All software
minimism
A minimal distributed MPI port from UFEMISM, used as a basis for UFEMISM2.0
- Finite volume method
- ice sheet
- MPI
- + 1
- Fortran
- MATLAB
- Mathematica
- + 4
MINTED
MINTED (Making Identifiers Necessary for Tracking Evolving Data) aims to apply dataset citation Digital Object Identifiers (DOIs) and researcher ORCIDs into ONC's Oceans 3.0 digital infrastructure.
- oceanography
- Oceans
- persistent identifiers
Mixed Meal Model SBML
This software generates the SBML version of the Mixed Meal Model, for predicting the glucose level evolution after the intake of a meal.
- Digital Twins
- modelling
- Python
- Shell
mkdocs rich argparse
An MkDocs plugin to generate documentation for a rich argparse parser. It renders commands, sub commands and sub-sub commands which can have rich help messages.
- python
- Python
MPET
This software is designed to run simulations of batteries with porous electrodes using porous electrode theory, which is a volume-averaged, multiscale approach to capture the coupled behavior of electrolyte and active material within electrodes
- Python
- Dockerfile
MSS-IMProv
An Integrative Modeling Platform
- mass spectrometry
- Modeling
- proteins
NanopubJL
JupyterLab extension to aid in searching and publishing of Nanopublications in a python notebook
- Inter-operability & linked data
- TypeScript
- Python
- JavaScript
- + 3
Nature Counts
The NatureCounts platform allows users to collect, archive, interpret and access wildlife data to advance the understanding of bird populations across the Western Hemisphere.
- bird monitoring
- conservation science
- open data
- R
- CSS
nedextract
nedextract is a python library that helps you to extract information on person names and organisations mentioned in Dutch (annual report) PDF files.
- Python
- Jupyter Notebook
- Shell
NetCDF2LittleR
An application to convert NetCDF files to the Little-R format
- Fortran
- CMake
- Pascal
NeuroAnalyzer
NeuroAnalyzer is a Julia toolbox for analyzing neurophysiological data.
- EEG
- fNIRS
- MEG
- + 2
NeuroGym
NeuroGym is a curated collection of neuroscience tasks with a common interface. The goal is to facilitate the training of neural network models on neuroscience tasks.
- deep learning
- Machine learning
- Neuroscience
- + 3
- Python
NPLinker eScience Workshop GenMetMine Materials
These materials were used as a part of the NPLinker eScience Workshop on Natural Product Genome & Metabolome Mining: https://www.wur.nl/en/research-results/chair-groups/plant-sciences/bioinformatics/teaching/nplinker_workshop.htm Most materials are available in a format facilitating its reuse.
- Data mining
- genomics
- Inter-operability & linked data
- + 4
Nunaliit
The Nunaliit Atlas Framework aims to make it easy to tell stories and highlight relationships between many different forms of information from a variety of sources, using maps as a central way to connect and interact with the data.
- atlas
- cartography
- database
- + 6
- JavaScript
- Java
- HTML
- + 9
OBiBa Agate
Agate is a web application that offers users related services to the OBiBa software stack.
- authentication
- Epidemiology
- Java
- FreeMarker
- Vue
- + 7
OBiBa Mica
Mica is OBiBa's software application that is used to create data web portals for large-scale epidemiological studies or multiple-study consortia.
- euCanSHare, software integration
- Java
- JavaScript
- FreeMarker
- + 6
OBiBa Opal
Opal is OBiBa's core data repository application for epidemiological studies.
- euCanSHare, software integration
- Java
- Vue
- JavaScript
- + 8
Ocean Networks Canada
By bringing data to the surface, ONC provides ocean intelligence to scientists, governments, organizations, and citizens. Ocean data are archived, processed and made freely available via ONC’s data management system, Oceans 3.0.
OCTSEG
Analyze retinal optical coherence tomography images.
- Image processing
- MATLAB
- M
One button compute
Web application for running a CWL workflow on a bunch of files.
- Optimized data handling
- Workflow technologies
- Python
- HTML
- Common Workflow Language
OpenDA
Open data assimilation toolbox. OpenDA is an open interface standard for a set of tools to quickly implement data-assimilation and calibration for arbitrary numerical models.
- Optimized data handling
- Java
- Fortran
- Python
- + 22
Open Matrices Stimulus Set (omss)
omss is a Python package for generating matrix reasoning puzzles, inspired by Raven's Progressive Matrices. It allows users to generate an unlimited number of customizable puzzles across a range of difficulty levels by setting rules for visual elements.
