JOSS collection | Ecosyste.ms: Summary

https://github.com/shirtsgroup/physical_validation

Physical validation of molecular simulations

molecular-dynamics molecular-mechanics molecular-simulation physical-validation python

Last synced: 29 Sep 2026

https://github.com/jessecambon/tidygeocoder

Geocoding Made Easy

geocoding r rspatial rstats tidyverse

Last synced: 29 Sep 2026

https://github.com/vnmabus/rdata

A Python library for R datasets.

conversion python python3 r rda rdata rds

Last synced: 29 Sep 2026

https://github.com/bjodah/pyodesys

∫ Straightforward numerical integration of systems of ordinary differential equations

code-generation initial-value-problem numerical-codes ordinary-differential-equations symbolic-manipulation sympy

Last synced: 29 Sep 2026

https://github.com/capytaine/capytaine

Python BEM solver for linear potential flow, based on Nemoh.

boundary-element-method fortran hydrodynamics potential-flow python sea-keeping water-wave wave-energy

Last synced: 29 Sep 2026

https://github.com/CliMA/EnsembleKalmanProcesses.jl

Derivative-free parameter calibration and uncertainty quantification for expensive models using ensemble Kalman methods

bayesian-inference calibration data-assimilation derivative-free-optimization ensemble-kalman-filter ensemble-kalman-inversion inverse-problems julia machine-learning optimization parameter-estimation scientific-computing uncertainty-quantification

Last synced: 29 Sep 2026

https://github.com/Deltares/hydromt

HydroMT: Automated and reproducible model building and analysis

geoscience hydrodynamics hydrology modeling

Last synced: 29 Sep 2026

https://github.com/r-cas/ryacas

Ryacas: R Interface to the Yacas Computer Algebra System

Last synced: 29 Sep 2026

https://github.com/finsberg/pulse

A software for solving problems in cardiac mechanics

Last synced: 29 Sep 2026

https://github.com/vferat/pycrostates

eeg eeg-analysis

Last synced: 29 Sep 2026

https://github.com/cwinpy/cwinpy

CW Inference in Python

Last synced: 29 Sep 2026

https://github.com/vprusso/toqito

|toqito> (Theory of Quantum Information Toolkit) is a Python library for research in quantum information theory.

convex-optimization entanglement linear-algebra matrix-analysis nonlocal-game physics python python-3 quantum quantum-channels quantum-computing quantum-information quantum-information-science quantum-information-theory quantum-measurements quantum-physics quantum-programming quantum-states research semidefinite-programming

Last synced: 29 Sep 2026

https://github.com/devsim/devsim

TCAD Semiconductor Device Simulator

c-plus-plus devsim finite-volume pde python semiconductor semiconductor-physics tcad tcad-device-simulator

Last synced: 29 Sep 2026

https://github.com/nifty-ppl/nifty

Probabilistic programming framework for signal inference algorithms that operate regardless of the underlying grids and their resolutions

Last synced: 29 Sep 2026

https://github.com/PyAutoLabs/PyAutoLens

PyAutoLens: Open-Source Strong Gravitational Lensing

astronomy astrophysics bayesian-inference cosmology galaxy gravitational-lensing python

Last synced: 29 Sep 2026

https://github.com/aiidateam/kiwipy

A python messaging library for RPC, task queues and broadcasts

python rabbitmq

Last synced: 29 Sep 2026

https://github.com/Degiacomi-Lab/molearn

protein conformational spaces meet machine learning

machine-learning molecular-dynamics molecular-modeling protein-structure

Last synced: 29 Sep 2026

https://github.com/adrn/schwimmbad

A common interface to processing pools.

mpi multiprocessing parallel-computing

Last synced: 29 Sep 2026

https://gitlab.com/picos-api/picos

A Python interface to conic optimization solvers.

math optimization python

Last synced: 29 Sep 2026

https://github.com/benmaier/netwulf

Interactive visualization of networks based on Ulf Aslak's d3 web app.

d3 network-visualization networkx python

Last synced: 29 Sep 2026

https://github.com/pachadotdev/gravity

R package that provides estimation methods for Gravity Models

bvu bvw ddm econometrics glm gpml gravity international-trade lm maximum-likelihood nbpml nls ols ppml r sils tobit trade

