Software | Research Software Directory

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

5

ColorIce: Automated in-plane ice thin section analysis tool

birefringence
crossed-polarization
grain boundary
+ 5

2

5

Dataset of human gait in a domestic setup collected with an LFMCW MIMO radar

doppler signature
fmcw radar
gait
+ 4

4

5

Inductive 3D printer XY calibration GUI

3D printer
calibration
FDM
+ 8

3

5

learningcurvefitting

Code supporting the publication: Learning Learning Curves

expected error
extrapolation
Interpolation
+ 2

(Markdown)
(Other)
(Python)

4

5

Matlab scripts and MuseScore scripts accompanying the book "The Perceptual Structure of Sound"

sound design

1

5

NetLogo model: "Agent-Based Simulation of Short-Term Peer-to-Peer Rentals: Evidence from the Amsterdam Housing Market"

agent-based modelling
Airbnb
Amsterdam
+ 4

2

5

SNAPWF

Code underlying the publication: Automated Python workflow for generating Sentinel-1 PSI and SBAS interferometric stacks using SNAP on Geospatial Computing Platform

InSAR
Interferometric Stacks
Open-Source Tools
+ 2

("Jupyter Notebook")
(Markdown)
(Python)
+ 1

7

5

Source code for INCS (Iterative Nonlinear Contrast Source)

INCS
medical ultrasound
microbubbles
+ 1

(Automake)
(C)
(Fortran)
+ 5

2

5

Summation of currents electromagnetic solver

Coil
FEM
Inductive
+ 6

3

5

Task-aware-connectivity-learning-for-incoming-nodes-over-growing-graphs

Code underlying the publication: Task-aware-connectivity-learning-for-incoming-nodes-over-growing-graphs

expanding graph
graph signal processing
incoming nodes
+ 2

(Matlab)

1

5

eEecology Classification

Automatic classification of accelerometer data using a supervised learning approach.

Machine learning

(Batchfile)
(CSS)
(HTML)
+ 3

1

5

MagnumPI - Potential Integrator

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

Inter-operability & linked data
Visualization

(C++)
(CMake)
(M4Sugar)
+ 1

6

5

mexca

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

Audio processing
Image processing
Machine learning
+ 1

(Dockerfile)
(Python)
(Shell)

5

nanomesh

Python workflow tool for generating meshes from 2D and 3D microscopy image data

Image processing
Visualization
Workflow technologies

("Jupyter Notebook")
(PowerShell)
(Python)
+ 1

3

5

PerfectFit

This is a virtual coach system that coaches users into being more physically active and stop smoking.

Big data
health

(Gherkin)
(JavaScript)
(Shell)

5

PIQMIe

A web tool for mass spectrometry-based proteomics data analyses

Data Analysis
mass spectrometry
Optimized data handling
+ 2

(Dockerfile)
(HTML)
(JavaScript)
+ 3

1

5

SedTRAILS

SedTRAILS is a Lagrangian particle-tracking model for simulating and visualizing coastal sediment pathways and connectivity. Initial public release forthcoming ~February 2026.

Coastal Engineering
coastal processes
connectivity
+ 5

(Python)

2

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

(C)
(R)

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 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 publication: Parametric excitation and friction modulation for a forced 2-dof system

effective friction
Friction-induced oscillations
Negative damping
+ 2

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

Code underlying the publication: "Self-Supervised PPG Representation Learning Shows High Inter-Subject Variability"

Autoencoder
Human Activity Recognition
Inter-Subject Variability
+ 3

(JSON)
(Markdown)
(Other)
+ 1

3

4

Data and code underlying Chapter 4 of the PhD thesis "Advanced Magnetocaloric Regenerators for Heat Pump Applications"

active magnetocaloric regenerator
layered AMR
magnetocaloric heat pump
+ 5

(Other)
(Python)

4

endogenous-macrodynamics-in-algorithmic-recourse

Software and data underlying the publication: Endogenous Macrodynamics in Algorithmic Recourse

