JOSS collection | Ecosyste.ms: Summary

https://github.com/scikit-hep/root_numpy

The interface between ROOT and NumPy

cern cython hep numpy python root

Last synced: 20 Aug 2026

https://github.com/Pele-Suite/PeleLMeX

An adaptive mesh hydrodynamics simulation code for low Mach number reacting flows without level sub-cycling.

amrex combustion gpu-acceleration low-mach-number pele

Last synced: 21 Aug 2026

https://github.com/meenakshi-kushwaha/mmaqshiny

R-Shiny package to explore Air-Pollution Mobile Monitoring data

Last synced: 20 Aug 2026

https://github.com/ben-aaron188/netanos

NETANOS: Named entity-based Text Anonymization for Open Science'

Last synced: 20 Aug 2026

https://github.com/gridap/GridapDistributed.jl/

Parallel distributed-memory version of Gridap

distributed finite-elements mpi parallel parallel-computing partial-differential-equations

Last synced: 20 Aug 2026

https://github.com/arfc/osier

Justice oriented energy system optimization framework

Last synced: 20 Aug 2026

https://github.com/orbisgis/geoclimate/

Geospatial processing toolbox for environmental and climate studies

climate-change environment gis

Last synced: 20 Aug 2026

https://github.com/1oly/AeroAcoustics.jl

A Julia package for Aeroacoustics

Last synced: 21 Aug 2026

https://github.com/SAFRAN-LAB/HODLR

A fast, accurate direct solver and determinant computation for dense linear systems

c-plus-plus fast-algorithms hierarchical-matrix kernel matrices solver

Last synced: 20 Aug 2026

https://github.com/TomHilder/wakeflow

Generate and manipulate semi-analytic models of planet wakes

analytical astronomy astronomy-astrophysics astrophysics modelling numerical planet-formation protoplanetary-discs protoplanetary-disks python

Last synced: 20 Aug 2026

https://github.com/mrc-ide/individual

R Package for individual based epidemiological models

agent-based-modeling epidemiology individual-based-modelling infectious-diseases r r-package rstats

Last synced: 21 Aug 2026

https://github.com/sagepublishing/rejected_article_tracker_pkg

Last synced: 20 Aug 2026

https://github.com/andreasmang/claire

Constrained Large Deformation Diffeomorphic Image Registration (CLAIRE)

image-registration medical-image-computing parallel-computing

Last synced: 20 Aug 2026

https://github.com/ggonnella/fastsubtrees

Python library and command line script , for fast extraction of subtrees of fairly large trees, consisting of millions of nodes, such as the NCBI taxonomy tree.

bioinformatics ncbi-taxonomy python subtree subtree-extraction subtree-query taxonomy tree

Last synced: 20 Aug 2026

https://github.com/AMReX-Astro/MAESTROeX

A C++ low Mach number stellar hydrodynamics code

amrex astrophysical-simulation

Last synced: 20 Aug 2026

https://github.com/mjacob1002/Eir

Eir is a package that helps researchers simulate the spread of epidemics, mainly focusing on discrete-time Markovian spatial models.

Last synced: 21 Aug 2026

https://github.com/volfpeter/localclustering

Python 3 implementation and documentation of the Hermina-Janos local graph clustering algorithm.

cluster cluster-analysis clustering clustering-algorithm graph-algorithms graph-theory hierarchical-clustering local-clustering python python3 ranking social-network-analysis

Last synced: 20 Aug 2026

https://github.com/wvanzeist/riroriro

A code for simulating gravitational waves and evaluating their detectability.

bpass gravitational-waves

Last synced: 21 Aug 2026

https://github.com/mendezVKI/SPICY_VKI

The repository contains the codes linked to the SPICY project (Super-resolution and Pressure from Image Velocimetry)

Last synced: 21 Aug 2026

https://github.com/rvhonorato/cazy-parser

A way to extract specific information from CAZy

carbohydrates cazy data-mining enzymes scrapper text-mining

Last synced: 20 Aug 2026

https://github.com/neurogeriatricskiel/KielMAT

Python based toolbox for processing motion data

Last synced: 20 Aug 2026

https://github.com/yupidevs/pactus

Framework to evaluate Trajectory Classification Algorithms

classification classification-models evaluation-framework python trajectory trajectory-analysis transformers

