit for Single-cell Proteomics and multi-omics analysis - Published in JOSS (2026)
BayCauRETM: R package for Bayesian Causal Inference for Recurrent Event Outcomes
BayCauRETM: R package for Bayesian Causal Inference for Recurrent Event Outcomes - Published in JOSS (2026)
YACHT: Software for an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample
YACHT: Software for an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample - Published in JOSS (2026)
DeGAUSS: Decentralized Geomarker Assessment for Multi-Site Studies
DeGAUSS: Decentralized Geomarker Assessment for Multi-Site Studies - Published in JOSS (2018)
Komodo: Cryptographically-proven Erasure Coding
Komodo: Cryptographically-proven Erasure Coding - Published in JOSS (2026)
fgivenx: A Python package for functional posterior plotting
fgivenx: A Python package for functional posterior plotting - Published in JOSS (2018)
mixR: An R package for Finite Mixture Modeling for Both Raw and Binned Data
mixR: An R package for Finite Mixture Modeling for Both Raw and Binned Data - Published in JOSS (2022)
ReciPies: A Lightweight Data Transformation Pipeline for Reproducible ML
ReciPies: A Lightweight Data Transformation Pipeline for Reproducible ML - Published in JOSS (2026)
Calzone: A Geant4 Python wrapper for the simulation of outdoor particle detectors
Calzone: A Geant4 Python wrapper for the simulation of outdoor particle detectors - Published in JOSS (2025)
AMaze: a benchmark generator for sighted maze-navigating agents
AMaze: a benchmark generator for sighted maze-navigating agents - Published in JOSS (2025)
Visualization of Multi-Dimensional Data -- The data-slicer Package
Visualization of Multi-Dimensional Data -- The data-slicer Package - Published in JOSS (2021)
rtimicropem: an R package supporting the analysis of RTI MicroPEM output files
rtimicropem: an R package supporting the analysis of RTI MicroPEM output files - Published in JOSS (2017)
GPP, the Generic Preprocessor
GPP, the Generic Preprocessor - Published in JOSS (2020)
Oceananigans.jl: Fast and friendly geophysical fluid dynamics on GPUs
Oceananigans.jl: Fast and friendly geophysical fluid dynamics on GPUs - Published in JOSS (2020)
areal: An R package for areal weighted interpolation
areal: An R package for areal weighted interpolation - Published in JOSS (2019)
ERAD: A Graph-Based Tool for Energy Resilience Analysis of Electric Distribution Systems
ERAD: A Graph-Based Tool for Energy Resilience Analysis of Electric Distribution Systems - Published in JOSS (2025)
Diff Studio: Ecosystem for Interactive Modeling by Ordinary Differential Equations
Diff Studio: Ecosystem for Interactive Modeling by Ordinary Differential Equations - Published in JOSS (2026)
ccostr: An R package for estimating mean costs with censored data
ccostr: An R package for estimating mean costs with censored data - Published in JOSS (2019)
SenSARP: A pipeline to pre-process Sentinel-1 SLC data by using ESA SNAP Sentinel-1 Toolbox
SenSARP: A pipeline to pre-process Sentinel-1 SLC data by using ESA SNAP Sentinel-1 Toolbox - Published in JOSS (2022)
ShakeNBreak: Navigating the defect configurational landscape
ShakeNBreak: Navigating the defect configurational landscape - Published in JOSS (2022)
PySWMM: The Python Interface to Stormwater Management Model (SWMM)
PySWMM: The Python Interface to Stormwater Management Model (SWMM) - Published in JOSS (2020)
sweater: Speedy Word Embedding Association Test and Extras Using R
sweater: Speedy Word Embedding Association Test and Extras Using R - Published in JOSS (2022)
turtleFSI: A Robust and Monolithic FEniCS-based Fluid-Structure Interaction Solver
turtleFSI: A Robust and Monolithic FEniCS-based Fluid-Structure Interaction Solver - Published in JOSS (2020)
SlideRule: Enabling rapid, scalable, open science for the NASA ICESat-2 mission and beyond
SlideRule: Enabling rapid, scalable, open science for the NASA ICESat-2 mission and beyond - Published in JOSS (2023)
tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data
tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data - Published in JOSS (2019)
PureML: a transparent NumPy-only deep learning framework for teaching and prototyping
PureML: a transparent NumPy-only deep learning framework for teaching and prototyping - Published in JOSS (2026)
Nuclear Morphology Analysis 2.0.0: Improved image analysis software for measuring nuclear shape
Nuclear Morphology Analysis 2.0.0: Improved image analysis software for measuring nuclear shape - Published in JOSS (2022)
pyCLINE: A Python package using the CLINE method for discovery of nullcline structures in oscillatory dynamics
pyCLINE: A Python package using the CLINE method for discovery of nullcline structures in oscillatory dynamics - Published in JOSS (2025)
samplics: a Python Package for selecting, weighting and analyzing data from complex sampling designs.
