UWGeodynamics
UWGeodynamics: A teaching and research tool for numerical geodynamic modelling - Published in JOSS (2019)
PyKronecker
PyKronecker: A Python Library for the Efficient Manipulation of Kronecker Products and Related Structures - Published in JOSS (2023)
NeuroAnalyzer
NeuroAnalyzer: Julia toolbox for analyzing neurophysiological data - Published in JOSS (2025)
X-PSI
X-PSI: A Python package for neutron star X-ray pulse simulation and inference - Published in JOSS (2023)
bíogo/ncbi
bíogo/ncbi: interfaces to NCBI services for the Go language - Published in JOSS (2017)
covidregionaldata
covidregionaldata: Subnational data for COVID-19 epidemiology - Published in JOSS (2021)
libscientific
libscientific: A Powerful C Library for Multivariate Analysis - Published in JOSS (2023)
PFEIFER
PFEIFER: Preprocessing Framework for Electrograms Intermittently Fiducialized from Experimental Recordings - Published in JOSS (2018)
pathways
pathways: life cycle assessment of energy transition scenarios - Published in JOSS (2024)
NCBImeta
NCBImeta: efficient and comprehensive metadata retrieval from NCBI databases - Published in JOSS (2020)
Aletheia
Aletheia: an open-source toolbox for steganalysis - Published in JOSS (2024)
AliNe
AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignment - Published in JOSS (2025)
MRdataset
MRdataset : A unified and user-friendly interface to medical imaging datasets - Published in JOSS (2024)
LFSpy
LFSpy: A Python Implementation of Local Feature Selection for Data Classification with scikit-learn Compatibility - Published in JOSS (2020)
AutoGAMESS
AutoGAMESS: A Python package for automation of GAMESS(US) Raman calculations - Published in JOSS (2019)
The ARC-OPT Library for Whole-Body Control of Robotic Systems
The ARC-OPT Library for Whole-Body Control of Robotic Systems - Published in JOSS (2024)
swift-emulator
swift-emulator: A Python package for emulation of simulated scaling relations - Published in JOSS (2022)
Instrbuilder
Instrbuilder: A Python package for electrical instrument control - Published in JOSS (2019)
Qlunc
Qlunc: Quantification of lidar uncertainty - Published in JOSS (2021)
rfasst
rfasst: An R tool to estimate air pollution impacts on health and agriculture - Published in JOSS (2022)
PyFPT
PyFPT: A Python package for first-passage times - Published in JOSS (2023)
mcMST
mcMST: A Toolbox for the Multi-Criteria Minimum Spanning Tree Problem - Published in JOSS (2017)
serp
serp: An R package for smoothing in ordinal regression - Published in JOSS (2021)
RCzechia
RCzechia: Spatial Objects of the Czech Republic - Published in JOSS (2023)
Geometric nested sampling
Geometric nested sampling: sampling from distributions defined on non-trivial geometries - Published in JOSS (2020)
skedm
skedm: Empirical Dynamic Modeling - Published in JOSS (2017)
STReNGTHS, a Python package to model and simulate complex reaction-diffusion systems
STReNGTHS, a Python package to model and simulate complex reaction-diffusion systems - Published in JOSS (2024)
PyView
PyView: A general purpose tool for analyzing calcium imaging data - Published in JOSS (2023)
array_split
array_split: Multi-dimensional array partitioning - Published in JOSS (2017)
Maelstrom
Maelstrom: A Python package for identifying companions to pulsating stars from their light travel time variations - Published in JOSS (2020)
Thing Directory
Thing Directory: Simple and lightweight registry of IoT device metadata - Published in JOSS (2021)
Kindel
Kindel: indel-aware consensus for nucleotide sequence alignments - Published in JOSS (2017)
ACTIN
ACTIN: A tool to calculate stellar activity indices - Published in JOSS (2018)
mcbette
mcbette: model comparison using babette - Published in JOSS (2020)
BifacialSimu
BifacialSimu: Holistic Simulation of large-scale Bifacial Photovoltaic Systems - Published in JOSS (2022)
pyMultiFit: A Python library for fitting data with multiple models
pyMultiFit: A Python library for fitting data with multiple models - Published in JOSS (2025)
pymgpipe
pymgpipe: microbiome metabolic modeling in Python - Published in JOSS (2023)
pygen-structures
pygen-structures: A Python package to generate 3D molecular structures for simulations using the CHARMM forcefield - Published in JOSS (2020)
TimeSeriesClustering
TimeSeriesClustering: An extensible framework in Julia - Published in JOSS (2019)
GFAKluge
GFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formats - Published in JOSS (2019)
Synthia
Synthia: multidimensional synthetic data generation in Python - Published in JOSS (2021)
bikedata
bikedata - Published in JOSS (2017)
openaerostruct
OpenAeroStruct is a lightweight tool that performs aerostructural optimization using OpenMDAO.