- Intelligence
- Matrices
- python
- + 1
- Python
OpenSim Creator
A UI for building OpenSim models
- biomechanical engineering
- opensim
- Simulation
- C++
- GLSL
- CMake
- + 5
Orange3 Argument Mining Add-on
This open-source Python package facilitates the processing, analysis, and visualization of argument corpora. Additionally, It offers user-friendly GUIs integrated into the Orange3 scientific workflow platform, enabling non-programmers to utilize its capabilities.
- Argument mining
- Natural Language Processing
- python
- + 1
- Python
Orange3 Story Navigator
Add-on providing quantitative textual story analysis based on principles in narrative psychology
- narrative psychology
- orange3
- text analysis
- Python
Orange Hackathon
Orange modules for text processing in the project What Works When for Whom
- Jupyter Notebook
- Python
- CSS
- + 2
Osmium
Start, stop and monitor applications remotely via a HTTP interface.
- High performance computing
- Java
- API Blueprint
oTree Demo Experiments
oTree demo experiment: Public goods game
- behavioral research
- oTree
- Workflow technologies
- HTML
- Python
- JavaScript
- + 1
oTree Development Environment
A Docker environment for programming against multiple oTree server
- oTree
- Makefile
- Shell
- Dockerfile
oTree Waiting Room
A load balancer for oTree servers.
- oTree
- JavaScript
- HTML
- Shell
Overture Arranger
Data can be messy, let Arranger organize it for you.
- JavaScript
- TypeScript
- CSS
- + 3
Overture Data Management System
Overture is a collection of open-source, extendable solutions for big-data genomic science that research institutions and individual researchers can use to support their work.
- authentication
- cloud storage
- genomics
- + 2
- Java
- Shell
- Dockerfile
- + 1
Overture Ego
A stateless authorization and user management service.
- Data Indexing
- Elasticsearch Automation
- Java
- Shell
- Makefile
- + 1
Overture Maestro
Organizing your distributed data into one index.
- Data Indexing
- Elasticsearch Automation
- Java
- Groovy
- Makefile
- + 1
Overture Score
Transfer data quickly and easily to and from any cloud-based storage system.
- Cancer Genomics
- Cloud Storage & Transfer
- Java
- Shell
- Makefile
- + 1
Overture Song
Quickly and reliably track genome metadata scattered across multiple Cloud storage systems.
- Cancer Genomics
- Metadata Management
- Metadata Validation
- Java
- Python
- Shell
- + 7
PACTE
A Collaborative Electronic Text Annotation Platform
- collaborative
- corpus
- disambiguation
- + 5
PanTools-pipeline-v4
General purpose Snakemake pipeline for PanTools v4.
- Data Analysis
- genomics
- pangenomics
- Python
- Dockerfile
- Shell
paradigma
A toolbox to calculate digital biomarkers for wearable sensors in Parkinson's disease.
- Python
- Jupyter Notebook
parareal
This package runs the parareal algorithm on a black-box simulator. Parallelisation is managed through Dask.
- High performance computing
- Numerical analysis
- CSS
- Jupyter Notebook
- Python
- + 5
ParticleDA.jl
Julia package to perform data assimilation with particle filters, supporting both thread-based parallelism and distributed processing using MPI.
- Data assimilation
- Julia Package
- Particle filter
- Julia
- Jupyter Notebook
- Shell
PartitionedArrays.jl
This package provides distributed (a.k.a. partitioned) vectors and sparse matrices like the ones needed in distributed finite differences, finite volumes, or finite element computations.
- GPU
- High performance computing
- Julia Package
- Julia
- Shell
PattyAnalytics
Library for aligning and scaling one point cloud to an other.
- Big data
- Point Cloud
- Python
PBI
An open-source python package to identify breakthrough innovations within patents.
- Breakthrough innovations
- jupyter notebooks
- parallel computing
- + 2
- Python
pdbtbx-ts
Want to parse Protein Data Bank files in JavaScript
- Optimized data handling
- Rust
- JavaScript
- TypeScript
Petri Nets on Hyperledger
Decentralized coordination of multi-domain workflows using Hyperledger Fabric blockchain and Petri nets.
- Blockchain
- hyperledger
- Petri net
- + 1
- JavaScript
- CSS
- HTML
- + 1
PhysicalConstants.jl
Collection of fundamental physical constants with uncertainties. It supports arbitrary-precision constants.
- Julia Package
- Physics
- Julia
PlanEO Dashboard
Provides an interactive interface for visualizing geographical data relevant to the MINE-DD project, including pathogen distribution, risk factors, and demographic analysis through both point data and raster overlays.
- Data Analysis
- Demographic Analysis
- Geographic Visualization
- + 8
- TypeScript
- Svelte
- Python
- + 5