Software | Research Software Directory

PoreSpy

PoreSpy is a collection of image analysis tools used to extract information from 3D images of porous materials (typically obtained from X-ray tomography).

image analysis
porous media
tomography

(Batchfile)
(Python)
(Shell)

2

1

qumia-train-scripts

Scripts and files related to ML training for the QUMIA project

Machine learning
Neuromuscular
ultrasound imaging

("Jupyter Notebook")
(Python)
(Shell)

3

1

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.

("OpenEdge ABL")
(Prolog)
(Python)
+ 1

2

1

ROBIST

Robust Optimization by Iterative Scenario Sampling and Statistical Testing

optimization
python

(Python)

2

1

Rocket

Rocket is a framework for efficient execution of all-pair applications on heterogeneous platforms.

Big data
GPU
High performance computing
+ 1

(C++)
(Cuda)
(Java)
+ 2

1

rocrate-action-recorder

Python package to record calls of Python CLI commands into a Research Object Crate (RO-Crate). Supports RO-Crate 1.1 specification. Specifically the Process Run Crate profile.

Inter-operability & linked data
Workflow technologies

(Python)

1

Rucio deployment for KM3NeT

This repository contains the Rucio deployment for KM3NeT. It can be used as an example of how to deploy Rucio.

Big data
High performance computing

3

1

SalientDescriptor-matlab

If you need to automate your image matching tasks for the purposes of object detection or photo-identification in an easy way, the SalientDescriptor-matlab is right for you

Image processing

(HTML)
(MATLAB)

1

SARXarray

An Xarray extension to process coregistered Single Look Complex (SLC) image stacks acquired by Synthetic Aperture Radar (SAR).

Dask
InSAR
Interferometry
+ 6

(Python)
(ReScript)
(TeX)

4

1

scriptcwl

Create CWL workflows by writing a simple Python script.

CWL
Workflow technologies

("Common Workflow Language")
(Python)

8

1

self-hosted runners

Collection of resources to set up GitHub runners on self-hosted infrastructure

High performance computing

(Dockerfile)
(Shell)

5

1

SimVascular

The only fully open source software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis.

Cardiovascular
Fluid mechanics
Medical image computing
+ 1

(Batchfile)
(C)
(C++)
+ 9

4

1

sirup

Sirup is an open-source Python package that makes it easy to connect to, and rotate across, VPN servers provided by services such as ProtonVPN and Surfshark.

ip-rotation
openvpn
python
+ 1

(Python)
(Shell)

1

SlicerIGT

Software toolkit for rapid development of image-guided therapy systems - for minimally invasive medical procedures, where operators rely on computer-generated images rather than direct sight of the target organs.

3D Slicer
deep learning
Medical image computing
+ 2

(C++)
(CMake)
(Python)

2

1

snakemake-wrf

A snakemake workflow to run WRF, including pre- and postprocessing. See our blog post for a detailed description.

geospatial
High performance computing
python
+ 1

("Jupyter Notebook")
(Python)
(Shell)

2

1

TaxoTagger

DNA barcode identification, powered by semantic searching.

Fungi
Machine learning
semantic search
+ 3

(Makefile)
(Mustache)
(Python)

1

Umple

Umple allows generation of code in Java, PHP and other languages from a textual representation of UML state machines, associations and other modeling constructs, thus saving coding effort

Code Generation
Software Modeling
State Machines
+ 1

(Batchfile)
(C++)
(CSS)
+ 19

14

1

ValidSense

The ValidSense toolbox aims to assess the agreement between two quantitative methods using the Limits of Agreement analysis, aka the Bland-Altman analysis. Four existing variants are available. Moreover, a Longitudinal analysis is developed to assess agreement over time.

Agreement Analysis
Bland-Altman
Limits of Agreement
+ 1

(Python)

4

1

WAM2layers

WAM2layers is an atmospheric moisture-tracking model that can be used to determine where precipitation originally evaporated (backtracking), or where evaporated moisture eventually ends up (forward tracking).

atmospheric rivers
ERA5
hydrological cycle
+ 4

("Jupyter Notebook")
(Python)
(Shell)

4

1

Workflomics

Web platform for workflow exploration and benchmarking in bioinformatics

Inter-operability & linked data
Workflow technologies

(CSS)
(HTML)
(JavaScript)
+ 1

7

1

WRF-runner

Simple shell script to run a complete WPS/WRF experiment in one go

climate
Forecasting
workflow
+ 1

(Shell)

2

1

Angle-and-step random walk

An Python implementation of random walk in 2D space based on agent angle orientation and step distance. It defines an agent class `Walker` capable of random walk movement based on random angle and movement step distance in a continuous 2D space.

1

0

Random walk in data frames

Collection of methods for producing random walks in two-dimensional space outputting position coordinates in data frames, including alternatives for grid and non-grid space. In R, it uses tidyverse "tibble" to construct the data frames that store trajectories.