HydDown
HydDown: A Python package for calculation of hydrogen (or other gas) pressure vessel filling and discharge - Published in JOSS (2021)
Lexicon-Mono-Seq, DOM Text Based Async MSA Viewer
Lexicon-Mono-Seq, DOM Text Based Async MSA Viewer - Published in JOSS (2019)
shmlast
shmlast: An improved implementation of Conditional Reciprocal Best Hits with LAST and Python - Published in JOSS (2017)
PASCal Python
PASCal Python: A Principal Axis Strain Calculator - Published in JOSS (2023)
Systole
Systole: A python package for cardiac signal synchrony and analysis - Published in JOSS (2022)
FHI-vibes
FHI-vibes: Ab Initio Vibrational Simulations - Published in JOSS (2020)
disksurf
disksurf: Extracting the 3D Structure of Protoplanetary Disks - Published in JOSS (2021)
Castor
Castor: A C++ library to code "à la Matlab" - Published in JOSS (2022)
repytah
repytah: An Open-Source Python Package for Building Aligned Hierarchies for Sequential Data - Published in JOSS (2023)
Heta compiler
Heta compiler: a software tool for the development of large-scale QSP models and compilation into simulation formats - Published in JOSS (2021)
A framework for generating interactive reports for cancer genome analysis
A framework for generating interactive reports for cancer genome analysis - Published in JOSS (2017)
SeqTools
SeqTools: A python package for easy transformation, combination and evaluation of large datasets. - Published in JOSS (2018)
xrdfit
xrdfit: A Python package for fitting synchrotron X-ray diffraction spectra - Published in JOSS (2020)
HSImage
HSImage: A Python and C++ library to allow interaction with ENVI-BIL hyperspectral images - Published in JOSS (2018)
Chi
Chi: A Python package for treatment response modelling - Published in JOSS (2024)
OpenDrop
OpenDrop: Open-source software for pendant drop tensiometry & contact angle measurements - Published in JOSS (2021)
OPSDN
OPSDN: an enhanced SDN simulation framework for OPNET Modeler - Published in JOSS (2023)
GB code
GB code: A grain boundary generation code - Published in JOSS (2018)
Ipyannotator
Ipyannotator: the infinitely hackable annotation framework - Published in JOSS (2022)
Analytic continuation component of the GreenX library
Analytic continuation component of the GreenX library: robust Padé approximants with symmetry constraints - Published in JOSS (2025)
bistablehistory
bistablehistory: an R package for history-dependent analysis of perceptual time series - Published in JOSS (2022)
svFSI
svFSI: A Multiphysics Package for Integrated Cardiac Modeling - Published in JOSS (2022)
SyntheticEddyMethod.jl
SyntheticEddyMethod.jl: A Julia package for the creation of inlet flow conditions for LES - Published in JOSS (2023)
modeLLtest
modeLLtest: An R Package for Unbiased Model Comparison using Cross Validation - Published in JOSS (2019)
Vlasiator.jl
Vlasiator.jl: A Julia package for processing Vlasiator data - Published in JOSS (2023)
ChainConsumer
ChainConsumer - Published in JOSS (2016)
Mayawaves
Mayawaves: Python Library for Interacting with the Einstein Toolkit and the MAYA Catalog - Published in JOSS (2024)
vSmartMOM.jl
vSmartMOM.jl: an Open-Source Julia Package for Atmospheric Radiative Transfer and Remote Sensing Tools - Published in JOSS (2022)
QMKPy
QMKPy: A Python Testbed for the Quadratic Multiple Knapsack Problem - Published in JOSS (2022)
DetectorChecker
DetectorChecker: analyzing patterns of defects in detector screens - Published in JOSS (2020)
MarSwitching.jl
MarSwitching.jl: A Julia package for Markov switching dynamic models - Published in JOSS (2024)
BioProv - A provenance library for bioinformatics workflows
BioProv - A provenance library for bioinformatics workflows - Published in JOSS (2021)
R3D2
R3D2: Relativistic Reactive Riemann problem solver for Deflagrations and Detonations - Published in JOSS (2016)
gym-saturation
gym-saturation: an OpenAI Gym environment for saturation provers - Published in JOSS (2022)
CarrierCapture.jl
CarrierCapture.jl: Anharmonic Carrier Capture - Published in JOSS (2020)
DE-Sim
DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python - Published in JOSS (2020)
nnde
nnde: A Python package for solving differential equations using neural networks - Published in JOSS (2022)
PyCurious
PyCurious: A Python module for computing the Curie depth from the magnetic anomaly. - Published in JOSS (2019)
Lightshow
Lightshow: a Python package for generating computational x-ray absorption spectroscopy input files - Published in JOSS (2023)
pySBeLT
pySBeLT: A Python software package for stochastic sediment transport under rarefied conditions - Published in JOSS (2022)
Mallob
Mallob: Scalable SAT Solving On Demand With Decentralized Job Scheduling - Published in JOSS (2022)
PYCV
PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python - Published in JOSS (2019)
VAST
VAST: the Void Analysis Software Toolkit - Published in JOSS (2022)
coronagraph
coronagraph: Telescope Noise Modeling for Exoplanets in Python - Published in JOSS (2019)
graynet
graynet: single-subject morphometric networks for neuroscience connectivity applications - Published in JOSS (2018)
AutoClassWrapper
AutoClassWrapper: a Python wrapper for AutoClass C classification - Published in JOSS (2019)
BART-Survival
BART-Survival: A Bayesian machine learning approach to survival analyses in Python - Published in JOSS (2025)