Software | Research Software Directory

WRFpy

WRFpy is a python application that provides an easy way to set up, run, and monitor Weather Research and Forecasting simulations

Data Simulation
python

Python

4

8

Code supporting the paper: A Bayesian finite-element trained machine learning approach for predicting post-burn contraction

Feed-forward neural network
Machine learning
MATLAB
+ 5

3

7

Code underlying the publication: Forecasting estuarine salt intrusion in the Rhine-Meuse delta using an LSTM model

chloride
Delta
estuary
+ 7

4

7

MATLAB scripts created during the work on "Multi-Δt approach for peak-locking error correction and uncertainty quantification in PIV"

PIV (Particle Image Velocimetry)
Uncertainty Quantification

3

7

Source code of the SWAN model: Free Infragravity Waves in the North Sea

coastal waters
Infragravity waves
inland waters
+ 3

3

7

SWMM_GNN_Repository_Paper_version

SWMM GNN metamodel – Code for paper: Transferable and Data Efficient Metamodeling of Storm Water System Nodal Depths Using Auto-Regressive Graph Neural Networks

GNN
Graph neural networks
Machine learning
+ 5

Other
Python
Jupyter Notebook
+ 2

4

7

Bacting

Bacting is an open-source platform for chemo- and bioinformatics based on Bioclipse that defines a number of common domain objects and wraps common functionality, providing a toolkit independent, scriptable solution to handle data from the life sciences.

bioinformatics
Cheminformatics

Java
TeX

1

7

ece2cmor3

Process EC-Earth output to publish for CMIP6

Big data
High performance computing
Optimized data handling

Shell
Python

2

7

jaspProcess

A JASP implementation of the PROCESS macro for SPSS

Data Analysis
Statistics
Visualization

R
QML

2

7

MultilayerGraphs.jl

A Julia package for the creation, manipulation and analysis of the structure, dynamics and functions of multilayer graphs.

Graphs
Graph Theory
Hierarchical Graphs
+ 10

Julia

2

7

nlppln

A flexible solution to build text mining workflows that allows you to quickly combine Natural Language Processing tools from different sources.

Text analysis & natural language processing

Python
Common Workflow Language
Dockerfile

2

7

orbitN

Symplectic integrator for near-Keplerian planetary systems

astronomical solution
astronomy
N-body
+ 2

1

7

Turing Data Safe Haven

Data Safe Haven is an open-source framework for creating Trusted Research Environments (TREs) to analyse sensitive data. It provides a set of scripts that will allow you to deploy, administer and use your own TRE on Microsoft Azure cloud.

Cloud
cloud storage
Infrastructure as code
+ 3

Python
Shell
Jinja
+ 3

29

7

xtas

the eXtensible Text Analysis Suite

Text analysis & natural language processing

Python
Shell
Java

2

7

Blade Element Momentum Theory Code for Positive and Negative Thrust Propellers

BEM
BEMT
Blade Element Momentum Theory
+ 2

1

6

Code supporting the paper: Sensitivity and feasibility of a one-dimensional morphoelastic model for post-burn contraction

Burns
Feasibility
MATLAB
+ 4

3

6

Data/software underlying the publication: Robust quantum-network memory based on spin qubits in isotopically engineered diamond

distributed quantum computation
entanglement distillation

12

6

Framework for the publication: MirrorLabs – creating similar learning environments for students all over Europe for human-robot coproduction

Augmented Reality
Interactive Visualization
robotics
+ 2

2

6

Learning_on_SCs

Code underlying: Hodge-Aware Convolutional Learning on Simplicial Complexes

Hodge theorem
neural networks
simplicial complexes

Other
Python
Markdown
+ 1

1

6

Microscopy data, code and analysis underlying the publication "Optical STEM detection for scanning electron microscopy"

Electron Detection
Instrumentation Development
Scanning Electron Microscopy
+ 2

Other
Markdown
Jupyter Notebook
+ 2

6

Source, documentation, tests: MACE: Automated Assessment of Stereochemistry of Transition Metal Complexes and its Applications in Computational Catalysis

automation
chemoinformatics
Computational Chemistry
+ 6

Chemical XYZ
Other
Jupyter Notebook
+ 5

2

6

eEcology Annotation Tool

Visualize and annotate GPS measurements of bird movements.

Inter-operability & linked data
Visualization

HTML
Python
Mako
+ 5

1

6

PSSMGen

Generates consistent PSSM and PDB files for protein-protein complexes

Big data
High performance computing
Optimized data handling

Python
Makefile

2

6

PuReGoMe

Analyzes social media messages for polarity and stance towards governmental COVID-19 measures

Machine learning
Social media

Jupyter Notebook
Python
Shell

3

6

SPOT

SPOT is an interactive visualization tool for multi-dimensional data. It allows quick analysis of complex datasets and easy identification of correlations between variables.

