JOSS collection | Ecosyste.ms: Summary

https://github.com/MFaymon/spINAR

Semiparametric and parametric estimation and bootstrapping of integer-valued autoregressive (INAR) models.

bootstrapping count-data parametric-estimation penalization semiparametric-estimation simulation time-series validation

Last synced: 15 Aug 2026

https://github.com/EdyVision/pii-codex

A research python package for detecting, categorizing, and assessing the severity of personal identifiable information (PII)

analysis data-analysis personal-identifiable-information pii pii-detection poetry presidio python python3 research research-software research-tool

Last synced: 14 Aug 2026

https://github.com/casics/nostril

Nostril: Nonsense String Evaluator

detector gibberish identifier-string identifiers inference mining-software-repositories nonsense nonsense-string-evaluator source-code text-processing

Last synced: 14 Aug 2026

https://github.com/FraunhoferIWES/foxes

Farm Optimization and eXtended yield Evaluation Software

Last synced: 15 Aug 2026

https://github.com/TeaspoonTDA/teaspoon

Topological Signal Processing in Python

persistent-homology persistent-homology-graphs python signal-processing tda tda-python topological-data-analysis topological-signal-processing

Last synced: 14 Aug 2026

https://github.com/EnvModellingGroup/hrds

Hierarchical raster data set: smooth interpolation of raster files at different resolutions for multiscale modelling

gis modelling numerical-modelling science-research

Last synced: 14 Aug 2026

https://github.com/nasa/ncompare

Compare the structure of two netCDF (or HDF5) files

data-comparison hierarchical-data netcdf

Last synced: 15 Aug 2026

https://github.com/expfactory/expfactory

software to generate a reproducible container with a battery of experiments

battery container experiment-factory experiments expfactory psychology reproducible singularity

Last synced: 14 Aug 2026

https://github.com/ThomasMBury/ewstools

Python package for early warning signals (EWS) of bifurcations in time series data.

autocorrelation bifurcation bootstrapping complex-systems critical-transitions early-warning-indicators early-warning-signals forecasting ipynb power-spectrum python resilience-indicators time-series tipping-point visualization

Last synced: 14 Aug 2026

https://github.com/SMTG-Bham/easyunfold

Band structure unfolding made easy!

ab-initio band-structure-unfolding computational-chemistry computational-materials-science defects dft disorder electronic-structure symmetry-breaking unfolding vasp

Last synced: 14 Aug 2026

https://github.com/AndreWeiner/flowtorch

flowTorch - a Python library for analysis and reduced-order modeling of fluid flows

csv dmd jupyter openfoam pod pytorch spod tau

Last synced: 15 Aug 2026

https://github.com/RECETOX/RIAssigner

RIAssigner is a python tool for retention index (RI) computation for GC-MS data.

gc-ms hacktoberfest mass-spectrometry python

Last synced: 14 Aug 2026

https://github.com/raamana/pyradigm

Research data management in biomedical and machine learning applications

automation biomedical data-integration data-structures datascience datastructures machine-learning machine-learning-workflows medical-data neuroimaging neuroinformatics neuroscience pandas python userfriendly workflow

Last synced: 14 Aug 2026

https://github.com/mad-lab-fau/imucal

A Python library to calibrate 6 DOF IMUs

Last synced: 14 Aug 2026

https://github.com/mzy2240/ESA

Easy SimAuto (ESA): An easy-to-use Power System Analysis Automation Environment atop PowerWorld Simulator Automation Server (SimAuto)

automation contingency-analysis esa graph-analysis hpc numba numpy pandas power-flow powersystem powerworld powerworld-simulator python pythran simauto simulator simulator-automation-server smart-grid transient-stability

Last synced: 14 Aug 2026

https://github.com/silvandeleemput/memcnn

PyTorch Framework for Developing Memory Efficient Deep Invertible Networks

deep-learning machine-learning python3 pytorch

Last synced: 14 Aug 2026

https://github.com/a-slide/pycoQC

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

computing-metrics generates-plots jupyter-notebook nanopore

Last synced: 14 Aug 2026

https://github.com/ropensci/opentripplanner

An R package to set up and use OpenTripPlanner (OTP) as a local or remote multimodal trip planner.

data isochrones java opentripplanner otp public-transport r routing transport transportation-planning

Last synced: 14 Aug 2026

https://github.com/sepandhaghighi/pyrgg

🔧 Python Random Graph Generator

beerpay generator gpu graph-computing graph-generation graph-generator gtgraph math mathematics python python3 script

Last synced: 14 Aug 2026

https://github.com/spjuhel/BoARIO

Python implementation of ARIO model

Last synced: 15 Aug 2026

https://gitlab.com/vibes-developers/vibes

[FHI-vibes](https://vibes-developers.gitlab.io/vibes/): Vibrational simulations with python powered by ASE and FHI-aims.

