JOSS collection | Ecosyste.ms: Summary

https://github.com/edawson/gfakluge

A C++ library and utilities for manipulating the Graphical Fragment Assembly format.

genomics gfa graph-representation parsing

Last synced: 26 Aug 2026

https://github.com/szwiep/py_SBeLT

A Markov-type numerical model of sediment particle transport in rivers

Last synced: 27 Aug 2026

https://github.com/quantum-exeter/SpiDy.jl

:spider: Non-Markovian stochastic SPIn (and harmonic oscillator) DYnamics.

harmonic-oscillator open-systems spin-dynamics stochastic

Last synced: 27 Aug 2026

https://github.com/pyomeca/pyomeca/

Python toolbox for biomechanics analysis

biomechanics biomechanics-analysis dynamics kinematics kinetics python xarray

Last synced: 27 Aug 2026

https://github.com/lcpp-org/RustBCA

A free, open-source Binary Collision Approximation (BCA) code for ion-material interactions including sputtering, implantation, and reflection

bca bca-codes binary-collision-approximation binary-collisions bohdansky electronic-stopping fusion implantation incident-ion ion-material-interactions ion-solid-interactions materials-science nuclear-fusion nuclear-stopping plasma-material-interactions range rust simulation sputtering yamamura

Last synced: 26 Aug 2026

https://github.com/pylops/pyproximal/

PyProximal – Proximal Operators and Algorithms in Python

inverse-problems linear-algebra proximal-algorithms python

Last synced: 27 Aug 2026

https://github.com/lahovniktadej/gatree

Evolutionary decision trees

decision-tree evolutionary-algorithm genetic-algorithm machine-learning

Last synced: 26 Aug 2026

https://github.com/ropensci/bikedata

:bike: Extract data from public hire bicycle systems

bicycle-hire bicycle-hire-systems bike-data bike-hire database peer-reviewed r r-package rstats

Last synced: 26 Aug 2026

https://github.com/jackmwolf/tehtuner

An R Package to Fit and Tune to Models to Detect Treatment Effect Heterogeneity

clinical-trials heterogeneity-of-treatment-effect r subgroup-identification

Last synced: 27 Aug 2026

https://github.com/PhysioLabXR/PhysioLabXR-Community

Last synced: 27 Aug 2026

https://github.com/ialbert/genescape-central

Gene Ontology subgraph visualizations

Last synced: 27 Aug 2026

https://github.com/isakro/shoredate

R package for shoreline dating coastal Stone Age sites

archaeology relative-sea-level-change shoreline-dating south-eastern-norway

Last synced: 26 Aug 2026

https://github.com/SchmidtDSE/afscgap

Python-based tools for NOAA AFSC GAP marine species surveys data

biodiversity biology fish fisheries noaa

Last synced: 27 Aug 2026

https://github.com/sibirrer/lenstronomy

multi-purpose lens modeling software package

Last synced: 26 Aug 2026

https://github.com/leprojetcastor/castor

Last synced: 27 Aug 2026

https://github.com/SimVascular/svFSI

A multi-physics finite element solver for patient-specific blood flow simulation including fluid-structure interaction and cardiac electrophysiology

Last synced: 27 Aug 2026

https://github.com/Romain-Thomas-Shef/dfitspy

FITS file header search and display

Last synced: 26 Aug 2026

https://github.com/rchartra/NcCut

A GUI for visualizing and transecting 3D data.

Last synced: 27 Aug 2026

https://gitlab.com/ampere2/metalwalls

Last synced: 26 Aug 2026

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

Functions and data dependencies for loading various word embeddings (Word2Vec, FastText, GLoVE)

Last synced: 27 Aug 2026

https://github.com/WAVI-ice-sheet-model/WAVI.jl

WAVI ice sheet model

Last synced: 27 Aug 2026

https://gitlab.com/energyincities/besos/

Core functionality of the BESOS platform (besos.uvic.ca), including building energy simulation via EnergyPlus, optimization via Platypus and surrogate-modelling via scikit-learn.

Last synced: 27 Aug 2026

https://github.com/maxrousseau/pfla

pfla: Python Facial Landmark Analysis

computer-vision machine-learning medical-image-processing statistics

Last synced: 26 Aug 2026

https://github.com/pygbe/pygbe

PyGBe: Python, GPUs and Boundary elements for electrostatics

Last synced: 26 Aug 2026

https://github.com/nomad-coe/greenX

Library for Green’s function based electronic structure theory calculations

exascale fortran greens-functions

Last synced: 27 Aug 2026

https://github.com/raamana/hiwenet

Histogram-weighted Networks for Connectivity & Advanced Analysis in Neuroscience

biomarkers connectivity feature-extraction graph histogram-weighted-networks machine-learning neuroimaging neuroscience

Last synced: 26 Aug 2026

https://github.com/Sydney-Informatics-Hub/geodata-harvester

Jumpstart your geospatial analysis with a ready-made set of spatial-temporal aligned raster maps and data frames

Last synced: 27 Aug 2026

https://github.com/giorginolab/plumed2-pycv/

PYCV module for PLUMED2. See the src/pycv directory.