Last synced: 21 Aug 2026

https://github.com/AdaptInfer/Contextualized

An SKLearn-style toolbox for estimating and analyzing models, distributions, and functions with context-specific parameters.

bioinformatics machine-learning medical-informatics statistics

Last synced: 21 Aug 2026

https://github.com/JonasRieger/ldaPrototype

Determine a Prototype from a number of runs of Latent Dirichlet Allocation.

latent-dirichlet-allocation lda model-selection modelselection reliability text-mining textdata topic-model topic-models topic-similarities topicmodeling topicmodelling

Last synced: 20 Aug 2026

https://github.com/occupationMeasurement/occupationMeasurement

A package to help with the (interactive) coding and measurement of occupations

Last synced: 21 Aug 2026

https://github.com/rhenkin/visxhclust

A Shiny app and functions for visual exploration of hierarchical clustering.

clustering data-analysis data-science r r-package r-shiny rstats shiny-apps

Last synced: 21 Aug 2026

https://github.com/elyiorgos/sleeppy

Last synced: 20 Aug 2026

https://github.com/IBM/complex-linear-network-analyzer

Computes analytically the output of complex valued, linear networks.

Last synced: 20 Aug 2026

https://github.com/groupmm/libfmp

A Python package for teaching and learning Fundamentals of Music Processing (FMP)

audio beat chord dtw f0 fourier hmm mir music nmf onset processing python retrieval synchronization tempo

Last synced: 21 Aug 2026

https://github.com/CompNet/Renard

Relationship Extraction from NARrative Documents

alias-resolution character-networks coreference-resolution ner network-extraction novels speaker-attribution

Last synced: 21 Aug 2026

https://github.com/alexriss/SpmImageTycoon.jl

Organize Scanning Probe Microscopy (SPM, STM, AFM) Images and Spectra.

afm electron javascript julia julialang spectroscopy spm stm

Last synced: 21 Aug 2026

https://github.com/anowacki/SeisModels.jl

Seismic models of the interior of the Earth and other planets

earth geophysics julia seismology

Last synced: 20 Aug 2026

https://github.com/IBM/topography-searcher

This Python package is designed for mapping the solution space of machine learning models. An understanding of the organisation of the solution space can answer important questions about the reproducibility, explainability and performance of ML methods.

Last synced: 20 Aug 2026

https://gitlab.com/wpettersson/kep_solver

A Python package for reading and solving single instances of kidney exchange problems.

Last synced: 20 Aug 2026

https://github.com/ulf1/bwsample

Sampling algorithm for best-worst scaling sets.

best-worst-scaling bws-sets extracting-pairs logical-inference pairwise-comparison ranking sampling-algorithm

Last synced: 21 Aug 2026

https://github.com/FRBCesab/chessboard

:package: Create network connections based on chess moves

connectivity-matrix directed-networks neighborhood network one-dimensional-networks r-package spatial-networks two-dimensional-networks undirected-networks

Last synced: 21 Aug 2026

https://github.com/IslasGECI/nerd

NERD: Numerical Estimation of Rodenticide Density

Last synced: 21 Aug 2026

https://github.com/geoelements/gns

Graph Network Simulator

deep-learning graph-network-simulator machine-learning pytorch

Last synced: 21 Aug 2026

https://github.com/xpsi-group/xpsi

X-PSI: X-ray Pulse Simulation and Inference

astronomical-algorithms astronomy astrophysical-simulation astrophysics likelihood-functions modeling parameter-estimation posterior-sampling sampling statistics-modeling x-ray-astronomy

Last synced: 20 Aug 2026

https://gitlab.com/cmbm-ethz/pourbaix-diagrams

A Python library to create Pourbaix diagrams

Last synced: 21 Aug 2026

https://github.com/OpenTerrace/openterrace-python

OpenTerrace: A fast, flexible and extendable Python framework for packed bed thermal energy storage simulations

carnot-battery energy-storage heat-transfer multiphase-flow numerical packed-bed phase-change-materials python