Big data
Visualization

JavaScript
Pug
Stylus
+ 2

7

6

Reference evapotranspiration (FAO-56)

Calculate a daily value of reference evapotranspiration, useful for vegetation (incl. crop) models. The module code is based on FAO-56 Penman-Monteith method.

1

5

3D Slicer

3D Slicer is a free, open source software for visualization, processing, segmentation, registration, and analysis of medical, biomedical, and other 3D images and meshes; and planning and navigating image-guided procedures.

3D
3DSlicer
Extension
+ 7

C++
Python
CMake
+ 5

4

5

Code complementing the paper "Feasibility Analysis of a Self-Reinforcing Electroadhesive Rotational Clutch"

Clutch
Electroadhesion
self-reinforcement
+ 2

3

5

Code supporting the paper: Sensitivity of a two-dimensional biomorphoelastic model for post-burn contraction

burn
cell proliferation
MATLAB
+ 4

4

5

Code supporting the paper: Stability of a one-dimensional morphoelastic model for post-burn contraction

Burns
MATLAB
Morphoelasticity
+ 3

3

5

Hanson's Model in Frequency Domain - Tonal Noise of Rotors in Uniform Inflow

Hanson's model
Propeller Aeroacoustics
Propeller Noise
+ 1

1

5

Software supporting the publication: Background Electromagnetic Noise Received via Ionospheric Propagation in a Remote Rural Location in Spain (set 1)

ambient noise
electromagnetic noise
ionosphere
+ 3

4

5

eEecology Classification

Automatic classification of accelerometer data using a supervised learning approach.

Machine learning

Java
JavaScript
HTML
+ 3

1

5

IncompressibleNavierStokes

This package implements energy-conserving solvers for the incompressible Navier-Stokes equations on a staggered Cartesian grid. It is based on the Matlab package INS2D/INS3D. The simulations can be run on the single/multithreaded CPUs or Nvidia GPUs.

HPC
Scientific machine learning

Julia

5

MagnumPI - Potential Integrator

A package for the calculation of scattering angles and cross sections.

Inter-operability & linked data
Visualization

C++
Mathematica
Python
+ 2

6

5

mexca

Capture emotion expressions from video, audio, and text with a single pipeline.

Audio processing
Image processing
Machine learning
+ 1

Python
Dockerfile
Shell

5

PIQMIe

A web tool for mass spectrometry-based proteomics data analyses

Data Analysis
mass spectrometry
Optimized data handling
+ 2

HTML
JavaScript
Python
+ 3

1

5

sv-channels

Genome-wide detection of structural variants using deep learning

Machine learning

Python
Jupyter Notebook
R
+ 1

4

5

TIMP

TIMP is an R package for fitting superposition models that implements the partitioned variable projection algorithm. The package has been extensively applied to modeling spectroscopy and Fluorescence Lifetime Imaging Microscopy (FLIM) datasets. It serves as the backend for the Glotaran software.

global analysis
target analysis
time-resolved spectroscopy

R
C

2

5

Get fertility rates (females, 5-year cohort)

This NetLogo code snippet provides fertility estimates of females for use in demographic simulations. The figures used are based on two different sources, and will be assigned per 5-year age cohort.

1

4

Livestock demography

This submodel simulates livestock herd demography and slaughter effects. Initially part of the ROMFARMS model for animal husbandry on the Dutch Roman frontier, it focused on cattle, sheep, and horses. However, the code is adaptable for various animals, regions, and historical periods.

2

4

Artefact of: JavaBIP meets VerCors: Towards the Safety of Concurrent Software Systems in Java

concurrent systems
Deductive verification
formal methods
+ 3

5

4

Code and data underlying the publication: Symmetrization of 2D Polygonal Shapes Using Mixed-Integer Programming

Design
Digitalization
Shape optimization
+ 1

C
C++
Other
+ 3

3

4

Code and test data set underlying the publication: Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with a multiplexed magnetic tweezers

Dwell Time Analysis
magnetic tweezers
RdRP activity
+ 1

3

4

Code for the paper "Synergizing cycling and transit: Strategic placement of cycling infrastructure to enhance job accessibility"

code
cycling infrastructure
job accessibility

1

4

Code to produce the results of the publication: “Disentangling acceleration-, velocity- and duration-dependency of the short- and medium-latency stretch reflexes in the ankle plantarflexors”

Group Ia afferents
M1-M2 stretch reflex
Motoneuron pool
+ 1

1

4

Code to produce the results of the publication: “Neurophysiological Validation of Simultaneous Intrinsic and Reflexive Joint Impedance Estimates”

Electromyography
Joint resistance
Parallel-Cascade model
+ 2

1

4

MATLAB script and COMSOL models of the article "An efficient multiscale method for subwavelength transient analysis of acoustic metamaterials"

Equivalent fluid model
Homogenisation
Locally resonant acoustic metamaterials
+ 1

Other
Matlab
Markdown

4

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