Last synced: 26 Aug 2026

https://github.com/LLNL/Abmarl/

Agent Based Modeling and Reinforcement Learning

machine-learning

Last synced: 27 Aug 2026

https://github.com/openneuropet/PET2BIDS/

PET2BIDS helps you convert your PET data into BIDS! raw PET scanner files (e.g. ecat, dicom) and additional side files like .e.g excel sheets -- paper @JOSS https://doi.org/10.21105/joss.06067

bids converter json metadata

Last synced: 26 Aug 2026

https://github.com/jorisparet/partycls

Unsupervised learning of structure in systems of interacting particles.

clustering machine-learning molecular-dynamics physics python

Last synced: 27 Aug 2026

https://github.com/BjoernBiltzinger/pyspi

Pure python tools for interfacing with INTEGRAL SPI data. It also provides a 3ML plugin for performing full forward folding spectral analysis of GRBs. The documentation with a few examples is available at https://pyspi.readthedocs.io/.

3ml python spi-data

Last synced: 27 Aug 2026

https://github.com/aksholokhov/pysr3

SciKit-Learn compatible library for training mixed-effects models.

Last synced: 26 Aug 2026

https://github.com/neuralgraphs/diman

A Clojure library for applying dimensional analysis.

Last synced: 26 Aug 2026

https://github.com/schalkdaniel/compboost

C++ implementation and R API for componentwise boosting

boosting-framework interpretable-machine-learning machine-learning

Last synced: 26 Aug 2026

https://github.com/opensim-org/SCONE

Open Source Software for Predictive Simulation of Biological Motion.

musculoskeletal-models optimization simulation tutorials

Last synced: 26 Aug 2026

https://github.com/ExObsSim/ExoRad2-public

ExoRad, the generic point source radiometric model.

Last synced: 27 Aug 2026

https://github.com/barbagroup/geoclaw-landspill

An oil land-spill and overland flow simulator for pipeline rupture events

geoclaw land-spill overland-flow pipeline pipeline-ruptures shallow-water-equations

Last synced: 26 Aug 2026

https://github.com/AI-multimodal/Lightshow

A one-stop-shop for handling data in computational spectroscopy

Last synced: 27 Aug 2026

https://github.com/ericfell/rfbzero

Redox flow battery electrochemical cycling models in Python

batteries battery-models microkinetics python rfbzero simulation

Last synced: 26 Aug 2026

https://github.com/tne-lab/py-behav-box-v2

Pybehave is an open source software interface and framework for controlling behavioral experiments in neuroscience and psychology.

Last synced: 27 Aug 2026

https://github.com/WMD-group/CarrierCapture.jl

Julia package to compute trap-assisted electron and hole capture in semiconductors

defects electronic-structure materials-design semiconductors solar-cells

Last synced: 27 Aug 2026

https://github.com/COSIMA/regional-mom6/

Automatic generation of regional configurations of the Modular Ocean Model 6 (MOM6) in Python

mom6 ocean-modelling python regional-model

Last synced: 26 Aug 2026

https://github.com/seamplex/feenox/

Cloud-first free no-fee no-X uniX-like finite-element(ish) computational engineering tool

finite-elements hpc numerical-methods ode-solver pde-solver

Last synced: 27 Aug 2026

https://github.com/anmuller/CusToM

Last synced: 26 Aug 2026

https://github.com/suneeshjacob/ACRoD

Automatic Computation for Robot Design

Last synced: 27 Aug 2026

https://github.com/Samsung/mTower

mTower is Trusted Execution Environment specially designed to be used on MicroController Units (MCUs) supporting ARM TrustZone technology (e.g., Cortex-M23/33/35p). mTower operates well under restrictions typical for such environment – small RAM and ROM sizes, relatively low performance, absence of rich OSes providing variety of services available on PCs or in enterprise environments. mTower is intended for usage in IoT, embedded devices, Smart Home applications, distributed heterogeneous networks and other environments where secure processing of sensitive data is necessary.

bootloader cortex-m23 freertos gcc iot m2351 makefile microcontroller numaker-pfm-m2351 nuvoton risc-v secure smarthome trusted-execution-environment trustzone