Last synced: 21 Aug 2026

https://github.com/maxibor/sam2lca

Lowest Common Ancestor from a SAM/BAM/CRAM alignment file

Last synced: 21 Aug 2026

https://github.com/samaygarg/fuelcell

Electrochemical data analysis package

Last synced: 20 Aug 2026

https://github.com/JuliaText/WordTokenizers.jl/

High performance tokenizers for natural language processing and other related tasks

data-mining information-retrieval lexer nlp tokenization

Last synced: 20 Aug 2026

https://github.com/pnavaro/HOODESolver.jl

High Oscillatory Ordinary Differential Equation Solver in Julia

adams-bashforth-methods fft high-oscillatory julia ode-solver

Last synced: 20 Aug 2026

https://github.com/bbye98/mdcraft

A Python assistant for performing and analyzing molecular dynamics simulations of soft matter systems

Last synced: 20 Aug 2026

https://github.com/3d-pli/SLIX

Scattered Light Imaging ToolboX (SLIX) – an open-source Python package that allows a fully automated evaluation of SLI measurements and the generation of different parameter maps

Last synced: 20 Aug 2026

https://github.com/beardymcjohnface/Koverage

Quickly get coverage statistics given reads and an assembly

Last synced: 21 Aug 2026

https://github.com/kuadrat/growR

R implementation of the grassland model ModVege.

agronomy grass grassland modelling simulation-modeling

Last synced: 21 Aug 2026

https://github.com/npucino/sandpyper

Tools for beach volumetric and behavioral dynamics monitoring from multitemporal UAV-SfM datasets.

beach coastal-dynamics erosion remote-sensing satellite-data shoreline uav-imagery

Last synced: 21 Aug 2026

https://github.com/RemieJanssen/phylox

A python package with tools for constructing, manipulating, and analyzing phylogenetic networks.

Last synced: 20 Aug 2026

https://github.com/rodluger/starry_process

interpretable gaussian processes for stellar light curves

gaussian-processes lightcurves stars timeseries-analysis

Last synced: 20 Aug 2026

https://github.com/gomesdasilva/ACTIN

ACTIN is a Python program to calculate stellar activity indices

exoplanets radial-velocity spectroscopy stellar-activity

Last synced: 20 Aug 2026

https://github.com/dfki-ric/ugv_nav4d

A 4D (X,Y,Z, Theta) Planner for Unmanned Ground Vehicles

navigation planning-algorithms robotics sbpl

Last synced: 20 Aug 2026

https://github.com/JamesPaynter/PyGRB

Gamma-ray burst analysis library

astrophysics gamma-ray-astronomy gamma-ray-burst

Last synced: 20 Aug 2026

https://github.com/Deech08/whampy

Python Package to Interact with, Visualize, and Analyze the Wisconsin H-Alpha Mapper - Sky Survey

Last synced: 20 Aug 2026

https://github.com/homerjed/sbiax

Fast, lightweight and parallelised simulation-based inference in JAX.

generative-models jax normalizing-flows simulation-based-inference

Last synced: 21 Aug 2026

https://github.com/RadioAstronomySoftwareGroup/pyuvsim/

A ultra-high precision package for simulating radio interferometers in python on compute clusters.

Last synced: 20 Aug 2026

https://github.com/cire-thk/BifacialSimu

Simulation of bifacial PV

Last synced: 21 Aug 2026

https://github.com/josejimenezluna/pyGPGO

Bayesian optimization for Python

bayesian machine-learning optimization

Last synced: 20 Aug 2026

https://github.com/fruzsinaagocs/riccati

A package implementing the adaptive Riccati defect correction (ARDC) method for solving oscillatory second order linear ODEs.