Algorithmic Recourse
Counterfactual Explanations
Dynamic Systems
+ 1

(CSS)
(HTML)
(JavaScript)
+ 8

3

4

mason_constitutive_model

MASON (Masonry Advanced Softening cONtact) source code

cyclicity
distinct element method
explicit integration scheme
+ 3

(C)
(C++)
(Markdown)
+ 1

1

4

Script underlying the paper "On Robustly Convergent and Efficient Iterative Methods for Anisotropic Radiative Transfer"

acceleration
anisotropic
preconditioning
+ 3

3

4

AstronomicAL

An interactive dashboard for visualisation, integration and classification of data using Active Learning.

Active Learning
Classification
Data Analysis
+ 11

(Python)
(TeX)

1

4

cffconvert

Command line tool to convert CITATION.cff files to various formats used by reference managers such as Zotero and JabRef.

(Dockerfile)
(HTML)
(Python)
+ 1

5

4

cffinit

A web form to initialize CITATION.cff files which you can use to include citation information into your software repository.

Software Citation

(CSS)
(HTML)
(JavaScript)
+ 3

7

4

eAstroViz

This tool can convert and visualize radio astronomy measurement sets, as well as most LOFAR intermediate data products. It also performs RFI mitigation.

LOFAR
radio astronomy
RFI

(C)
(C++)
(Cuda)
+ 3

1

4

evidence

doc2vec-based assisted close reading with support for abstract concept-based search and context-based search

Text analysis & natural language processing

(CSS)
(Dockerfile)
(Go)
+ 5

9

4

howfairis

Command line tool to analyze a git repository's compliance with the fair-software.eu recommendations.

(Dockerfile)
(HTML)
(Python)
+ 1

7

4

LUE

LUE is software for storing and manipulating large amounts of information for large numbers of objects. The software is useful, and currently mainly used, in the context of environmental modelling of biological and physical systems, represented by agents and fields.

Agent-based modeling
environmental modelling
field based modelling
+ 6

(Batchfile)
(C)
(C++)
+ 6

3

4

Noodles

Task-based parallel programming model in Python that offers the same intuitive interface when running complex workflows on your laptop or on large computer clusters.

High performance computing
Workflow technologies

(HTML)
("Jupyter Notebook")
(Lua)
+ 2

9

4

Hercules

Retrieve recent tweets from certain users and classify them with machine learning

Machine learning
Text analysis & natural language processing

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

1

4

PowerSensor3

PowerSensor is a low-cost, custom-built device that measures the instantaneous power consumption of GPUs and other devices at a high time resolution.

GPU
High performance computing

(C)
(C++)
(CMake)
+ 3

6

4

WEARDA

WEARDA: recording wearable sensor data for human activity monitoring.

embedded software
GPS
Human activity monitoring
+ 4

(C)
(TeX)

2

4

Xenon gRPC server

Run applications remotely via a gRPC interface.

High performance computing

(Java)

3

4

Network structures

A draft model with some useful code for creating different network structures using the Netlogo NW extension: small-world, preferential attachment, circular, star, wheel, lattice, random, nearest neighbours.

1

3

Artifact for the Paper "Fast Verified SCCs for Probabilistic Model Checking"

Correct-by-construction
Gabow
IRF
+ 13

3

BrazilClim: script to gauge-calibrate the surfaces

Bioclimatic variables
Brazil
land surface temperatures
+ 4

5

3

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

Burns
MATLAB
Morphoelasticity
+ 3

3

Code supporting the publication: BAN: detecting backdoors activated by adversarial neuron noise.

Adversarial Noise
Backdoor Defense
Backdoor Trigger Inversion
+ 3

(JSON)
("Jupyter Notebook")
(Markdown)
+ 3

3

Code to produce the results of the publication: “Examining the Role of Intrinsic and Reflexive Contributions to Ankle Joint Hyper-Resistance Treated with Botulinum Toxin-A”

BoNT-A injections
Instrumented SPAT
Joint resistance
+ 2

1

3