Last synced: 26 Aug 2026

https://github.com/lskatz/mashtree

:deciduous_tree: Create a tree using Mash distances

bioperl mash mash-distances tree

Last synced: 27 Aug 2026

https://github.com/henrikmelin/h3ppy

A python package for modelling and fitting H3+ spectra

astronomy data-analysis planetary-science python3 spectroscopy

Last synced: 27 Aug 2026

https://gitlab.com/fame-framework/fame-core

Core library of FAME written in Java

FAME

Last synced: 26 Aug 2026

https://github.com/Merck/rtdpy

Residence Time Distribution modeling in Python.

process-development python residence-time-distribution

Last synced: 26 Aug 2026

https://github.com/DIDSR/DICaugment

Last synced: 27 Aug 2026

https://github.com/joaomcteixeira/taurenmd

A command-line interface for analysis of Molecular Dynamics simulations.

Last synced: 26 Aug 2026

https://gitlab.com/habermann_lab/phasik

Scientific tools for extracting cyclic data via hierarchical clustering

Last synced: 27 Aug 2026

https://github.com/xuanxu/starmatrix

Modelling nucleosynthesis of galactic chemical elements

astrophysics galaxies

Last synced: 27 Aug 2026

https://github.com/JuliaStats/HiddenMarkovModels.jl

A Julia package for simulation, inference and learning of Hidden Markov Models.

baum-welch forward-backward hidden-markov-model hmm julia markov statistics viterbi

Last synced: 27 Aug 2026

https://github.com/zoran-cuckovic/QGIS-visibility-analysis

Quantum GIS plugin for visibility analysis

qgis qgis2-python-plugins qgis3-plugin visibility-analysis

Last synced: 26 Aug 2026

https://github.com/Mat-dp/mat-dp-core

Mat-dp core cotains the key methods used in the broader Mat-dp model. Mat-dp aims to deliver user-friendly and open-access software to study the environmental implications of materials used for building low-carbon systems.

bulk-materials critical-materials embodied-emissions low-carbon-systems material-demand modelling-tool

Last synced: 27 Aug 2026

https://github.com/ur-whitelab/hoomd-tf/

A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD

machine-learning molecular-dynamics tensorflow

Last synced: 27 Aug 2026

https://github.com/sisl/PyroRL

An RL environment made for wildfire evacuation.

Last synced: 27 Aug 2026

https://github.com/rodoulak/desalsim

Techno-economic models for desalination and brine treatment technologies

brine desalination resource-recovery techno-economic-analysis

Last synced: 27 Aug 2026

https://github.com/itpplasma/GORILLA

GORILLA: Guiding-center ORbit Integration with Local Linearization Approach

fusion-reactor guiding-center hamiltonian-systems kinetic-modeling numerical-integration numerical-methods plasma-physics simulation stellarator tokamak

Last synced: 27 Aug 2026

https://github.com/kungfugo/BellDiagonalQudits.jl

Last synced: 26 Aug 2026

https://github.com/tobiasschoch/wbacon

Weighted BACON algorithms

outlier outlier-detection r-package robust-regression statistics

Last synced: 26 Aug 2026

https://github.com/pyscal/pyscal

Python library written in C++ for calculation of local atomic structural environment

bond-order-parameters lammps molecular-dynamics nucleation order-parameters solid-state-physics steinhardt steinhardt-bond-order-parameters

Last synced: 26 Aug 2026

https://github.com/labsquare/CutePeaks

CutePeaks is a standalone Sanger trace viewer steered by a modern and user-friendly UI.

ab1 sanger-chromatograms scf

Last synced: 27 Aug 2026

https://github.com/adriancorrendo/metrica/

Prediction Performance Metrics

Last synced: 27 Aug 2026

https://github.com/padster/pyNeuroTrace

Python code for processing neural timeseries

analytics neuroscience timeseries

Last synced: 26 Aug 2026

https://github.com/range-et/PGL

The Plebeian Graph Library: A WebGL based network visusalisation and diagnostics package

data-visualization graph graph-theory visualization webgl

Last synced: 27 Aug 2026

https://github.com/kanaverse/kana

Single cell analysis in the browser

bioinformatics cite-seq exploratory-data-analysis interactive-analysis interactive-visualizations rna-seq single-cell webassembly

Last synced: 27 Aug 2026

https://github.com/harpolea/r3d2

Last synced: 26 Aug 2026

https://github.com/SuperKam91/gns

Geometric nested sampling algorithm

Last synced: 26 Aug 2026

https://github.com/UM-KevinHe/surtvep

Last synced: 26 Aug 2026

https://github.com/dblarremore/webweb

MATLAB and Python + d3js. Webweb is a tool for creating interactive visualizations of networks on the web.

