All software
Islandora
Islandora is an open-source software framework designed to help institutions and organizations and their audiences collaboratively manage, and discover digital assets using a best-practices framework.
- Drupal
- Fedora
- open source
- + 1
- PHP
- JavaScript
- Twig
- + 1
i-VRESSE jupyterlab haddock3 configurator
Jupter Lab extension to create/edit haddock3 configuration file.
- Inter-operability & linked data
- TypeScript
- Python
- JavaScript
- + 1
JASP modules app
A web application that allows you to search/filter all the available JASP modules and install them.
- TypeScript
- HTML
- CSS
JUBE
JUBE is a generic, lightweight, configurable environment to run, monitor and analyse application execution in a systematic way. This software is commonly used to execute benchmarks and complex workflows on High Performance Computers, but is not limited to these systems.
- Benchmarking
- High performance computing
- HPC
- + 4
- Python
- Shell
- C
JupyterDaskOnSLURM
A Dask cluster and a Jupyter server on a SLURM system
- Big data
- High performance computing
- jupyter notebooks
- + 1
- Python
- Shell
JupyterLab dataset browser for THREDDS
A browser that allows you to include NetCDF data stored in THREDDS catalog into a Jupyter Notebook.
- Big data
- Optimized data handling
- Python
- TypeScript
- Jupyter Notebook
- + 2
JURI
JURI (Jülich Reporting Interface) provides a template-driven fully client-based web framework to visualise data lists and associated data graphs.
- JavaScript
- HTML
- CSS
- + 5
Kernel Float
C++ Header-only library for CUDA that simplifies working with vector types and reduced precision floating-point arithmetic in GPU code.
- AI
- Big data
- GPU
- + 1
- C++
- Cuda
- Python
- + 3
Kernel Launcher
Dynamically compile GPU kernels and launch them easily and safely using C++ magic. Tight integration with Kernel Tuner results in blazing fast CUDA code that is maintainable and performance portable.
- auto-tuning
- CUDA
- GPU
- + 2
- C++
- Python
- CMake
- + 3
KMM
KMM is a lightweight C++ middleware for accelerated computing.
- GPU
- High performance computing
- C++
- Cuda
- CMake
- + 1
kunefe
A Python package that helps users run containerized applications on HPC systems
- Agent-based modeling
- Apptainer
- containers
- + 5
- Python
- Shell
- Dockerfile
LARA
LARA (Laboratory Automation Robotic Assistant) is an open source Research Data Management Suite and 2nd generation Electronic Lab Notebook with that provides a rich infrastructure for lab communication, orchestration, data/metadata storage, evaluation and exchange.
- laboratory automatization
Laserfarm
Laserfarm: Laserchicken Framework for Applications in Research in Macroecology. Leverage Laserchicken in distributed fashion to use continental scale point cloud datasets for research.
- Python
- Jupyter Notebook
- Dockerfile
Ldot
Workflow and participant registration support
- GDPR
- participant information
- storage
- + 2
leakybucket
A Python BMI leaky bucket model 🪣
- Jupyter Notebook
- Python
- Dockerfile
LHAPDF
LHAPDF (The Les Houches Accord PDFs) is a standardised library for accessing parton distribution functions (PDFs) in high-energy physics. It provides a common interface to a wide range of PDF sets, enabling consistent and reproducible predictions in collider simulations and analyses.
- Collider physics
- Deep Inelastic Scattering
- Interpolation
- + 1
- C++
- Python
- M4Sugar
- + 2
LifelinesCSV2CDF
This tool converts Lifelines cohort study data from CSV to CDF/JSON, a format used in the MyDigiTwin project. Lifelines tracks health data over time, but variables are often scattered across files, making analysis difficult. CDF organizes data per participant, enabling FHIR/MedMij-compliant analysis
- Data Harmonization
- Lifelines
- MyDigiTwin
- Python
- Shell
LimeSurvey
LimeSurvey is a free and open-source online survey platform in 80+ countries worldwide. It offers features like conditional logic, question branching, customizable templates, multilingual support, and GDPR compliance.
- questionnaire
- survey
- JavaScript
- PHP
- CSS
- + 11
LLview
LLview is a set of software components to monitor clusters that are controlled by a resource manager and a scheduler system.
- High performance computing
- HPC
- Monitoring
- + 2
- Perl
- Python
- Shell
lofar-ld
Publish LOFAR catalog as Linked Data.
- Inter-operability & linked data
- Makefile
Lofar Predictive Maintenance
Software tool to cluster outputs of different baselines within a specific observation. There are often over 1500 baselines in a single observation which takes a lot of time to inspect. This tool makes inspecting output of baselines more productive.
Lokum
Deploy GlusterFS, Docker, Spark and JupyterHub services on bare-metal cluster.
- Big data
- High performance computing
- Optimized data handling
- Python
- HCL
- Shell
- + 2
LombScargle.jl
Compute Lomb-Scargle periodogram, suitable for unevenly sampled data. It supports multi-threading
- astronomy
- Astrophysics
- Julia Package
- Julia
LXCat
An open-access website for collecting, displaying, and downloading electron and ion scattering cross sections for modeling low temperature plasmas.
- Optimized data handling
- TypeScript
- Rust
- CSS
- + 2
LXCat schema
Type, JSON schema and validator for cross section set used in low-temperature plasma community.
m4ma
An R package containing C++ implementations to speed up the simulation and parameter estimation of the Predictive Pedestrian model.
- geospatial
- High performance computing
- Real time data analysis
- C++
- R
- C
Magic Castle
Magic Castle aims to recreate the HPC user experience in public clouds.
- CERN
- HPC
- research software
- + 1
- HCL
- Shell
- Python
marzipan
Deploying clusters of VMs on bare metal using OpenNebula, provisioning, and running services made easy by fully configurable scalable automation
- High performance computing
- Python
- Dockerfile
- Smarty
- + 1
Mass Spec Studio for Clinical Proteomics
A fusion of the popular OpenMS suite of functionality with the powerful Mass Spec Studio. Users have access to OpenDIA and OpenPRM to support large scale processing of clinical proteomics data sets.
- mass spectrometry
- proteins
- proteomics
Medical Image Processing in Python
This lesson introduces some specifics of medical image processing with popular Python libraries such as SimpleITK, Pydicom and NiBabel. Reconstruction algorithms, image and DICOM anonymization, registration, segmentation, data augmentation and generative AI are covered.
- Image processing
- medical
- radiology
mibibio
Collection of microbial analysis workflows to investigate microbiological community structure, characteristics and their degradation potential.
mibiremo
MiBiReMo (Microbiome Bioremediation Reaction Module) is a Python interface to the PhreeqcRM library. The package is designed to be coupled with transport models to simulate reactive transport in porous media, with applications in environmental and geochemical engineering.
- Python
- Makefile
mibiscreen
Data handling and screening package of the Microbiome based remediation Prediction Tool
- Data Analysis
- Multi-scale & multi model simulations
- python
- Python
- Jupyter Notebook
- Shell
mibitrans
A collection of analytical and semi-semianalytical solutions for hydrogeological transport phenomena
- Multi-scale & multi model simulations
- python
- Python
- Shell
Mimetic Operators Library Enhanced (MOLE)
MOLE is a high-quality (C++ & MATLAB/Octave) library of high-order mimetic operators to solve partial differential equations. It provides discrete analogs of vector calculus operators: Gradient, Divergence, Laplacian, Bilaplacian, and Curl. These operators satisfy local and global conservation laws.
- Mathematical Software
- Mimetic Operators
- Partial differential equations
- MATLAB
- C++
- CMake
- + 2
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