Last synced: 29 Sep 2026

https://github.com/NiaOrg/NiaPy

Python microframework for building nature-inspired algorithms. Official docs: https://niapy.org

hacktoberfest microframework nature-inspired-algorithms optimization-algorithms python swarm-intelligence

Last synced: 29 Sep 2026

https://github.com/dcr-unibe-ch/presize

Precision Based Sample Size Calculation

confidence-intervals precision sample-size-calculation shiny-app

Last synced: 29 Sep 2026

https://github.com/lab-cosmo/chemiscope

An interactive structure/property explorer for materials and molecules

hacktoberfest materials-science molecule visualization web

Last synced: 29 Sep 2026

https://github.com/nipy/nitransforms

a standalone fork of nipy/nibabel#656

Last synced: 29 Sep 2026

https://github.com/anhoej/qicharts2

R package: Quality improvement charts

Last synced: 29 Sep 2026

https://github.com/ropensci/cffr

Create and manage Citation File Format (CFF) files in R, including CFF ↔ BibTeX conversion.

attribution cff citation citation-file-format citation-files cran metadata r r-cran r-package ropensci rstats

Last synced: 29 Sep 2026

https://github.com/neurodsp-tools/neurodsp

Digital signal processing for neural time series.

Last synced: 29 Sep 2026

https://github.com/DidierMurilloF/FielDHub

FielDHub is an R Shiny design of experiments (DOE) app that aids in the creation of traditional, unreplicated, augmented and partially replicated (p-rep) designs applied to agriculture, plant breeding, forestry, animal and biological sciences.

agricultural breeding design doe experimental plantbreeding r rstats shiny

Last synced: 29 Sep 2026

https://github.com/CHOP-CGTInformatics/REDCapTidieR

Makes it easy to read REDCap Projects into R

r redcap redcap-api tidy-data

Last synced: 29 Sep 2026

https://github.com/wrenfold/wrenfold

Toolkit for generating code from symbolic math expressions.

code-generation computer-vision mathematics robotics symbolic-math

Last synced: 29 Sep 2026

https://github.com/KingsburyLab/pyEQL

A Python library for solution chemistry

Last synced: 29 Sep 2026

https://github.com/jrzaurin/pytorch-widedeep

A flexible package for multimodal-deep-learning to combine tabular data with text and images using Wide and Deep models in Pytorch

deep-learning images model-hub multimodal-deep-learning python pytorch pytorch-cv pytorch-nlp pytorch-tabular-data pytorch-transformers tabular-data text

Last synced: 29 Sep 2026

https://github.com/JuliaDynamics/DynamicalSystems.jl

Award winning software library for nonlinear dynamics and nonlinear timeseries analysis

attractor chaos complexity delay-coordinates dynamical-systems entropy fractal-dimension hacktoberfest lyapunov mathematics nonlinear nonlinear-dynamics physics

Last synced: 29 Sep 2026

https://github.com/GeoStat-Framework/pentapy

A Python toolbox for pentadiagonal linear systems

linear-algebra linear-systems math matrix pentadiagonal-linear-systems python solvers toolbox

Last synced: 29 Sep 2026

https://github.com/ropensci/osfr

R interface to the Open Science Framework (OSF)

open-science osf reproducible-research

Last synced: 29 Sep 2026

https://github.com/parmoo/parmoo

Python library for parallel multiobjective simulation optimization

blackbox-optimization mathematical-software multicriteria-optimization multiobjective multiobjective-optimization numerical-optimization python3 response-surface-methodology simulation-based-optimization simulation-optimization surrogate-based-optimization

Last synced: 29 Sep 2026

https://github.com/KVSlab/turtleFSI

Monolithic Fluid-Structure Interaction (FSI) solver

fenics fluid-structure-interaction python

Last synced: 29 Sep 2026

https://github.com/astorfi/speechpy

:speech_balloon: SpeechPy - A Library for Speech Processing and Recognition: http://speechpy.readthedocs.io/en/latest/

feature-extraction python speech-recognition speechpy

Last synced: 29 Sep 2026

https://github.com/bempp/bempp-cl

A fast Python based just-in-time compiling boundary element library

Last synced: 29 Sep 2026

https://github.com/rorynolan/filesstrings

A set of operations for manipulating strings in R, built on top of the stringr package and inspired by my struggles in trying to sensibly rename microscopy images.