Last synced: 14 Aug 2026

https://github.com/pmlmodelling/nctoolkit

A Python package for netCDF analysis and post-processing

cdo netcdf python

Last synced: 14 Aug 2026

https://github.com/AgrDataSci/climatrends

Climate Variability Indices for Ecological Modelling

climate-data climatology timeseries-analysis

Last synced: 14 Aug 2026

https://github.com/andim/noisyopt

Python library for optimizing noisy functions.

optimization

Last synced: 14 Aug 2026

https://github.com/NGSolve/ngsPETSc

ngsPETSc Docs

Last synced: 14 Aug 2026

https://gitlab.com/cosapp/cosapp

CoSApp core package

Last synced: 14 Aug 2026

https://github.com/UofABioinformaticsHub/strandCheckR

Last synced: 14 Aug 2026

https://gitlab.com/open-darts/open-darts

The DARTS framework is designed for forward and inverse modeling in geo-energy applications.

energy transition geothermal energy production modeling of CO2 sequestration

Last synced: 14 Aug 2026

https://github.com/hippylib/hippylib

An Extensible Software Framework for Large-Scale Inverse Problems

Last synced: 14 Aug 2026

https://github.com/MedMaxLab/selfEEG

selfEEG: a Python library for Self-Supervised Learning on Electroencephalography (EEG) data

deep-learning eeg self-supervised-learning

Last synced: 14 Aug 2026

https://github.com/lzkelley/kalepy

Kernel Density Estimation and (re)sampling

kde kernel-density-estimation pdfs python python3 resample resampling statistical-analysis statistics

Last synced: 14 Aug 2026

https://github.com/ajakef/gemlog

Data conversion software for the Gem Infrasound Logger

infrasound miniseed

Last synced: 14 Aug 2026

https://github.com/sylvaticus/BetaML.jl

Beta Machine Learning Toolkit

ai artificial-intelligence autoencoder classification clustering data-science decision-trees deep-learning feature-importance imputation julia machine-learning ml neural-networks pca random-forest regression

Last synced: 14 Aug 2026

https://github.com/FourierFlows/GeophysicalFlows.jl

Geophysical fluid dynamics pseudospectral solvers with Julia and FourierFlows.jl.

baroclinic fourierflows geophysical-fluid-dynamics gpu julia navier-stokes pdes qg quasigeostrophy sqg

Last synced: 14 Aug 2026

https://github.com/OSeMOSYS/otoole

OSeMOSYS Tools for Energy

energy energy-system energy-system-modelling osemosys

Last synced: 14 Aug 2026

https://github.com/mviereck/x11docker

Run GUI applications and desktops in docker and podman containers. Focus on security.

containers desktop docker gpu gui html5 nerdctl podman printer pulseaudio sandbox sound ssh vnc wayland webcam x x11 xorg xpra

Last synced: 14 Aug 2026

https://github.com/dianna-ai/dianna

Deep Insight And Neural Network Analysis

explainable-artificial-intelligence scientific-research

Last synced: 14 Aug 2026

https://github.com/jamesrhester/Lerche.jl

A Julia port of the Lark parser

Last synced: 15 Aug 2026

https://github.com/precice/micro-manager

A manager tool to facilitate two-scale coupling in multi-physics simulations using preCICE.

coupling macro-micro multiphysics multiscale research-and-development

Last synced: 15 Aug 2026

https://github.com/pdebuyl-lab/tidynamics

A tiny package to compute the dynamics of stochastic and molecular simulations

correlation molecular-dynamics numpy stochastic-process

Last synced: 14 Aug 2026

https://github.com/ianfhunter/GNOLL

GNOLL is an efficient dice notation parser for multiple programming languages that supports a wide set of dice notation

board-game c cpp dice dice-notation dice-roller dice-rolls go golang haskell java javascript js julia perl python r roleplaying-games rpg-dice-roller ttrpg

Last synced: 14 Aug 2026

https://github.com/automl/amltk

A build-it-yourself AutoML Framework

Last synced: 14 Aug 2026

https://github.com/mikegrudic/pytreegrav

Fast N-body gravitational force and potential in Python

Last synced: 14 Aug 2026

https://github.com/acerbilab/pybads

PyBADS: Bayesian Adaptive Direct Search optimization algorithm for model fitting in Python

bayesian-optimization log-likelihood noiseless-functions noisy-functions optimization-algorithms python

Last synced: 14 Aug 2026

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

A Julia package for generating timeseries surrogates

hacktoberfest hypothesis-testing julia nonlinear-time-series surrogate surrogates timeseries

