All software
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
- (Dockerfile)
- (Python)
- (Shell)
paradigma
A toolbox to calculate digital biomarkers for wearable sensors in Parkinson's disease.
- ("Jupyter Notebook")
- (Python)
parareal
This package runs the parareal algorithm on a black-box simulator. Parallelisation is managed through Dask.
- High performance computing
- Numerical analysis
- (CSS)
- (Dhall)
- (HTML)
- + 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
- (JavaScript)
- (Rust)
- (TypeScript)
Petri Nets on Hyperledger
Decentralized coordination of multi-domain workflows using Hyperledger Fabric blockchain and Petri nets.
- Blockchain
- hyperledger
- Petri net
- + 1
- (CSS)
- (HTML)
- (JavaScript)
- + 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
- (CSS)
- (Dockerfile)
- (HTML)
- + 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)
- (Makefile)
- (Python)
pybacting
Python wrapper around Bacting.
- Biology
- Chemistry
- python
- (Just)
- (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.
- (Dockerfile)
- (Python)
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
- (Dockerfile)
- ("Jupyter Notebook")
- (Python)
- + 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
- (C)
- (C++)
- (Makefile)
- + 2
PyXenon
Python wrapper for the Xenon programming interface to various compute and storage resources.
- (Batchfile)
- (Python)
- (Shell)
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
- (Dockerfile)
- (HCL)
- (Python)
- + 1
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
- ("Jupyter Notebook")
- (Python)
- (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
- (CMake)
- (Fortran)
- (Python)
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
- (CSS)
- (HTML)
- (JavaScript)
- + 3
rcoins
Identify continuous lines in a spatial network.
- geospatial
- Networks
- R
- (Python)
- (R)
rcrisp Shiny app
Shiny web app for the rcrisp software package.
- geospatial
- R
- shiny
- + 1
- (R)
rdfsolve
Extract RDF schemas from SPARQL endpoints and convert to multiple formats (VoID, LinkML, JSON-LD).
- (Dockerfile)
- ("Jupyter Notebook")
- (Python)
- + 1
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
- (Dockerfile)
- (Python)
- (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
- (HTML)
- ("Jupyter Notebook")
- (Python)
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
- (Batchfile)
- (Dockerfile)
- (Julia)
- + 3
repl-session
A script that runs a session on any Read-Eval-Print-Loop (REPL), following a description in a JSON file. The output JSON contains the commands entered including the results from the REPL session. This can be useful to drive documentation tests or literate programming tasks.
- Literate Programming
- python
- Workflow technologies
- (Nix)
- (Python)
Research Lifecycle Approach using Islandora
Islandora 8 is an open-source software framework designed to help organizations collaboratively manage and discover digital assets using a best-practices, standards-based preservation framework.
Research Portal for Secure Data Discovery, Access, and Collaboration
A Research Portal that can address these different usage models, while serving as website and gateway for authorized researchers to capture, query, and visualize patient data; communicate, collaborate and share datasets; and access support and training resources. platforms.
- Collaboration
- Data Access Request
- Data Sharing
- + 3
RESTful APE
RESTful API for the APE (Automated Pipeline Explorer) library.
- Java
- Program synthesis
- REST API
- + 1
- (Dockerfile)
- (Java)