samplics: a Python Package for selecting, weighting and analyzing data from complex sampling designs. - Published in JOSS (2021)
libRL: A Python library for the characterization of microwave absorption
libRL: A Python library for the characterization of microwave absorption - Published in JOSS (2019)
Virtual Bumblebees Artificial Life Simulation
Virtual Bumblebees Artificial Life Simulation - Published in JOSS (2017)
tidyLPA: An R Package to Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software
tidyLPA: An R Package to Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software - Published in JOSS (2018)
DEEPaaS API: a REST API for Machine Learning and Deep Learning models
DEEPaaS API: a REST API for Machine Learning and Deep Learning models - Published in JOSS (2019)
STUMPY: A Powerful and Scalable Python Library for Time Series Data Mining
STUMPY: A Powerful and Scalable Python Library for Time Series Data Mining - Published in JOSS (2019)
climpred: Verification of weather and climate forecasts
climpred: Verification of weather and climate forecasts - Published in JOSS (2021)
genomepy: download genomes the easy way
genomepy: download genomes the easy way - Published in JOSS (2017)
OceanSpy: A Python package to facilitate ocean model data analysis and visualization
OceanSpy: A Python package to facilitate ocean model data analysis and visualization - Published in JOSS (2019)
Ramble: Parser Combinator for R
Ramble: Parser Combinator for R - Published in JOSS (2017)
Pippin: A pipeline for supernova cosmology
Pippin: A pipeline for supernova cosmology - Published in JOSS (2020)
Weave.jl: Scientific Reports Using Julia
Weave.jl: Scientific Reports Using Julia - Published in JOSS (2017)
METISSE: METhod of Interpolation for Single Star Evolution
METISSE: METhod of Interpolation for Single Star Evolution - Published in JOSS (2025)
PySPOD: A Python package for Spectral Proper Orthogonal Decomposition (SPOD)
PySPOD: A Python package for Spectral Proper Orthogonal Decomposition (SPOD) - Published in JOSS (2021)
RealPaver 1.1: A C++ Library for Constraint Programming over Numeric or Mixed Discrete-Continuous Domains
RealPaver 1.1: A C++ Library for Constraint Programming over Numeric or Mixed Discrete-Continuous Domains - Published in JOSS (2026)
OrNet - a Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks
OrNet - a Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks - Published in JOSS (2020)
sourmash: a library for MinHash sketching of DNA
sourmash: a library for MinHash sketching of DNA - Published in JOSS (2016)
IAMReX: an adaptive framework for the multiphase flow and fluid-particle interaction problems
IAMReX: an adaptive framework for the multiphase flow and fluid-particle interaction problems - Published in JOSS (2025)
LAS: an integrated language analysis tool for multiple languages
LAS: an integrated language analysis tool for multiple languages - Published in JOSS (2016)
TopoChronia: A QGIS plugin for the creation of fully quantified palaeogeographic maps
TopoChronia: A QGIS plugin for the creation of fully quantified palaeogeographic maps - Published in JOSS (2026)
Chemiscope: interactive structure-property explorer for materials and molecules
Chemiscope: interactive structure-property explorer for materials and molecules - Published in JOSS (2020)
OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases.
OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases. - Published in JOSS (2021)
citesdb: An R package to support analysis of CITES Trade Database shipment-level data
citesdb: An R package to support analysis of CITES Trade Database shipment-level data - Published in JOSS (2019)
GFF3toEMBL: Preparing annotated assemblies for submission to EMBL
GFF3toEMBL: Preparing annotated assemblies for submission to EMBL - Published in JOSS (2016)
pylevin: efficient numerical integration of integrals containing up to three Bessel functions
pylevin: efficient numerical integration of integrals containing up to three Bessel functions - Published in JOSS (2025)
The psyplot interactive visualization framework
The psyplot interactive visualization framework - Published in JOSS (2017)
reflectorch: a deep learning package for X-ray and neutron reflectometry
reflectorch: a deep learning package for X-ray and neutron reflectometry - Published in JOSS (2025)
Container Tree: Software to Model Container Filesystems, Packages, and Inheritance
Container Tree: Software to Model Container Filesystems, Packages, and Inheritance - Published in JOSS (2019)
Annotation Sniffer: A tool to Extract Code Annotations Metrics
Annotation Sniffer: A tool to Extract Code Annotations Metrics - Published in JOSS (2020)
MaterialNet: A web-based graph explorer for materials science data
MaterialNet: A web-based graph explorer for materials science data - Published in JOSS (2020)
lawn: An R client for the Turf Javascript Library for Geospatial Analysis
lawn: An R client for the Turf Javascript Library for Geospatial Analysis - Published in JOSS (2017)
tidyqwi: A Tidy Approach to Accessing The US Census Bureau's Quarterly Workforce Indicators
tidyqwi: A Tidy Approach to Accessing The US Census Bureau's Quarterly Workforce Indicators - Published in JOSS (2019)
PyMarket - A simple library for simulating markets in Python
PyMarket - A simple library for simulating markets in Python - Published in JOSS (2020)
widgyts: Custom Jupyter Widgets for Interactive Data Exploration with yt
widgyts: Custom Jupyter Widgets for Interactive Data Exploration with yt - Published in JOSS (2020)
Sit2StandPy: An Open-Source Python Package for Detecting and Quantifying Sit-to-Stand Transitions Using an Accelerometer on the Lower Back
Sit2StandPy: An Open-Source Python Package for Detecting and Quantifying Sit-to-Stand Transitions Using an Accelerometer on the Lower Back - Published in JOSS (2020)
kiwiPy: Robust, high-volume, messaging for big-data and computational science workflows
kiwiPy: Robust, high-volume, messaging for big-data and computational science workflows - Published in JOSS (2020)