Last synced: 29 Sep 2026

https://github.com/ArdiaD/RiskPortfolios

Functions for the construction of risk-based portfolios

covariance optimization portfolio portfolio-optimization risk

Last synced: 29 Sep 2026

https://github.com/soundata/soundata

Python library for downloading, loading & working with sound datasets

audio bioacoustics dataset environmental-sound python urban-sound

Last synced: 29 Sep 2026

https://github.com/JuliaSymbolics/Metatheory.jl

Makes Julia reason with equations. General purpose metaprogramming, symbolic computation and algebraic equational reasoning library for the Julia programming language: E-Graphs & equality saturation, term rewriting and more.

compiler-construction compiler-optimization egraphs equality-saturation julia optimization programming-language symbolic symbolic-computation symbolic-manipulation term-rewriting

Last synced: 29 Sep 2026

https://github.com/wilsonrljr/sysidentpy

A Python Package For System Identification Using NARMAX Models

data-science dynamical-systems machine-learning narmax narx system-identification time-series

Last synced: 29 Sep 2026

https://github.com/duetosymmetry/qnm

Python package for computing Kerr quasinormal mode frequencies, separation constants, and spherical-spheroidal mixing coefficients

black-holes general-relativity numerical-methods physics python scientific-computing

Last synced: 29 Sep 2026

https://github.com/icb-dcm/pyabc

distributed, likelihood-free inference

abc approximate-bayesian-inference likelihood-free-inference parameter-inference

Last synced: 29 Sep 2026

https://github.com/BioSTEAMDevelopmentGroup/thermosteam

BioSTEAM's Premier Thermodynamic Engine

chemical chemical-engineering equations-of-state liquid-liquid-equilibrium material-and-energy-balance mixture properties reaction thermodynamics vapor-liquid-equilibrium

Last synced: 29 Sep 2026

https://github.com/changliao1025/pyflowline

A mesh independent river network generator for hydrologic models

earth-system-model gis graph hydrology river

Last synced: 29 Sep 2026

https://github.com/esteinig/nanoq

Minimal but speedy quality control for nanopore reads in Rust :bear:

Last synced: 29 Sep 2026

https://github.com/martibosch/detectree

Tree detection from aerial imagery in Python

image-segmentation python remote-sensing tree-canopy tree-detection tree-pixels

Last synced: 29 Sep 2026

https://github.com/labsyspharm/scimap

Spatial Single-Cell Analysis Toolkit

image-analysis pypi python single-cell-analysis spatial-analysis

Last synced: 29 Sep 2026

https://github.com/PyAutoLabs/PyAutoFit

PyAutoFit: Classy Probabilistic Programming

astronomy bayesian-inference bayesian-methods graphical-models mcmc model probabilistic-programming python statistical-analysis statistics stats

Last synced: 29 Sep 2026

https://github.com/ekiefl/pooltool

A sandbox billiards game that emphasizes realistic physics

billiards eight-ball panda3d physics pool python simulation snooker

Last synced: 29 Sep 2026

https://github.com/simupy/simupy

A framework for modeling and simulating dynamical systems

block-diagram python simulation simulation-framework simulation-modeling simulink

Last synced: 29 Sep 2026

https://github.com/kno10/python-kmedoids

Fast K-Medoids clustering in Python with FasterPAM

Last synced: 29 Sep 2026

https://github.com/lskatz/fasten

:construction_worker: Fasten toolkit, for streaming operations on fastq files

bioinformatics fastq-files rust

Last synced: 29 Sep 2026

https://github.com/furrer-lab/abn

Bayesian network analysis in R

bayesian-network binomial categorical-data gaussian grouped-datasets mixed-effects multinomial multivariate poisson structure-learning

Last synced: 29 Sep 2026

https://github.com/wright-group/WrightTools

Tools for loading, processing, and plotting multidimensional spectroscopy data.