Last synced: 15 Aug 2026

https://github.com/KennethEnevoldsen/augmenty

Augmenty is an augmentation library based on spaCy for augmenting texts.

augmentation natural-language-processing nlp nlproc python spacy spacy-extension spacy-nlp text-augmentation text-classification training-data

Last synced: 14 Aug 2026

https://github.com/TeamCOMPAS/COMPAS

COMPAS rapid binary population synthesis code

Last synced: 14 Aug 2026

https://github.com/MagneticParticleImaging/MPIFiles.jl

Julia Package for reading and writing MPI Files

julia mpi

Last synced: 14 Aug 2026

https://github.com/jeremiah-corrado/fem_2d

A rust library for 2D Finite Element Method computations

Last synced: 14 Aug 2026

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

Python package for input file creation for FAME models and digestion of FAME outputs. [Documentation](https://fame-framework.gitlab.io/fame-io/)

FAME

Last synced: 14 Aug 2026

https://github.com/undark-lab/swyft

A system for scientific simulation-based inference at scale.

likelihood-free-inference machine-learning marginal-neural-ratio-estimation neural-ratio-estimation parameter-estimation python pytorch simulation-based-inference truncated-neural-ratio-estimation

Last synced: 14 Aug 2026

https://github.com/arvestad/alv

A console-based alignment viewer

Last synced: 14 Aug 2026

https://github.com/ai4os/DEEPaaS

A REST API to serve machine learning and deep learning models

aiohttp artificial-intelligence data-science deep-hybrid-datacloud deep-learning deepaas-api h2020 http machine-learning machinelearning neural-network neural-networks rest-api restful-api

Last synced: 14 Aug 2026

https://github.com/athob/py-ananke

Python pipeline to generate mock astrometric and photometric catalogs of synthetic stars derived from particle-based simulated star populations

Last synced: 14 Aug 2026

https://github.com/Aarhus-Psychiatry-Research/timeseriesflattener

Converting irregularly spaced time series, such as eletronic health records, into dataframes for tabular classification.

electronic-healthcare-data irregular-time-series machine-learning python python3 time-series-analysis

Last synced: 14 Aug 2026

https://github.com/hauselin/ollama-r

R library to run Ollama language models

ai api llm llms ollama ollama-api r

Last synced: 14 Aug 2026

https://github.com/cdjellen/ndbc-api

A Python API for retrieving meteorological and oceanographic data from the National Data Buoy Center (NDBC).

climate-data data-science noaa python3

Last synced: 14 Aug 2026

https://github.com/Cloud-Drift/clouddrift

CloudDrift accelerates the use of Lagrangian data for atmospheric, oceanic, and climate sciences.

climate-data climate-science data-structures oceanography python

Last synced: 14 Aug 2026

https://github.com/stfbnc/fathon

python package for DFA (Detrended Fluctuation Analysis) and related algorithms

dcca detrended-fluctuation-analysis dfa hurst-exponent mfdfa multifractal-analysis multifractal-detrended-fluctuation multifractal-spectrum python scientific-software

Last synced: 14 Aug 2026

https://github.com/gallantlab/cottoncandy

sugar for s3

cloud-storage google-drive numpy-arrays python s3

Last synced: 14 Aug 2026

https://github.com/konfound-project/konfound

R package for carrying out sensitivity analysis

Last synced: 15 Aug 2026

https://github.com/dodge-research-group/thztools

Tools for terahertz time-domain spectroscopy (THz-TDS)

condensed-matter-physics data-analysis optics spectroscopy terahertz time-domain

Last synced: 14 Aug 2026

https://github.com/TeamLEGWORK/LEGWORK

Package for making predictions about stellar-origin sources in space-based gravitational wave detectors

astrophysics gravitational-waves lisa python

Last synced: 14 Aug 2026

https://github.com/BioPandas/biopandas

Working with molecular structures in pandas DataFrames

bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure

Last synced: 14 Aug 2026

https://github.com/DeepRank/deeprank2

An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.

convolutional-neural-networks deep-learning graph-neural-networks protein-protein-interfaces pytorch single-residue-variants structural-biology

Last synced: 15 Aug 2026

https://github.com/auctus-team/pycapacity

An efficient task-space capacity calculation package for robotics and biomechanics

biomechanics linear-algebra pip-package polytope real-time robotics

Last synced: 15 Aug 2026

https://github.com/masadcv/FastGeodis

Fast Implementation of Generalised Geodesic Distance Transform for CPU (OpenMP) and GPU (CUDA)

deep-learning gpu pytorch

Last synced: 14 Aug 2026

https://github.com/CoLRev-Environment/bib-dedupe

Last synced: 14 Aug 2026

https://github.com/Beuth-Erdelt/DBMS-Benchmarker

DBMS-Benchmarker is a Python-based application-level blackbox benchmark tool for Database Management Systems (DBMS). It connects to a given list of DBMS (via JDBC) and runs a given list of parametrized and randomized (SQL) benchmark queries. Evaluations are available via a Python interface and on an interactive multi-dimensional dashboard.

