geocat-examples
GeoCAT-examples provides a gallery of visualization examples demonstrating how to reproduce plots from NCL Applications scripts with packages in Python. It also includes some longer form examples demonstrating how to use functionality from various GeoCAT packages.
cytoscape-cose-bilkent
The CoSE layout for Cytoscape.js by Bilkent with enhanced compound node placement.
naturf
naturf: a package for generating urban parameters for numerical weather modeling - Published in JOSS (2024)
pypartmc
Python (and C++) interface to PartMC with Jupyter/Python, Julia and Matlab examples
IBBI: A Python package for the detection and classification of bark and ambrosia beetles
IBBI: A Python package for the detection and classification of bark and ambrosia beetles - Published in JOSS (2025)
DARE Platform
DARE Platform: a Developer-Friendly and Self-Optimising Workflows-as-a-Service Framework for e-Science on the Cloud - Published in JOSS (2020)
InsarViz
InsarViz: An open source Python package for the interactive visualization of satellite SAR interferometry data - Published in JOSS (2024)
autopytorch
Automatic architecture search and hyperparameter optimization for PyTorch
scarlet2: Astronomical scene modeling in JAX
scarlet2: Astronomical scene modeling in JAX - Published in JOSS (2026)
OnToCode
OnToCode: Template-based code-generation from ontologies - Published in JOSS (2019)
Biotrade
Biotrade: A Python package to access and analyse the international trade of bio-based products - Published in JOSS (2023)
Madym
Madym: A C++ toolkit for quantitative DCE-MRI analysis - Published in JOSS (2021)
Discovering the SUPER in computing - dagster-slurm for reproducible research on HPC
Discovering the SUPER in computing - dagster-slurm for reproducible research on HPC - Published in JOSS (2026)
MUQ
MUQ: The MIT Uncertainty Quantification Library - Published in JOSS (2021)
helm
Holistic Evaluation of Language Models (HELM) is an open source Python framework created by the Center for Research on Foundation Models (CRFM) at Stanford for holistic, reproducible and transparent evaluation of foundation models, including large language models (LLMs) and multimodal models.
Pop2net: Bipartite network generation for agent-based modeling
Pop2net: Bipartite network generation for agent-based modeling - Published in JOSS (2026)
pythermalcomfort
Package to calculate several thermal comfort indices (e.g. PMV, PPD, SET, adaptive) and convert physical variables.
dySEM: An <em>R</em> Package for Dyadic Structural Equation Modeling with Latent Variables
dySEM: An <em>R</em> Package for Dyadic Structural Equation Modeling with Latent Variables - Published in JOSS (2026)
tensorcircuit
Tensor network based quantum software framework for the NISQ era
idiolect: An R package for forensic authorship analysis
idiolect: An R package for forensic authorship analysis - Published in JOSS (2026)
Fast k-medoids Clustering in Rust and Python
Fast k-medoids Clustering in Rust and Python - Published in JOSS (2022)
H-RISK with NoiseModelling
H-RISK with NoiseModelling: a QGIS plugin to predict environmental noise and estimate health risks - Published in JOSS (2024)
Crux.jl: Deep Reinforcement Learning in Julia
Crux.jl: Deep Reinforcement Learning in Julia - Published in JOSS (2026)
Bijx: Bijections and normalizing flows with JAX/NNX
Bijx: Bijections and normalizing flows with JAX/NNX - Published in JOSS (2025)
Trixi
Trixi.jl: Adaptive high-order numerical simulations of conservation laws in Julia
maidr-legacy
[DEPRECATED prototype] Multimodal Access and Interactive Data Representation
DynamicPolynomials
Multivariate polynomials implementation of commutative and non-commutative variables
hatchet
Graph-indexed Pandas DataFrames for analyzing hierarchical performance data
NCDatasets.jl
NCDatasets.jl: a Julia package for manipulating netCDF data sets - Published in JOSS (2024)
ROSS - Rotordynamic Open Source Software
ROSS - Rotordynamic Open Source Software - Published in JOSS (2020)
BasicTools
BasicTools: a numerical simulation toolbox - Published in JOSS (2023)
isofit
Imaging Spectrometer Optimal FITting (ISOFIT) contains a set of routines and utilities for fitting surface, atmosphere and instrument models to imaging spectrometer data.
tts
🐸💬 - a deep learning toolkit for Text-to-Speech, battle-tested in research and production
climpred
climpred: Verification of weather and climate forecasts - Published in JOSS (2021)
AQCNES
AQCNES: A Quasi-Continuum Non-Equilibrium Solver - Published in JOSS (2024)
A-SLOTH
A-SLOTH: Ancient Stars and Local Observables by Tracing Halos - Published in JOSS (2022)
aimz: Scalable probabilistic impact modeling
aimz: Scalable probabilistic impact modeling - Published in JOSS (2026)
DuneCopasi
DuneCopasi: A multi-compartment reaction-diffusion simulator for systems biology - Published in JOSS (2024)
PowerSystems
Data structures in Julia to enable power systems analysis. Part of the Scalable Integrated Infrastructure Planning Initiative at the National Renewable Energy Lab.
PyCS3
PyCS3: A Python toolbox for time-delay measurements in lensed quasars - Published in JOSS (2020)
gkwreg: An R Package for Generalized Kumaraswamy Regression Models for Bounded Data
gkwreg: An R Package for Generalized Kumaraswamy Regression Models for Bounded Data - Published in JOSS (2026)
fars_cleaner: A Python package for downloading and pre-processing vehicle fatality data in the US
fars_cleaner: A Python package for downloading and pre-processing vehicle fatality data in the US - Published in JOSS (2022)
DeepTrees: Tree Crown Segmentation and Analysis in Remote Sensing Imagery with PyTorch
DeepTrees: Tree Crown Segmentation and Analysis in Remote Sensing Imagery with PyTorch - Published in JOSS (2025)
Synthesizer: Synthetic Observables for Modern Astronomy
Synthesizer: Synthetic Observables for Modern Astronomy - Published in JOSS (2026)
vidore-benchmark
Vision Document Retrieval (ViDoRe): Benchmark. Evaluation code for the ColPali paper.
fusion-blossom
A fast minimum-weight perfect matching solver for quantum error correction
RISE
RISE: An R package for RISE analysis - Published in JOSS (2018)
qmflows
This library tackles the construction and efficient execution of computational chemistry workflows
imaging-server-kit
Deploy image processing algorithms in FastAPI servers and easily run them in Napari, QuPath, and more.
Kamodo
Kamodo: A functional API for space weather models and data - Published in JOSS (2022)
The MarINvaders Toolkit
The MarINvaders Toolkit - Published in JOSS (2021)
gLBM
gLBM: A GPU enabled Lattice Boltzmann Method Library - Published in JOSS (2022)
integron_finder
Bioinformatics tool to find integrons in bacterial genomes
topoptlab: An Open and Modular Framework for Benchmarking and Research in Topology Optimization
topoptlab: An Open and Modular Framework for Benchmarking and Research in Topology Optimization - Published in JOSS (2026)
ccompass
A Neural Network Tool for Multi-Omic Classification of Cell Compartments
foyer
A package for atom-typing as well as applying and disseminating forcefields
shimmy
An API conversion tool for popular external reinforcement learning environments