All software
Orange Hackathon
Orange modules for text processing in the project What Works When for Whom
- (CSS)
- ("Jupyter Notebook")
- (Python)
- + 2
Orthanc
Orthanc is a Belgian, open-source, lightweight DICOM server for healthcare and medical research.
- Software Engineering and Data Infrastructure
OsiriX
Widely used DICOM viewer. Supports 2D, 3D, 4D, 5D viewing.
- Imaging and Image Processing
- (ActionScript)
- (AppleScript)
- (C)
- + 12
Osmium
Start, stop and monitor applications remotely via a HTTP interface.
- High performance computing
- ("API Blueprint")
- (Java)
oTree Demo Experiments
oTree demo experiment: Public goods game
- behavioral research
- oTree
- Workflow technologies
- (HTML)
- (JavaScript)
- (Procfile)
- + 1
oTree Development Environment
A Docker environment for programming against multiple oTree server
- oTree
- (Dockerfile)
- (Makefile)
- (Shell)
oTree Waiting Room
A load balancer for oTree servers.
- oTree
- (HTML)
- (JavaScript)
- (Shell)
Overture Arranger
Data can be messy, let Arranger organize it for you.
- (CSS)
- (HTML)
- (JavaScript)
- + 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
- (Dockerfile)
- (Java)
- (Makefile)
- + 1
Overture Ego
A stateless authorization and user management service.
- Data Indexing
- Elasticsearch Automation
- (Dockerfile)
- (Java)
- (Makefile)
- + 1
Overture Maestro
Organizing your distributed data into one index.
- Data Indexing
- Elasticsearch Automation
- (Dockerfile)
- (Groovy)
- (Java)
- + 1
Overture Score
Transfer data quickly and easily to and from any cloud-based storage system.
- Cancer Genomics
- Cloud Storage & Transfer
- (Dockerfile)
- (Java)
- (Makefile)
- + 1
Overture Song
Quickly and reliably track genome metadata scattered across multiple Cloud storage systems.
- Cancer Genomics
- Metadata Management
- Metadata Validation
- (Batchfile)
- (Dockerfile)
- (Go)
- + 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
- (Dockerfile)
- (Python)
- (Shell)
paradigma
A toolbox to calculate digital biomarkers for wearable sensors in Parkinson's disease.
- (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)
ParticlePhaseSpace
A set of tools for processing and analysing particle phase space files. Designed for use with Monte Carlo simulations, particularly for proton therapy.
- Treatment Planning and dosimetry
- (Batchfile)
- ("Jupyter Notebook")
- (Makefile)
- + 1
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)
PDFtoAria
A Cscript for converting PDF documents into a format that can be imported into Varian ARIA. Automates the process of adding documents to ARIA.
- Software Engineering and Data Infrastructure
- (C#)
PENELOPE
The computer code system penelope (version 2024) performs Monte Carlo simulation of coupled electron-photon transport in arbitrary materials for a wide energy range, from a few hundred eV to about 1 GeV.
- Treatment Planning and dosimetry
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)
PinPath
PinPath is an R package and web-based application for visualizing omics data, such as genomics, transcriptomics, proteomics, and metabolomics, onto pathway diagrams from WikiPathways, KEGG, and custom GPML/KGML files.
- bioinformatics
- KEGG
- Omics
- + 2
- (HTML)
- (R)
PlanCheck
A Varian Eclipse scripting plugin for treatment plan verification. Automates the process of checking a plan against a set of rules.
- Quality Assurance
- (C#)
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
PlanUNC
A program for performing dosimetry calculations in radiotherapy. The program is proprietary and not open source.
- Software Engineering and Data Infrastructure
Plastimatch
Focuses on high-performance volumetric registration, segmentation, and image processing of volumetric medical images. Supports DICOM and DICOM-RT import/export.
- Imaging and Image Processing
- (C)
- (C++)
- (CMake)
- + 2
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)
PlatiPy
Aims to simplify use, visualization, processing, and analysis of medical images. Built on SimpleITK, VTK.
- Imaging and Image Processing
- (CSS)
- (Dockerfile)
- (HTML)
- + 4
PortPy
PortPy, short for Planning and Optimization for Radiation Therapy, is an initiative aimed at creating an open-source Python library for cancer radiotherapy treatment planning optimization.
- Treatment Planning and dosimetry
- (CSS)
- (Python)
prfmodel
A modern Python implementation for population receptive field modelling.
- GPU
- Neuroscience
- optimization
- + 2
- (Python)
PRIMO
Simulates clinical linear accelerators and estimates absorbed dose distributions. Combines GUI with PENELOPE and DPM Monte Carlo codes.
- Treatment Planning and dosimetry
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)
pyanno4RT
pyanno4rt is a Python package for conventional and outcome prediction model-based inverse photon and proton treatment plan optimization, including radiobiological and machine learning (ML) models for tumor control probability (TCP) and normal tissue complication probability (NTCP).
- Treatment Planning and dosimetry
- (Python)
pybacting
Python wrapper around Bacting.
- Biology
- Chemistry
- python
- (Just)
- (Python)
PyBeam-QA
A Python library for performing beam quality assurance tests in radiotherapy. The software is in an early stage of development.
- Quality Assurance
- (HTML)
- (JavaScript)
- (Python)
- + 1
pyCERR
pyCERR provides convenient data structure for imaging metadata and their associations. Utilities are provided to to extract, transform, organize metadata and visualize results of image processing for image and dosimetry features, image processing for AI model training and inference.
- Treatment Planning and dosimetry
- (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)
Pydicer
Eases conversion of Radiotherapy DICOM data to research-ready format (NIfTI). Provides analysis functionality.
- Imaging and Image Processing
- (Makefile)
- (Python)
- (Shell)
pydicom
Reads, modifies, and writes DICOM data in a "pythonic" way. General-purpose framework, does not handle specifics of individual SOP classes.
- Software Engineering and Data Infrastructure
- (Makefile)
- (Python)
- (Shell)
PyELSEPA
Python wrapper for ELSEPA, a numeric code for computing elastic scattering cross-sections for electrons and positrons off neutral atoms.
- (Dockerfile)
- (Python)
pyESAPI
A Python wrapper for the Varian Eclipse Scripting API (ESAPI). Allows scripting of Eclipse functions using Python.
- Software Engineering and Data Infrastructure
- (PowerShell)
- (Python)