agplv3 benchmarking dbms jdbc python sql

Last synced: 15 Aug 2026

https://github.com/circuitgraph/circuitgraph

Tools for working with circuits as graphs in python

boolean-circuits eda graphs netlist python satisfiability

Last synced: 14 Aug 2026

https://github.com/bastistician/polyCub

An R package for numerical integration over polygonal domains

numerical-integration polygons r

Last synced: 14 Aug 2026

https://github.com/fieldtrip/fieldtrip

The MATLAB toolbox for MEG, EEG and iEEG analysis

analysis beamformer bids brain connectivity dipole donders ecog eeg fieldtrip ieeg matlab meg neuroimaging neuroscience seeg statistics time-frequency

Last synced: 15 Aug 2026

https://github.com/hugoledoux/startinpy

A Python library for modelling and processing 2.5D terrains using a (2D) Delaunay triangulation.

delaunay-triangulation gis interpolation terrain tin

Last synced: 14 Aug 2026

https://github.com/SatelliteShorelines/CoastSeg

An interactive toolbox for downloading satellite imagery, applying image segmentation models, mapping shoreline positions and more. The mapping extension for CoastSat and Zoo.

colab earth-engine jupyter landsat python

Last synced: 14 Aug 2026

https://github.com/mwalmsley/zoobot

Classifies galaxy morphology with Bayesian CNN

Last synced: 14 Aug 2026

https://github.com/bjmorgan/py-sc-fermi

py-sc-fermi is a materials modelling code for calculating self-consistent Fermi energies and defect concentrations under thermodynamic equilibrium (or quasi-equilibrium) given defect formation energies.

Last synced: 14 Aug 2026

https://github.com/SteveMacenski/slam_toolbox

Slam Toolbox for lifelong mapping and localization in potentially massive maps with ROS

Last synced: 14 Aug 2026

https://github.com/Sm00thix/IKPLS

Fast CPU and GPU Python implementations of Improved Kernel Partial Least Squares (PLS) by Dayal and MacGregor (1997) and Fast Partition-Based Cross-Validation With Centering and Scaling for XTX and XTY by Engstrøm and Jensen (2025). This package also includes options to use sample weights for PLS modeling.

algorithm data-science gpu-support linear-regression partial-least-squares partial-least-squares-regression pls plsda plsr tpu-acceleration weighted-least-squares weighted-linear-regression weighted-regression

Last synced: 14 Aug 2026

https://github.com/OceanBioME/OceanBioME.jl

🌊 🦠 🌿 A fast and flexible modelling environment written in Julia for modelling the coupled interactions between ocean biogeochemistry, carbonate chemistry, and physics

biogeochemical-models biogeochemistry climate julia ocean ocean-modelling ocean-sciences oceanography

Last synced: 15 Aug 2026

https://github.com/rhenanbartels/hrv

A Python package for heart rate variability analysis

data-science hacktoberfest hrv python signal-processing

Last synced: 14 Aug 2026

https://github.com/rivasiker/PhaseTypeR

General-purpose phase-type functions

Last synced: 14 Aug 2026

https://github.com/upb-lea/openmodelica-microgrid-gym

OpenModelica Microgrid Gym (OMG): An OpenAI Gym Environment for Microgrids

control electrical-engineering energy-system-modeling engineering machine-learning microgrid modelica openai-gym openai-gym-environments openmodelica power-electronics power-supply power-systems python reinforcement-learning simulation smart-grids

Last synced: 14 Aug 2026

https://github.com/DeltaRCM/pyDeltaRCM

Delta model with a reduced-complexity approach

Last synced: 14 Aug 2026

https://github.com/bihealth/altamisa

AltamISA: a Python API for ISA-Tab files

bioinformatics isa isa-tab

Last synced: 14 Aug 2026

https://github.com/1313e/PRISM

An alternative to MCMC for rapid analysis of models

analysis-pipeline emulator model model-analysis python python3 regression

Last synced: 14 Aug 2026

https://github.com/online-ml/deep-river

data-science deep-learning incremental-learning machine-learning neural-network online-deep-learning online-learning outlier-detection pytorch stream

Last synced: 14 Aug 2026

https://github.com/DTUComputeStatisticsAndDataAnalysis/MBPLS

(Multiblock) Partial Least Squares Regression for Python

bioinformatics chemometrics data-fusion data-integration data-science machine-learning metabolomics multivariate-analysis multivariate-statistics pattern-recognition subspace-learning supervised-learning