python

Last synced: 28 Sep 2026

https://github.com/cbrnr/sleepecg

Sleep stage detection using ECG

ecg heartrate peak-detection python sleep-staging

Last synced: 29 Sep 2026

https://github.com/r-cas/caracas

Computer algebra in R

Last synced: 29 Sep 2026

https://github.com/torressa/cspy

A collection of algorithms for the (Resource) Constrained Shortest Path problem in Python / C++ / C#

bidirectional-labeling-algorithm csp-problem operations-research optimization optimization-algorithms optimization-library resource-constrained-shortest-path

Last synced: 29 Sep 2026

https://github.com/pypeit/PypeIt

The Python Spectroscopic Data Reduction Pipeline

Last synced: 29 Sep 2026

https://github.com/davemlz/eemont

A python package that extends Google Earth Engine.

earth-engine geographic-information-systems gis google google-earth-engine python python3 raster remote-sensing satellite-imagery satellite-images spectral-indices

Last synced: 29 Sep 2026

https://github.com/IndrajeetPatil/statsExpressions

Tidy data frames and expressions with statistical summaries 📜

bayesian-inference bayesian-statistics contingency-table correlation effectsize meta-analysis parametric robust robust-statistics statistical-details statistical-tests tidy

Last synced: 29 Sep 2026

https://github.com/neuralhydrology/neuralhydrology

Python library to train neural networks with a strong focus on hydrological applications.

Last synced: 29 Sep 2026

https://github.com/Chilipp/straditize

⛔️ Python package for digitizing pollen diagrams

Last synced: 29 Sep 2026

https://github.com/NeuroDiffGym/neurodiffeq

A library for solving differential equations using neural networks based on PyTorch, used by multiple research groups around the world, including at Harvard IACS.

artificial-intelligence boundary-value-problem deep-learning differential-equations initial-value-problem mathematical-modelling neural-networks ode odes pde-solver physics-informed-neural-networks pinn pypi pytorch scientific-computing time-series

Last synced: 29 Sep 2026

https://github.com/vocalpy/crowsetta

A tool to work with any format for annotating animal sounds

animal-communication animal-vocalizations annotation annotation-format bioacoustic-analysis bioacoustics birdsong csv dataset python python3

Last synced: 29 Sep 2026

https://github.com/ropensci/ijtiff

An R Package for general purpose TIFF file I/O which plays nice with ImageJ

image-manipulation imagej peer-reviewed r r-package rstats tiff-files tiff-images

Last synced: 29 Sep 2026

https://github.com/exoplanet-dev/exoplanet

Fast & scalable MCMC for all your exoplanet needs!

astronomy astrophysics bayesian-inference exoplanet exoplanet-radial-velocities exoplanet-transits exoplanets gaussian-processes mcmc pymc3 time-series time-series-analysis

Last synced: 29 Sep 2026

https://github.com/ni1o1/transbigdata

A Python package develop for transportation spatio-temporal big data processing, analysis and visualization.

bike-sharing-data bus-gps-data data-analysis data-pre-processing data-quality-analysis data-visualization geospatial-data python spatio-temporal-data taxi-gps-data transportation

Last synced: 29 Sep 2026

https://github.com/morganjwilliams/pyrolite

A set of tools for getting the most from your geochemical data.

chemistry data-science geochemical-data geochemistry geoscience pyrolite ternary-diagrams

Last synced: 29 Sep 2026

https://github.com/salabim/salabim

salabim - discrete event simulation

animation discrete-event-simulation logistics python

Last synced: 29 Sep 2026

https://github.com/opengeos/HyperCoast

A Python Package for Visualizing and Analyzing Hyperspectral Data in Coastal Environments

aviris coastal emit geospatial hyperspectral ipyleaflet ipywidgets leafmap nasa nasa-pace neon pace python

Last synced: 29 Sep 2026

https://github.com/ropensci/hydroscoper

R interface to the Greek National Data Bank for Hydrometeorological Information

climate greece hydrology hydrometeorology hydroscope meteorological-data meteorological-stations peer-reviewed r r-package rstats tidy-data time-series water-resources

Last synced: 29 Sep 2026

https://github.com/WebFuzzing/EvoMaster

The first open-source AI-driven tool for automatically generating system-level test cases (also known as fuzzing) for web/enterprise applications. Currently targeting whitebox and blackbox testing of Web APIs, like REST, GraphQL and RPC (e.g., gRPC and Thrift).