Last synced: 20 Aug 2026

https://github.com/pydemull/activAnalyzer

accelerometer actigraph app monitor r shiny

Last synced: 21 Aug 2026

https://github.com/milnus/Magphi

Tool intended to pull out sequences and annotations between insertion sites specified by the user.

annotations bacterial-genomes insertion-sites mobile-genetic-elements prokaryotic-genomes

Last synced: 21 Aug 2026

https://github.com/BRAIN-TO/GIRFReco.jl

An Open-Source End-to-End Pipeline for Spiral Magnetic Resonance Image (MRI) Reconstruction in Julia

mri mri-brain mri-reconstruction

Last synced: 21 Aug 2026

https://github.com/YoungFaithful/CapacityExpansion.jl

Capacity Expansion Problem Formulation for Julia

california capacity-expansion-planning clustering energy energy-optimization-model germany julia jump

Last synced: 20 Aug 2026

https://github.com/gesel-inc/gesel.js

Client-side gene set queries.

Last synced: 21 Aug 2026

https://github.com/sequana/sequana/

Sequana: a set of Snakemake NGS pipelines

coverage de-novo ngs pacbio rna-seq sequanix snakemake taxonomy variant-calling

Last synced: 20 Aug 2026

https://github.com/ranocha/SummationByPartsOperators.jl

A Julia library of summation-by-parts (SBP) operators used in finite difference, Fourier pseudospectral, continuous Galerkin, and discontinuous Galerkin methods to get provably stable semidiscretizations, paying special attention to boundary conditions.

boundary-conditions cgsem continuous-galerkin derivative-operator dgsem discontinuous-galerkin finite-difference fourier hacktoberfest julia sbp summation-by-parts

Last synced: 20 Aug 2026

https://github.com/HofstadterTools/HofstadterTools

A Python package for analyzing the Hofstadter model.

band-theory condensed-matter-physics electromagnetism fractals mathematical-physics quantum-hall-effect quantum-physics theoretical-physics topological-materials topological-order

Last synced: 21 Aug 2026

https://github.com/openeventdata/petrarch2

Another next-generation event coding platform.

Last synced: 20 Aug 2026

https://github.com/tdep-developers/tdep

The Temperature Dependent Effective Potentials (TDEP) code

Last synced: 21 Aug 2026

https://github.com/calebweinreb/SNUB

Last synced: 21 Aug 2026

https://github.com/WinVector/vtreat/

vtreat is a data frame processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner. Distributed under choice of GPL-2 or GPL-3 license.

categorical-variables machine-learning-algorithms nested-models prepare-data r

Last synced: 20 Aug 2026

https://github.com/tupui/scipy

Scipy library main repository

Last synced: 20 Aug 2026

https://github.com/viash-io/viash

script + metadata = standalone component

Last synced: 21 Aug 2026

https://github.com/edsonportosilva/OptiCommPy/

Simulate optical communications systems with Python.

adaptive-equalization bit-error-rate cupy digital-modulation digital-signal-processing eye-diagrams fiber-optic-communications jupyter-notebook ldpc modulation-techniques numba ofdm optical-communications photonics python split-step-fourier-method

Last synced: 21 Aug 2026

https://github.com/souzamonteiro/cnatool

Complex Network Analysis Tool

Last synced: 21 Aug 2026

https://github.com/bjmorgan/pyscses

PYthon Space-Charge Site-Explicit Solver

Last synced: 20 Aug 2026

https://github.com/ArneTillmann/AuDoLab

Last synced: 20 Aug 2026

https://github.com/dfki-ric-underactuated-lab/torque_limited_simple_pendulum

Torque Limited Simple Pendulum Underactuated System

Last synced: 20 Aug 2026

https://github.com/JorenSix/Panako

The Panako acoustic fingerprinting system.

acoustic-fingerprinting audio-processing duplicate-detection music-information-retrieval

Last synced: 21 Aug 2026

https://github.com/McMasterRS/LFSpy

Last synced: 20 Aug 2026

https://github.com/michellab/BioSimSpace

Code and resources for the EPSRC BioSimSpace project.

biomolecular-simulation ccpbiosim computational-biology computational-chemistry computational-physics interoperability molecular-dynamics reproducibility reproducible-research

Last synced: 20 Aug 2026