Software | Research Software Directory

Landscape and Land Cover Generation

This algorithm generates landscapes and landcovers in contiguous zones. Users can define different landscape types, landcovers and rules for settlement placement in the setup procedure. It is designed to allow flexible configuration of environmental and social parameters.

1

2

SyGMa

SyGMa provides fast and lightweight predictions of human metabolites to support discovery scientists design better and safer drugs

Workflow technologies

(Python)

2

agda-core

Code underlying the publication: Building a Correct-By-Construction Type Checker for a Dependently Typed Core Language

core language
Dependent Types
type-checking
+ 2

(Haskell)
(Markdown)
(Other)
+ 1

2

Code supporting the paper: High-speed predictions of post-burn contraction using a neural network trained on 2D-finite element simulations

Feedforward neural network
Machine learning
Monte Carlo simulations
+ 2

3

2

Code to produce the results of the publication: “Reducing the Soleus Stretch Reflex with Conditioning: Exploring Game- and Impedance-based Biofeedback”

Electromyography (EMG)
Gamification
operant conditioning
+ 2

1

2

Code underlying the publication: Exploiting Learned Symmetries in Group Equivariant Convolutions

equivariance
equivariant convolutions
separable convolutions

(Markdown)
(Other)
(Python)

2

Code underlying the publication: "Humans disagree with the IoU for measuring object detector localization error."

Human preference
Intersection over Union (IoU)
Object detection

("Jupyter Notebook")
(Markdown)
(Other)

3

2

Data underlying the publication/thesis chapter: Scale Learning in Scale-Equivariant Convolutional Networks

computer vision
Convolutional neural network (CNN)
equivariance
+ 3

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

6

2

Dynamic-Graph-Decomposition

Code underlying the publication: Tensor Graph Decomposition for Temporal Networks

decomposition
dynamic graphs
graph signal processing
+ 1

(Matlab)
(Other)

2

mo-tas

Truck Appointment Systems - Multi-Objective model

Collaboration
Multi-Agent Systems
prioritized planning
+ 2

(Markdown)
(Python)

1

2

OFF framework, code underlying the publication A dynamic open-source model to investigate wake dynamics in response to wind farm flow control strategies

dynamic parametric wake model
surrogate wake model
wind farm flow control
+ 1

(CSS)
(HTML)
(JavaScript)
+ 7

2

oraqle

Oraqle: A Depth-Aware Secure Computation Compiler

arithmetization
compiler
cryptography
+ 1

(C++)
("Jupyter Notebook")
(Markdown)
+ 4

1

2

PETsChallenge

Code underlying: Privacy-Preserving Membership Queries for Federated Anomaly Detection

Anomaly detection
cryptography
elliptic curves
+ 4

(HTML)
(Markdown)
(Other)
+ 4

8

2

SO-CRYSTAL

Code underlying: Shape Optimization of Scintillation Crystals through GEANT4 and NSGAII (SO-CRYSTAL)

Finite-difference time-domain method
Genetic algorithms
Material properties
+ 2

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

1

2

Software for "Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body"

Architectural RNA
Morphological Sorting
NEAT1
+ 6

8

2

stable-dmpc-pwa

Software underlying publication: Distributed model predictive control for piecewise affine systems based on switching ADMM

Alternating direction method of multipliers (ADMM)
distributed model predictive control (MPC)
networked systems
+ 1

(Markdown)
(Matlab)
(Other)
+ 1

1

2

TU/e Microscopic Energy Consumption PRediction tOol 0.1 (TU/e MECPRO 0.1)

Automotive Engineering
Battery Electric Vehicle
Electric Vehicle (EV)
+ 3

4

2

Visible vapor plumes in a tropical wet forest: R script

forest evaporation
lifting condensation layer
R script
+ 2

4

2

adhtools

Use adhtools for analyzing Arabic corpora.

Text analysis & natural language processing
Visualization
Workflow technologies

("Common Workflow Language")
(Java)
("Jupyter Notebook")
+ 1

2

Data Storytelling

Developing consistent, structured ways to present data across projects. Using LLMs and interactive tools to turn results into clear, engaging stories. Applying this approach to selected eScience projects, especially those in the upcoming center-wide evaluation.

application
llm
storytelling
+ 1

(CSS)
(HTML)
(JavaScript)
+ 3

3

2

dhdt

A photohypsometric Python library to estimate glacier elevation change via optical remote sensing imagery

geospatial
Glacier
image
+ 2

(Python)
(TeX)

2

duqtools

Duqtools is a tool for Dynamic Uncertainty Quantification for Tokamak reactor simulations modelling.

fusion-reactor
modelling
python
+ 2

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

2

eEcology Tracker calendar

Calendar overview with daily statistics of GPS-trackers used to track bird movements.