api-rest api-testing evolutionary-algorithms fuzzer fuzzing graphql grpc java kotlin rest rpc-api search-based-software-testing test-case-generation testing thrift

Last synced: 29 Sep 2026

https://github.com/sewardlee337/finreportr

R package - Financial Data from U.S. Securities and Exchange Commission

balance-sheet cash-flow finance financial-data financial-statement financial-statements income-statement r sec stock-ticker-symbol

Last synced: 29 Sep 2026

https://github.com/mprib/caliscope

Multicamera Calibration for Motion Capture Workflows

bundle-adjustment camera-calibration extrinsic-calibration intrinsic-calibration motion-capture-mocap motion-capture-processing open-source

Last synced: 29 Sep 2026

https://github.com/sherbold/autorank

Last synced: 29 Sep 2026

https://github.com/cbrnr/mnelab

MNELAB – a GUI for MNE-Python

eeg gui ica meg mne python qt6 xdf

Last synced: 29 Sep 2026

https://github.com/caseyyoungflesh/MCMCvis

R package to visualize, manipulate, and summarize MCMC output

Last synced: 29 Sep 2026

https://github.com/IMMM-SFA/mosartwmpy

Python translation of MOSART-WM: a water routing and management model

Last synced: 29 Sep 2026

https://github.com/skypyproject/skypy

SkyPy: A package for modelling the Universe.

astronomy astrophysics cosmology forward-modeling skypy

Last synced: 29 Sep 2026

https://github.com/nialov/fractopo

fractopo is a Python package with tools for validating and analyzing lineament and fracture trace maps

analysis fractopo fracture geology geometry python spatial-analysis topology

Last synced: 29 Sep 2026

https://github.com/damask-multiphysics/DAMASK

Düsseldorf Advanced Material Simulation Kit (Read-only mirror)

crystal-plasticity engineering material materials materials-science metallurgy multi-physics physics plasticity science simulation

Last synced: 29 Sep 2026

https://github.com/dmentipl/plonk

Smoothed particle hydrodynamics analysis and visualization with Python.

astronomy python smoothed-particle-hydrodynamics visualization

Last synced: 29 Sep 2026

https://github.com/castelao/GSW-rs

Unofficial Gibbs Sea Water Oceanographic Toolbox of TEOS-10 in Rust

data ocean ocean-sciences oceanography rust

Last synced: 29 Sep 2026

https://gitlab.com/pvst/asi

Atomic Simulations Interface

Last synced: 29 Sep 2026

https://github.com/brandondube/prysm

physical optics: integrated modeling, phase retrieval, segmented systems, polynomials and fitting, sequential raytracing...

4d diffraction forbes-polynomial gpu-computing modeling mtf mtf-mapper optics phase-retrieval phasecam propagation psf python q-polynomial raytracing trioptics wavefront wavefront-sensing zernike zygo

Last synced: 29 Sep 2026

https://github.com/paulgovan/BayesianNetwork

Bayesian Network Modeling and Analysis

bayesian-networks learning-algorithm network-measures r

Last synced: 29 Sep 2026

https://github.com/idaholab/MontePy

MontePy is the most user friendly Python library (API) to read, edit, and write MCNP input files.

api mcnp mcnp6 monte-carlo neutronics radiation-transport

Last synced: 29 Sep 2026

https://github.com/upb-lea/gym-electric-motor

Gym Electric Motor (GEM): An OpenAI Gym Environment for Electric Motors

benchmark converters electric-drive electrical-engineering gym-environment machinelearning motor-models openai openai-gym openai-gym-environments pmsm reinforcement-learning

Last synced: 29 Sep 2026

https://github.com/pyiron/executorlib

Up-scale python functions for high-performance computing (HPC)

concurrent-futures distributed-computing flux gpu hpc hpc-cluster mpi mpi4py multiprocessing parallel-computing pyiron python scientific-computing slurm task-scheduler

Last synced: 29 Sep 2026

https://github.com/willyfh/visualtorch

VisualTorch aims to help visualize Torch-based neural network architectures.

architecture-diagram architecture-visualization artificial-intelligence deep-learning machine-learning neural-network pytorch torch visualization visualtorch

Last synced: 29 Sep 2026