chise
A web application to visualize and edit the pathway models represented by SBGN Process Description Notation
AMIRIS
AMIRIS: Agent-based Market model for the Investigation of Renewable and Integrated energy Systems - Published in JOSS (2023)
EPICpy
EPICpy: A Python Interface for EPIC Computational Cognitive Modeling - Published in JOSS (2022)
rehype-citation
Rehype plugin to add citation and bibliography from bibtex files
PileupCaller: A command-line tool to sample genotypes from low-coverage sequencing data of ancient DNA
PileupCaller: A command-line tool to sample genotypes from low-coverage sequencing data of ancient DNA - Published in JOSS (2026)
LiGuard
LiGuard: Interactively and Rapidly Create Point-Cloud and Image Processing Pipelines - Published in JOSS (2025)
openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
graphannis
This is a new backend implementation of the ANNIS linguistic search and visualization system.
ado: a Python framework for computational experimentation and benchmarking
ado: a Python framework for computational experimentation and benchmarking - Published in JOSS (2026)
biolink-model
Schema and generated objects for biolink data model and upper ontology
SIMIO-continuum
SIMIO-continuum: Connecting simulations to ALMA observations - Published in JOSS (2024)
KinESim
KinESim: Pre-equilibrium kinetic simulation of electrochemical reactions - Published in JOSS (2019)
riversCentralAsia
riversCentralAsia: An R package to support data pre- and postprocessing for hydrological modelling with RS MINERVE - Published in JOSS (2023)
DataRepExp
DataRepExp: a R shiny Application that makes Data FAIR for Data Repositories - Published in JOSS (2024)
OpenPelt
OpenPelt: Python Framework for Thermoelectric Temperature Control System Development - Published in JOSS (2022)