pyam
pyam: a Python Package for the Analysis and Visualization of Models of the Interaction of Climate, Human, and Environmental Systems - Published in JOSS (2019)
Physics-Informed Neural networks for Advanced modeling
Physics-Informed Neural networks for Advanced modeling - Published in JOSS (2023)
GemGIS - Spatial Data Processing for Geomodeling
GemGIS - Spatial Data Processing for Geomodeling - Published in JOSS (2022)
t8code - modular adaptive mesh refinement in the exascale era
t8code - modular adaptive mesh refinement in the exascale era - Published in JOSS (2025)
HydroMT
HydroMT: Automated and reproducible model building and analysis - Published in JOSS (2023)
dython: A Set of Analysis and Visualization Tools for Data and Variables in Python
dython: A Set of Analysis and Visualization Tools for Data and Variables in Python - Published in JOSS (2025)
prysm
prysm: A Python optics module - Published in JOSS (2019)
Emiproc
Emiproc: A Python package for emission inventory processing - Published in JOSS (2025)
ProgPy
ProgPy: Python Packages for Prognostics and Health Management of Engineering Systems - Published in JOSS (2023)
geostan
geostan: An R package for Bayesian spatial analysis - Published in JOSS (2022)
AIBECS.jl
AIBECS.jl: A tool for exploring global marine biogeochemical cycles. - Published in JOSS (2022)
PlantSimEngine
PlantSimEngine: A Simulation Engine For The Soil-Plant-Atmosphere System - Published in JOSS (2023)
OpenCMP
OpenCMP: An Open-Source Computational Multiphysics Package - Published in JOSS (2022)
Telewavesim
Telewavesim: Python software for teleseismic body wave modeling - Published in JOSS (2019)
X-PSI
X-PSI: A Python package for neutron star X-ray pulse simulation and inference - Published in JOSS (2023)
pymgpipe
pymgpipe: microbiome metabolic modeling in Python - Published in JOSS (2023)
FIPS
FIPS: An R Package for Biomathematical Modelling of Human Fatigue Related Impairment - Published in JOSS (2020)
FijiRelax
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t - Published in JOSS (2023)
simpeg
Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.
amici
High-performance sensitivity analysis for large ordinary differential equation models
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
retomaton
PyTorch code for the RetoMaton paper: "Neuro-Symbolic Language Modeling with Automaton-augmented Retrieval" (ICML 2022)
https://github.com/bluebrain/snap
The Blue Brain Pythonic Simulation and Network Analysis Productivity layer
cobra
COBRApy is a package for constraint-based modeling of metabolic networks.
opengeode-core
Open source framework for representing and manipulating geometric models
overreact
⚛️📈 Create and analyze chemical microkinetic models built from computational chemistry data. Crafted at the @geem-lab.
contrabass
Constraint-based model vulnerabilities analysis - Python analysis tool http://contrabass.unizar.es
rsofun
Implements the Simulating Optimal FUNctioning framework for site-scale simulations of ecosystem processes, including model calibration. It contains Fortran 90 modules for the P-model, SPLASH, and BiomeE models.
mst-himalaya
Assessing the Shyft Modelling Framework in Nepal: Impact of Snow Routines and Terrain Representation on Simulated Water Balance Components
glacier-flow-model
Modeling glaciers on a digital elevation model (DEM) based on mass balance and a modified D8 flow algorithm applied to ice.
wrf-mosit
This BASH script installs all the required libraries, packages, software, dependencies, etc for the Weather Research & Forecasting model suite.
pommesdispatch
A bottom-up fundamental power market model for the German electricity sector
hydrotools
Suite of tools for retrieving USGS NWIS observations and evaluating National Water Model (NWM) data.
https://github.com/usnistgov/fipy
FiPy is a Finite Volume PDE solver written in Python
toxpiR
toxpiR R package for the Toxicological Priority Index (ToxPi) algorithm.
https://github.com/radonpy/radonpy
RadonPy is a Python library to automate physical property calculations for polymer informatics.
mip
Python-MIP: collection of Python tools for the modeling and solution of Mixed-Integer Linear programs
epistasis
A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
https://github.com/usnistgov/pyprism
A framework for conducting polymer reference interaction site model (PRISM) calculations
leaf
Simulator for modeling energy consumption in cloud, fog, and edge computing environments 🌱
lime
Local Interpretable Model-Agnostic Explanations (R port of original Python package)
climatemodels.jl
Julia interface to climate models + tracked workflow framework
https://github.com/austinjhunt/petrinet-webgme-designstudio
A custom design studio for modeling and simulating distributed systems as Petri (place/transition) Nets, built with JointJS, WebGME, and NodeJS.
ForestVegetationSimulator
Forest Vegetation Simulation (FVS) - Growth and Yield Modeling software
biomodelos-sdm
BioModelos is a collaborative online system to map species distributions. This repository stores functions to automate the construction of Species Distribution Models (SDM) from databases gathered, managed and curated by The Alexander Von Humboldt Institute and a network of experts in order to be evaluated and refined.
varycoef
The R package varycoef implements Gaussian processes spatially varying coefficient models.
https://github.com/andrew-hossack/dash-tools
DashTools - Plotly Dash Command Line Tools - Create, Run and Deploy Templated Python Apps from Terminal
https://github.com/algebraicjulia/structured-epidemic-modeling
Results and software for our paper on structured epidemic modeling
https://github.com/cthoyt/biomodels-metadata-analysis
Generate a summary of metadata annotations in the BioModels database
https://github.com/bvhpatel/gi-review-dataset
Dataset associated with our review manuscript on the constitutive modeling of GI tissues
https://github.com/cdcgov/pyrenew-flu-light
A replication in Python and PyRenew of a renewal model written in Epidemia for forecasting influenza hospital admissions.
https://github.com/alleninstitute/dipde
Numerical solver for coupled population density equations
https://github.com/benmaier/boarding_school_sir
Fit SIR dynamics to the prevalence curve of an H1N1 outbreak of a British boarding school in 1978.