edsnlp
Modular, fast NLP framework, compatible with Pytorch and spaCy, offering tailored support for French clinical notes.
r3f
r3f: Rotation of 3-dimensional Reference Frames - Published in JOSS (2025)
ABSESpy: An agent-based modeling framework for social-ecological systems
ABSESpy: An agent-based modeling framework for social-ecological systems - Published in JOSS (2024)
Habfuzz
Habfuzz: A tool to calculate the instream hydraulic habitat suitability using fuzzy logic and fuzzy Bayesian inference - Published in JOSS (2016)
Algorithms for SEM-EDS Mineral Dust Classification
Algorithms for SEM-EDS Mineral Dust Classification - Published in JOSS (2025)
fff_segmenter
fff_segmenter: A signal segmentation script for acoustic FFF fabrication data in MATLAB - Published in JOSS (2024)
Bioassays
Bioassays: a new package in R for analyzing cellular assays - Published in JOSS (2020)
YoungTab
YoungTab - Published in JOSS (2017)
OpenEPSim
OpenEPSim: An Open Exclusion Process Simulation Tool - Published in JOSS (2018)
CRED
CRED: a rapid peak caller for Chem-seq data - Published in JOSS (2019)
gitlab2prov
🔍️ Extract provenance information (W3C PROV) from GitLab projects.
BCEA
Bayesian Cost Effectiveness Analysis. Given the results of a Bayesian model (possibly based on MCMC) in the form of simulations from the posterior distributions of suitable variables of costs and clinical benefits for two or more interventions, produces a health economic evaluation. Compares one of the interventions (the "reference") to the others ("comparators"). Produces many summary and plots to analyse the results
esmvaltool
ESMValTool: A community diagnostic and performance metrics tool for routine evaluation of Earth system models in CMIP
NiTransforms
NiTransforms: A Python tool to read, represent, manipulate, and apply $n$-dimensional spatial transforms - Published in JOSS (2021)
@kit-data-manager/react-pid-component
The PID-Component is a web component that can be used to display PIDs, ORCiDs, and possibly other identifiers in a user-friendly way. It is easily extensible to support other identifier types.
parcels
Main code for Parcels - a highly customisable Lagrangian simulation framework
DEVSIM
DEVSIM: A TCAD Semiconductor Device Simulator - Published in JOSS (2022)
pettingzoo
An API standard for multi-agent reinforcement learning environments, with popular reference environments and related utilities
flaml
A fast library for AutoML and tuning. Join our Discord: https://discord.gg/Cppx2vSPVP.
pyGPGO: Bayesian Optimization for Python
pyGPGO: Bayesian Optimization for Python - Published in JOSS (2017)
esmvalcore
ESMValCore: A community tool for pre-processing data from Earth system models in CMIP and running analysis scripts.
Multiple Inference
Multiple Inference: A Python package for comparing multiple parameters - Published in JOSS (2022)
heat
Distributed tensors and Machine Learning framework with GPU and MPI acceleration in Python
specreduce
Tools for the reduction of spectroscopic observations from Optical and NIR instruments
SEP: Source Extractor as a library
SEP: Source Extractor as a library - Published in JOSS (2016)
cebra
Learnable latent embeddings for joint behavioral and neural analysis - Official implementation of CEBRA
aiapy
aiapy: A Python Package for Analyzing Solar EUV Image Data from AIA - Published in JOSS (2020)
spam
spam: Software for Practical Analysis of Materials - Published in JOSS (2020)
kerasR
kerasR: R Interface to the Keras Deep Learning Library - Published in JOSS (2017)
Automated Sleep Stage Scoring Using k-Nearest Neighbors Classifier
Automated Sleep Stage Scoring Using k-Nearest Neighbors Classifier - Published in JOSS (2020)
CITapp - a response time-based Concealed Information Test lie detector web application
CITapp - a response time-based Concealed Information Test lie detector web application - Published in JOSS (2019)
gofcat
gofcat: An R package for goodness-of-fit of categorical response models - Published in JOSS (2022)
Discrete Laplace mixture model with applications in forensic genetics
Discrete Laplace mixture model with applications in forensic genetics - Published in JOSS (2018)
fitODBOD
fitODBOD: An R Package to Model Binomial Outcome Data using Binomial Mixture and Alternate Binomial Distributions. - Published in JOSS (2019)
serverless-benchmarks
SeBS: serverless benchmarking suite for automatic performance analysis of FaaS platforms.
