jsPsych
jsPsych: Enabling an Open-Source Collaborative Ecosystem of Behavioral Experiments - Published in JOSS (2023)
toqito -- Theory of quantum information toolkit
toqito -- Theory of quantum information toolkit: A Python package for studying quantum information - Published in JOSS (2021)
New developments in PySDM and PySDM-examples v2
New developments in PySDM and PySDM-examples v2: collisional breakup, immersion freezing, dry aerosol initialization, and adaptive time-stepping - Published in JOSS (2023)
abcvoting
abcvoting: A Python package for approval-based multi-winner voting rules - Published in JOSS (2023)
Nextclade
Nextclade: clade assignment, mutation calling and quality control for viral genomes - Published in JOSS (2021)
TipToft
TipToft: detecting plasmids contained in uncorrected long read sequencing data - Published in JOSS (2019)
PII-Codex
PII-Codex: a Python library for PII detection, categorization, and severity assessment - Published in JOSS (2023)
Multilocus sequence typing by blast from de novo assemblies against PubMLST
Multilocus sequence typing by blast from de novo assemblies against PubMLST - Published in JOSS (2016)
PySwarming
PySwarming: a research toolkit for Swarm Robotics - Published in JOSS (2023)
RidePy
RidePy: A fast and modular framework for simulating ridepooling systems - Published in JOSS (2024)
WRF-CMake
WRF-CMake: integrating CMake support into the Advanced Research WRF (ARW) modelling system - Published in JOSS (2019)
Statmanager-kr
Statmanager-kr: A User-friendly Statistical Package for Python in Pandas - Published in JOSS (2024)
Taguette
Taguette: open-source qualitative data analysis - Published in JOSS (2021)
SaffronTree
SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs. - Published in JOSS (2017)
GPUE
GPUE: Graphics Processing Unit Gross--Pitaevskii Equation solver - Published in JOSS (2018)
pymeasure
Scientific measurement library for instruments, experiments, and live-plotting
G'MIC
G'MIC: An Open-Source Self-Extending Framework for Image Processing - Published in JOSS (2025)
pypartmc
Python (and C++) interface to PartMC with Jupyter/Python, Julia and Matlab examples
sb3-contrib
Contrib package for Stable-Baselines3 - Experimental reinforcement learning (RL) code
https://github.com/adaptive-intelligent-robotics/qdax
Accelerated Quality-Diversity
datahugger
One downloader for many scientific data and code repositories! DOI :open_hands: Data
gpt-researcher
LLM based autonomous agent that conducts deep local and web research on any topic and generates a long report with citations.
https://github.com/bytedance/protenix
A trainable PyTorch reproduction of AlphaFold 3.
fsbrain
R library for structural neuroimaging. Provides high-level functions to access (read and write) and visualize surface-based brain morphometry data for individuals and groups.
catalyst
Accelerated deep learning R&D
zmap
ZMap is a fast single packet network scanner designed for Internet-wide network surveys.
infomeasure
Python package for calculating various information measures, including entropy, mutual information, transfer entropy, and more, with support for both discrete and continuous variables.
PyMPDATA v1
PyMPDATA v1: Numba-accelerated implementation of MPDATA with examples in Python, Julia and Matlab - Published in JOSS (2022)
euro-calliope
A workflow to build models of the European electricity system for Calliope.
harmony
The Harmony Python library: a research tool for psychologists to harmonise data and questionnaire items. Open source.
GFF3toEMBL
GFF3toEMBL: Preparing annotated assemblies for submission to EMBL - Published in JOSS (2016)
https://github.com/quakemigrate/quakemigrate
A Python package for automatic earthquake detection and location using waveform migration and stacking.
freesurferformats
GNU R package for reading and writing neuroimaging file formats. Not limited to FreeSurfer anymore, despite its name.
simona
simona is an agent-based discrete-event power system simulation model developed @ie3-institute
pysiral
python package for scientific computing (satellite radar altimetry over ice-covered ocean)
ccbs-study-3
Does Adolescent and Adult Training Impact Canine Behavior Outcomes?
findpapers
Findpapers: A tool for helping researchers who are looking for related works
https://github.com/facebookresearch/habitat-lab
A modular high-level library to train embodied AI agents across a variety of tasks and environments.
augur
Python library and web service for Open Source Software Health and Sustainability metrics & data collection. You can find our documentation and new contributor information easily here: https://oss-augur.readthedocs.io/en/main/
impactx
high-performance modeling of beam dynamics in particle accelerators with collective effects
gval
A high-level Python framework to evaluate the skill of geospatial datasets by comparing candidates to benchmark maps producing agreement maps and metrics.
Pybotics
Pybotics: Python Toolbox for Robotics - Published in JOSS (2019)
https://github.com/allenai/allenact
An open source framework for research in Embodied-AI from AI2.
https://github.com/cloudsimplus/cloudsimplus
State-of-the-art Framework 🏗 for Cloud Computing ⛅️ Simulation: a modern, full-featured, easier-to-use, highly extensible 🧩, faster 🚀 and more accurate ☕️ Java 24+ tool for cloud computing research 🎓 Examples: https://github.com/cloudsimplus/cloudsimplus-examples
https://github.com/khoj-ai/khoj
Your AI second brain. Self-hostable. Get answers from the web or your docs. Build custom agents, schedule automations, do deep research. Turn any online or local LLM into your personal, autonomous AI (gpt, claude, gemini, llama, qwen, mistral). Get started - free.
https://github.com/carla-simulator/carla
Open-source simulator for autonomous driving research.
harmony_examples
Example Jupyter notebook and R scripts using Harmony in real research problems
drone-data-in-agricultural-research
Lessons on working with multispectral drone based data in agricultural research settings
particula
Particula is an open-source, Python-based aerosol simulator. Particula captures gas-particle interactions, transformations, and dynamics to power predictive aerosol science.
https://github.com/bytedance/dplm
The Family of Diffusion Protein Language Models (DPLM)
https://github.com/bytedance/1d-tokenizer
This repo contains the code for 1D tokenizer and generator
https://github.com/dallinger/dallinger
Laboratory automation for the behavioral and social sciences; human culture on a chip.
https://github.com/learningcircuit/local-deep-research
Local Deep Research achieves ~95% on SimpleQA benchmark (tested with GPT-4.1-mini). Supports local and cloud LLMs (Ollama, Google, Anthropic, ...). Searches 10+ sources - arXiv, PubMed, web, and your private documents. Everything Local.
PSP
PSP-UFU (Power Systems Platform of Federal University of Uberlândia) is a cross-platform, multilingual, Free and Open-Source Software with advanced GUI features and CAD tools for electrical power system studies.
https://github.com/csinva/csinva.github.io
Slides, paper notes, class notes, blog posts, and research on ML 📉, statistics 📊, and AI 🤖.
obp
Open Bandit Pipeline: a python library for bandit algorithms and off-policy evaluation
phenodata
An acquisition and processing toolkit for open access phenology data.
https://github.com/jspsych/jspsych-contrib
An open repository of jsPsych plugins and extensions, without any official support
yoda
A system for reliable, long-term storing and archiving large amounts of research data during all stages of a study.
https://github.com/petermakus/seismic
SeisMIC is a python software suite to monitor phase velocity changes in time and space in seismology using ambient noise.
yellow-sticky-traps-detection
Code for our paper Faster R-CNN and EfficientNet for Accurate Insect Identification in a Relabeled Yellow Sticky Traps Dataset
