All software
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
- Jupyter Notebook
- Julia
- 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
Platalea
Platalea contains deep neural network architectures for modeling spoken language from multiple sources at once: audio, and simultaneously images, text or video. This can be used to learn about what different context sources add to the language acquisition process.
- Python
prfmodel
A modern Python implementation for population receptive field modelling.
- GPU
- Neuroscience
- optimization
- + 2
- Python
protein-detective
Python package to detect proteins in EM density maps.
- Python
PSRDADA python
If you want to do astrophysics in python, this could come in handy. Connect to a radiotelescope and process data in real-time.
- Cython
- Python
- Makefile
pybacting
Python wrapper around Bacting.
- Biology
- Chemistry
- python
- Python
Pycoeus
Pycoeus is a command-line tool and python package designed for exploration of multiband geospatial datasets. It lets the user iteratively train and retrain segmentation models in seconds. A combination of Deep learning and traditional machine learning is used, leveraging the best of both methods.
- deep learning
- gis
- Machine learning
- + 2
- Python
PyELSEPA
Python wrapper for ELSEPA, a numeric code for computing elastic scattering cross-sections for electrons and positrons off neutral atoms.
- Python
- Dockerfile
Pyspextools
Pyspextools is a collection of python tools for the SPEX X-ray spectral fitting package.
- Astrophysics
- Software
- Spectroscopy
- Python
PyStemmusScope
A python package for running the STEMMUS-SCOPE model
- Jupyter Notebook
- Python
- Shell
- + 1
pyTAMS
A physics-agnostic implementation of the Trajectory-Adataptive Multilevel Splitting (TAMS) algorithm for predicting transition probability in bi-stable dynamic problems.
- Rare event simulations
- Python
- Shell
python-pcl
Use the industry-standard Point Cloud Library from within Python.
- Big data
- High performance computing
- Python
- C++
- Makefile
- + 2
PyXenon
Python wrapper for the Xenon programming interface to various compute and storage resources.
- Python
- Shell
- Batchfile
pyZacros
A Python library to handle Kinetic Monte Carlo codes.
- Python
- Shell
qalcore
Core Library of the Quantum Application Lab
- python
- Quantum Computing
- Jupyter Notebook
- Python
- Shell
QANS
QANS (Questionnaire And Nomination Software) is a collection of software components to enable longitudinal research using sociometric (peer nomination, peer ranking) surveys.
- Peer Nomination
- questionnaire
- sociology
- + 2
qc2
Quantum Computing for Quantum Chemistry
- quantum chemistry
- Quantum Computing
- Jupyter Notebook
- Python
- Shell
q-cardIA
Quantitative cardiac image analysis
- cardiac image analysis
- deep learning
- Medical Imaging
QMCBlip
QMCBlip allows to couple Quantum Monte Carlo Simulations with Machine Learning Force Fields to accelerate Molecular Dynamics simulations
- Python
QMCTorch
Use and design neural network ansatz wave function for real-space quantum Monte Carlo simulations of molecular systems.
- Computational Chemistry
- GPU
- High performance computing
- + 2
- Python
- TeX
quafing
Questionnaire analysis using Fisher Information Non-Parametric Embedding. Explore high-dimensional continuous and discrete questionnaire data sets.
- Data Analysis
- python
- Statistics
- Python
- Jupyter Notebook
- Shell
Quantum Newton Raphson
The Quantum Newton Raphson package allows to leverage quantum computing routines to accelerate the Newton-Raphson algorithm.
- Numerical analysis
- Quantum Computing
- Python
- Shell
qubols
qubols allows to solve linear system using a QUBO approach that can be deployed on quantum annealers
- Numerical analysis
- Quantum Computing
- Jupyter Notebook
- Python
- Shell
qubops
qubops allows to solve polynomial system of equations using a QUBO approach that can be deployed on quantum annealers
- Numerical analysis
- Quantum Computing
- Jupyter Notebook
- Python
- Shell
QUICKLB
QUICKLB is a very efficient library that sacrifices optimality for speed. It shines in distributed applications that have unpredictable unbalanced computational peaks in their domains.
- Computational Fluid Dynamics (CFD)
- Fortran
- High performance computing
- + 2
- Fortran
- Python
- CMake
Radiam
Radiam helps researchers keep track of their data, regardless of where it is stored. There are multiple components working together, and most of them run within Docker containers.
- metadata
- RDM
- Python
- JavaScript
- HTML
- + 3
rcoins
Identify continuous lines in a spatial network.
- geospatial
- Networks
- R
- R
- Python
rcrisp Shiny app
Shiny web app for the rcrisp software package.
- geospatial
- R
- shiny
- + 1
- R
ReaxPro framework ontology
This application ontology is dedicated to the ReaxPro framework for the multi-scale modeling of catalytic materials.
- Multi-scale & multi model simulations
- ontology
- Workflow technologies
ReaxPro wrappers
This repository is a collection of wrappers used in the ReaxPro project. It holds wrappers for the Amsterdam Modeling Suite (AMS) and Zacros.
- Chemistry
- Multiscale modeling
- Multi-scale & multi model simulations
- Python
- Dockerfile
- Shell
REE-HDSC
Software developed in the project REE-HDSC (Recognizing Extracted Entities for the Historical Database Suriname Curacao, 2023-2024) of the Radboud University Nijmegen and the Netherlands eScience Center.
- hand-written text recognition
- named entity Recognition
- Jupyter Notebook
- Python
- HTML
Remote BMI
Remote BMI allows you to communicate with Basic Model Interface enabled numerical models using a RESTful API
- Basic Model Interface
- BMI
- julia
- + 4
- Julia
- Python
- R
- + 3