deltascf-aims
An application to automate core level spectroscopy simulations in FHI-aims
datalad-next
DataLad extension for new functionality and improved user experience
sfctools - A toolbox for stock-flow consistent, agent-based models
sfctools - A toolbox for stock-flow consistent, agent-based models - Published in JOSS (2023)
andes
Python toolbox / library for power system transient dynamics simulation with symbolic modeling and numerical analysis 🔥
KrylovKit
Krylov methods for linear problems, eigenvalues, singular values and matrix functions
geostatspy
GeostatsPy Python package for spatial data analytics and geostatistics. Started as a reimplementation of GSLIB, Geostatistical Library (Deutsch and Journel, 1992) from Fortran to Python, Geostatistics in a Python package. Now with many additional methods. I hope this resources is helpful, Prof. Michael Pyrcz
QComms QKD Software Toolkit
QComms QKD Software Toolkit - Published in JOSS (2019)
dm-meltingpot
A suite of test scenarios for multi-agent reinforcement learning.
DMT-core
DMT-core: A Python Toolkit for Semiconductor Device Engineers - Published in JOSS (2022)
SAILS
SAILS: Spectral Analysis In Linear Systems - Published in JOSS (2020)
splashsurf
Surface reconstruction library and CLI for particle data from SPH simulations, written in Rust.
ersilia
The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.
scikit-activeml
scikit-activeml: Python library for active learning on top of scikit-learn
mmgis
Multi-Mission Geographical Information System - Web-based Mapping and Spatial Data Infrastructure for Planetary Science Operations - https://nasa-ammos.github.io/MMGIS/
Altair
Altair: Interactive Statistical Visualizations for Python - Published in JOSS (2018)
fuxictr
A configurable, tunable, and reproducible library for CTR prediction https://fuxictr.github.io
ThermoCodegen
ThermoCodegen: a python/C++ package for the generation of custom thermodynamic models - Published in JOSS (2023)
Asimov
Asimov: A framework for coordinating parameter estimation workflows - Published in JOSS (2023)
Catalyst
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
binary_c-python
binary_c-python: A Python-based stellar population synthesis tool and interface to binary_c - Published in JOSS (2023)
GluPredKit: A Python Package for Blood Glucose Prediction and Evaluation
GluPredKit: A Python Package for Blood Glucose Prediction and Evaluation - Published in JOSS (2024)
mermaid
Generation of diagrams like flowcharts or sequence diagrams from text in a similar manner as markdown
quantus
Quantus is an eXplainable AI toolkit for responsible evaluation of neural network explanations
pyiron
pyiron - an integrated development environment (IDE) for computational materials science.
DEPP - Differential Evolution Parallel Program
DEPP - Differential Evolution Parallel Program - Published in JOSS (2020)
PyMS
PyMS: Python for Mycorrhizal Symbiosis data analysis - Published in JOSS (2019)
SeqPeelSort
SeqPeelSort: a spike sorting algorithm for single sensillum recordings - Published in JOSS (2018)
TEfits
TEfits: Nonlinear regression for time-evolving indices - Published in JOSS (2020)
autoStreamTree
autoStreamTree: Genomic variant data fitted to geospatial networks - Published in JOSS (2024)
SISSO++
SISSO++: A C++ Implementation of the Sure-Independence Screening and Sparsifying Operator Approach - Published in JOSS (2022)
scikit-maad
Open-source and modular toolbox for quantitative soundscape analysis in Python
deflake.rs: Detect Flaky Tests in Rust Projects using Execution Data
deflake.rs: Detect Flaky Tests in Rust Projects using Execution Data - Published in JOSS (2025)
kinisi: Bayesian analysis of mass transport from molecular dynamics simulations
kinisi: Bayesian analysis of mass transport from molecular dynamics simulations - Published in JOSS (2024)
BaderKit: A Python Package for Grid-based Bader Charge Analysis
BaderKit: A Python Package for Grid-based Bader Charge Analysis - Published in JOSS (2026)
cytoscape-expand-collapse
A Cytoscape.js extension to expand/collapse nodes for better management of complexity of compound graphs
pytest
The pytest framework makes it easy to write small tests, yet scales to support complex functional testing
decimer
DECIMER Image Transformer is a deep-learning-based tool designed for automated recognition of chemical structure images. Leveraging transformer architectures, the model converts chemical images into SMILES strings, enabling the digitization of chemical data from scanned documents, literature, and patents.
SOLWEIG-GPU: GPU-Accelerated Thermal Comfort Modeling Framework for Urban Digital Twins
SOLWEIG-GPU: GPU-Accelerated Thermal Comfort Modeling Framework for Urban Digital Twins - Published in JOSS (2026)
