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
- Julia
- Jupyter Notebook
- 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
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
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
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
qc2
Quantum Computing for Quantum Chemistry
- quantum chemistry
- Quantum Computing
- Jupyter Notebook
- Python
- Shell
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
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
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
RESTfull API for the APE (Automated Pipeline Explorer) library.
- Java
- Program synthesis
- REST API
- + 1
- Java
- Dockerfile
ReSurfEMG
ReSurfEMG is an open source collaborative python library for analysis of respiratory electromyography (EMG). The library includes functions for pre-processing, analysis and machine learning.
- electrophysiology
- EMG
- Machine learning
- + 1
- Jupyter Notebook
- Python
- TeX
- + 3
ReSurfEMG-dashboard
A dashboard for visualizing and analyzing respiratory EMG signal, making use of the ReSurfEMG library
- EMG
- Time Series Analysis
- Visualization
- Python
Review Argumentation at Scale
This package contains a scalable pipeline to perform argument reasoning on a dataset of product reviews, to identify the highest quality ones. By tuning both lossy and lossless parameters, it is possible to tune the pipeline to foster the accuracy of the computation or its speed.
- Python
- Prolog
- Shell
- + 1
Rivet
Rivet is a toolkit for validation and analysis of Monte Carlo event generators in particle physics. It provides a library of reusable analysis components and a large collection of published analyses, enabling precise, reproducible comparisons between theory and experimental data.
- Big data
- Collider physics
- Data Analysis
- + 2
- C++
- Gnuplot
- C
- + 2