Last synced: 26 Aug 2026

https://github.com/barbagroup/PetIBM

PetIBM - toolbox and applications of the immersed-boundary method on distributed-memory architectures

computational-fluid-dynamics gpu-computing immersed-boundary-method nvidia-amgx petsc

Last synced: 26 Aug 2026

https://github.com/NickC1/skedm

Empirical dynamic modeling in scikit-learn's style

Last synced: 26 Aug 2026

https://github.com/barbagroup/cuIBM

cuIBM: a GPU-based immersed boundary method code.

Last synced: 26 Aug 2026

https://github.com/PeerHerholz/BIDSonym/

a BIDS app for pseudo-anonymization of neuroimaging data

Last synced: 27 Aug 2026

https://github.com/groupmm/synctoolbox

A Python toolbox with reference implementations for efficient, robust, and accurate music synchronization based on dynamic time warping (DTW)

chromagram dtw music onset python synchronization

Last synced: 27 Aug 2026

https://github.com/ks905383/xagg/

Aggregating gridded data (xarray) to polygons

aggregation polygon python raster-data xarray

Last synced: 27 Aug 2026

https://github.com/virtual-vehicle/pointcloudset/

Efficient analysis of large datasets of point clouds recorded over time

4d-point-cloud convert las lidar lidar-point-cloud livox open3d ouster point-cloud pointcloud python riegl ros ros2 rosbag rostopic time-series time-series-analysis velodyne-sensor

Last synced: 26 Aug 2026

https://github.com/ElectionDataAnalysis/electiondata

Tools for consolidation and analysis of raw election results from the most reliable sources -- the election agencies themselves.

common-data-format election election-data

Last synced: 27 Aug 2026

https://github.com/Jacks0nJ/PyFPT

Stochastic first-passage time (FPT) simulations using importance sampling.

cosmology cython first-passage-times importance-sampling inflation stochastic

Last synced: 26 Aug 2026

https://github.com/ToyotaCRDL/mahos

Measurement Automation Handling and Orchestration System

Last synced: 27 Aug 2026

https://github.com/martibosch/swisslandstats-geopy

Python tools for preprocessing geodata from the Swiss Federal Statistical Office

Last synced: 26 Aug 2026

https://github.com/amberbiology/scribl

Semantic Capture of Relationships In Biological Literature (scribl)

computational-biology literature-mining network-biology systems-biology

Last synced: 26 Aug 2026

https://github.com/CEA-MetroCarac/pystack3d

Package to process images stacks (typically from 3D FIB-SEM)

Last synced: 26 Aug 2026

https://github.com/petermr/pygetpapers/

a Python version of getpapers

Last synced: 27 Aug 2026

https://github.com/rrrlw/helixvis

Visualize alpha-helical peptide sequences in R using helical wheels and wenxiang diagrams. See https://doi.org/10.21105/joss.01008 for more details.

biochemistry cran helical-wheels peptide-sequences r visualization wenxiang-diagrams

Last synced: 26 Aug 2026

https://github.com/wetransform-os/ProMCDA

A tool to estimate ranks of alternatives and their uncertainties based on the Multi Criteria Decision Analysis approach.

Last synced: 27 Aug 2026

https://github.com/Cohere-Labs-Community/rl

Generic reinforcement learning codebase in TensorFlow

machine-learning reinforcement-learning rl tensorflow

Last synced: 26 Aug 2026

https://github.com/unfoldtoolbox/UnfoldSim.jl

Simulate EEG / ERP data with overlap, non-linear effects, multiple regression

eeg erp julia simulation time-series

Last synced: 27 Aug 2026

https://github.com/TrashBirdEcology/bbsAssistant/

An R package for downloading and handling data and information from the North American Breeding Bird Survey.

bbs-data birds breeding-bird-survey data-downloader ecology ornithology point-count usgs

Last synced: 26 Aug 2026

https://github.com/DingshanDeng/ysoisochrone

This is the Python package that handles the isochrones for young stellar objects (YSOs). One of the primary goals of this package is to derive the stellar mass and ages from the isochrones.

Last synced: 27 Aug 2026

https://github.com/JuliaOcean/AIBECS.jl

The ideal tool for exploring global marine biogeochemical cycles.

awesome biogeochemical biogeochemical-model biogeochemistry fluxes global inverse-model julia marine marine-tracer model modeling models ocean ocean-circulation oceanography optimization pathways tracer transport