2

0

Resource exploitation procedure

This module takes an agent and lets it decide which resources to target and exploit. The agent moves to the patch to be harvested, takes the resources and returns home

1

0

Absorption Coefficient Estimator using Domain Adaptation

Code underlying the research project: Extracting absorption coefficients from a room impulse response using a convolutional neural network with domain adaptation

Absorption Coefficient
domain adaptation
Machine learning
+ 3

(Markdown)
(Matlab)
(Other)
+ 1

1

0

abstraction-mpc-integration

Code for publication: Temporal Logic Control of Nonlinear Stochastic Systems with Online Performance Optimization

Abstraction
formal methods
Hybrid Systems
+ 3

(CSS)
(HTML)
(JavaScript)
+ 4

5

0

ACDC-OpFlow

ACDC-OpFlow, Unified, Cross-Language Framework for AC/DC Optimal Power Flow Solutions

AC/DC power systems
Optimal Power Flow
power electronic converters

4

0

A demand management and frequency settings model for complying to the COVID-19 capacity limits in public transport operations

COVID-19
demand management
frequency settings
+ 3

1

0

AeoLiS v2.1.0

advection
aeolian sediment transport
coastal dunes
+ 5

9

0

Agent-based model software written for the master thesis Scaling Up, Staying Secure

Agent based modelling and simulation (ABMS)
CYBER SECURITY
Distributed energy resources (DER)
+ 2

1

0

A high spatial resolution Extended Spring Indices database over American and European regions

Citizen Science
Climate change
Cloud computing
+ 4

(Markdown)
(Other)
(Python)

2

0

AircraftDuctedFanOptimisation

The Unified Ducted Fan Code and Ducted Fan Optimisation Framework

Aircraft
Aircraft performance
Conceptual aircraft design
+ 7

(Markdown)
(Other)
(Python)

1

0

Air Traffic Control Reinforcement Learning Environment

Air Traffic Control (ATC)
Air traffic management (ATM)
Reinforcement Learning (RL)

4

0

A model for modifying the public transport service patterns to account for the imposed COVID-19 capacity

capacity
coronavirus
COVID-19
+ 7

1

0

AmpliDiff

Code underlying the publication: "AmpliDiff: An Optimized Amplicon Sequencing Approach to Estimating Lineage Abundances in Viral Metagenomes"

Abundance Estimation
Amplicon Sequencing
Primer Design
+ 1

(C)
(Markdown)
(Other)
+ 3

3

0

ANNESI: An open-source artificial neural network for estuarine salt intrusion

estuary
Neural Network
salt intrusion

1

0

Application of SDDTMPC to control a unicycle

MPC
nonlinear control
robotics
+ 2

(Markdown)
(Matlab)

1

0

ApPlyWood: a calculation tool supporting the design of plywood-based seismic retrofitting interventions on existing timber floors

Architectural conservation
Design tools
Earthquake engineering
+ 4

1

0

APS

APS: Asses Pedestrian model Speed framework

Computational Complexity
Model assessment framework
Pedestrian models
+ 1

(JSON)
(Markdown)
(Other)
+ 1

1

0

Argon Laser-Plasma Thruster - Design and Test of a Laboratory Model - Processing and Analysis Code

argon
laser
laser-sustained plasma
+ 4

(JSON)
("Jupyter Notebook")
(Markdown)
+ 5

1

0

Artefact for doctoral thesis "Verifying Optimised Parallel Code"

Deductive verification
formal methods
GPU
+ 2

(C)
(C++)
(Markdown)
+ 4

1

0

Artifact for paper (Alpinist: an Annotation-Aware GPU Program Optimizer)

Annotation-aware
Deductive verification
GPU
+ 2

4

0

Artifact for the paper "A Formally Verified IEEE 754 Floating-Point Implementation of Interval Iteration for MDPs"

Correct-by-construction
Floating-point
IEEE 754
+ 6

(C)
(C++)
(JSON)
+ 5

5

0

Artifact for the paper "Efficient Formally Verified Maximal End Component Decomposition for MDPs"

Correct-by-construction
Interactive Theorem Proving
Maximal End Components
+ 3

(C)
(C++)
(JSON)
+ 6

3

0

Artifact of Knor: reactive synthesis using Oink

binary decision diagrams
parity games
reactive synthesis

(Automake)
(C)
(C++)
+ 15

1

0

Artifact to the paper "A Fast and Verified Probabilistic Model Checking Pipeline for Minimal Reachability Probabilities"

Correct-by-construction
Interactive Theorem Proving
Markov decision process
+ 1

(C)
(C++)
(JSON)
+ 4

1

0

Assets for JOAN: a framework for human-automated vehicle interaction experiments in a virtual reality driving simulator

Carla simulator
Driving simulation
JOAN simulator
+ 1

5

0

ATHENS

ATHENS: Aerodynamic Tracer for High-altitude Environment Numerical Simulations

Direct Simulation Monte Carlo (DSMC)
free molecular flow
gas-surface interaction
+ 2

(C)
(C++)
(Markdown)
+ 3

1

0