Visualization

(CSS)
(JavaScript)
(Makefile)
+ 5

1

2

ewatercycle

The eWaterCycle package makes it easier to use hydrological models without having intimate knowledge about how to install and run the models.

Inter-operability & linked data
Multi-scale & multi model simulations
Optimized data handling
+ 1

(Dockerfile)
(Python)

10

2

fairtally

Create comprehensive reports on compliance with the fair-software.nl recommendations.

(Dockerfile)
(Python)
(Shell)

4

2

fairworkflows

A python library for constructing, annotating and publishing scientific workflows described using semantic technologies.

("Common Workflow Language")
(HTML)
(Python)
+ 1

5

2

frbcatdb

A database to store a catalog of Fast Radio Bursts and expose them as Virtual Observation Events.

Optimized data handling

(Python)
(Shell)

2

frbcat-web

Provides an easy to-use web frontend to browse and filter the Fast Radio Burst Catalogue.

Optimized data handling
Visualization

(CSS)
(HTML)
(JavaScript)

1

2

GridFormat

Header-only C++ Library for grid file I/O

Grid-based PDE methods
grid file I/O
mesh file I/O
+ 3

(C++)
(CMake)
(Dockerfile)
+ 1

2

MOTrainer

Measurement Operator Trainer for data assimilation purposes.

Data assimilation
High performance computing
Machine learning
+ 2

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

7

2

NEWSGAC platform

Software for running the online platform of the NEWSGAC project for running explainable machine learning models on textual data

Explainable AI
Machine learning
Text analysis & natural language processing

(CSS)
(Dockerfile)
(HTML)
+ 4

3

2

ochre

A tool to clean up text generated by OCR using individual words as well as their context.

Machine learning
Text analysis & natural language processing

("Common Workflow Language")
(HTML)
("Jupyter Notebook")
+ 2

1

2

PathVisio

PathVisio is a free open-source software to curate biological pathway models.

bioinformatics
PathVisio
Systems Biology
+ 2

(Batchfile)
(CSS)
(HTML)
+ 4

9

2

PIDIMEHS library

Showcases a diachronic analysis of the Dutch Royal Library's newspaper archive.

Big data
Real time data analysis
Text analysis & natural language processing
+ 1

2

protein-quest

Python package to search/retrieve/filter proteins and protein structures

(Python)

3

2

pyglotaran

A Python library for Global and Target Analysis of time-resolved spectroscopy data

biophysics
global analysis
glotaran
+ 3

(Nix)
(Python)

4

2

Ricgraph - Research in context graph

With Ricgraph (Research in context graph), you can create a graph from research information that is stored in various source systems. You can explore this graph and discover relations you were not aware of.

graph
graph database
research in context graph
+ 2

(CSS)
(Dockerfile)
(HTML)
+ 5

1

2

sfb-annotator

Annotate field books of natural history collections

Inter-operability & linked data

(CSS)
(Dockerfile)
(Java)
+ 4

3

2

ShiCo

A visualization that shows how the meaning we attach to a given concept shifts over time.

Text analysis & natural language processing
Visualization

(CSS)
(Dockerfile)
(HTML)
+ 3

1

2

tortellini

GitHub action to check whether any licensing issues exist for given software.

(JavaScript)
(TypeScript)

4

2

Pedestrian random walk in NetLogo (ch2.1)

A collection of methods for random walk in NetLogo, including various movement restrictions, biases, and algorithm alternatives.

4

1

Place them on the map

Multiple agent placement in specific geographical location. Set up an input number of agents (turtles) at an input location (cell or patch) in an grid holding the input spatial data (map).

5

1

Epidemic Network

Experimental environment for testing of large array of theoretical conditions for development epidemic event within various quantitative, spatial and connectedness (network structure) aspects.

2

1

Preferential Attachment Network

This NetLogo algorithm simulates network formation using preferential attachment. New nodes are more likely to connect to existing nodes with higher degrees, reflecting a "lottery" system where popular nodes attract more links.

1

Visualising GIS Rasters and Vector Data in NetLogo

This module provides a framework for importing and visualising GIS data in NetLogo. It supports continuous raster data visualised using colour gradients, binary and categorical raster data visualised using discrete colour assignments, and point-based vector data visualised as turtle agents.

1

auction-tas

Truck Appointment Systems - Auction Based

Auction
competition
Scheduling
+ 2

("Jupyter Notebook")
(large-text-file)
(Markdown)
+ 2

1

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

effective friction
Friction-induced oscillations
Negative damping
+ 2

1

Code underlying the publication: "Video BagNet: short temporal receptive fields increase robustness in long-term action recognition"

3D-CNN
Action recognition
BagNet
+ 2

(Markdown)
(Other)
(Python)
+ 1

4

1

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