Software | Research Software Directory

iScore

A framework and predictor based on support vector machine and random walk graph kernel for scoring protein-protein interfaces.

Big data
Machine learning
Protein-Protein Interaction

C++
Cuda
Makefile
+ 1

4

92

Code for Tiresias: Predicting Security Events Through Deep Learning

Event Analysis
Security

Markdown
Other
Python

1

90

DeepCASE

Code for DeepCASE: Semi-Supervised Contextual Analysis of Security Events

Event Analysis
Security

JSON
large-text-file
Markdown
+ 2

10

90

DeepLog

Code for DeepLog: Anomaly detection and diagnosis from system logs through deep learning

Event Analysis
Security

large-text-file
Markdown
Other
+ 1

1

90

Tillage-controlled Runoff Pattern model (TCRP) v1.1; a GIS model to adjust runoff patterns for tillage induced roughness in agricultural catchments

DEM
erosion pattern
modelling
+ 2

2

89

grlc

Builds a web API from SPARQL queries hosted on GitHub to accessing triple store data.

garlic
Inter-operability & linked data

CSS
Dockerfile
HTML
+ 4

3

89

4CAT Capture & Analysis Toolkit

The 4CAT Capture and Analysis Toolkit provides modular data capture & analysis for a variety of social media platforms. Its goal is to make the capture and analysis of data from these platforms accessible to people through a web interface, without requiring any programming or web scraping skills.

Big data
python
Social media
+ 1

CSS
Dockerfile
HTML
+ 4

3

86

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

distributed quantum computation
entanglement distillation

12

79

openAVEM (Open Aviation Emissions)

aircraft emissions
air pollution
aviation
+ 1

4

78

Twiqs

Software behind the web server twiqs.nl, which has provided free access to statistics about Dutch tweets since 2010

Big data
Text analysis & natural language processing
Visualization

HTML
Java
JavaScript
+ 3

1

75

CODaN

CODaN: Common Objects Day and Night, an image classification dataset.

color invariants
computer vision
day-night
+ 2

Markdown
Other
Python

4

73

Code underlying the publication: Zero-Shot Day-Night Domain Adaptation with a Physics Prior

color invariant convolution
color invariants
data efficient deep learning

Markdown
Other
Python

4

73

Gaussian FLORIDyn, Matlab implementation belonging to the paper: The revised FLORIDyn model: Implementation of heterogeneous flow and the Gaussian wake

FLOw Redirection and Induction Dynamics (FLORIDyn)
systems and control theory
wind currents
+ 1

1

73

NPLinker Web Application

This is the NPLinker web application, developed with Plotly Dash. It enables interactive visualization of NPLinker predictions and is designed to be run locally or in a containerized environment.

Data mining
Genome
Metabolome
+ 2

CSS
Dockerfile
Mustache
+ 1

13

73

powerfit

Rigid body fitting of atomic strucures in cryo-electron microscopy density maps

cryo-electron microscopy
macromolecular structure
map fitting

C
Cuda
Dockerfile
+ 3

6

72

dtscalibration

A Python package to load raw Distributed Temperature Sensing (DTS) files, perform a calibration, and plot the result.

calibration
DTS
fiber optic
+ 1

Jupyter Notebook
Python

2

71

PanTools

PanTools is a pangenomic toolkit for comparative analysis of large number of genomes. It is developed in the Bioinformatics Group of Wageningen University, the Netherlands. Please cite the relevant publication(s) from the list of publications if you use PanTools in your research.

Data Analysis
Gene classification
pangenomics

Java
Python
Roff Manpage
+ 1

3

70

Code to paper: Review of image segmentation techniques for the layup defect detection in the Automated Fiber Placement process

dlr
fiber placement
inspection

2

69

KG-tool: Python package for accessing the Chemical Engineering Knowledge Graph (ChemEngKG)

Artificial Intelligence
chemical engineering
chemical process development
+ 2

4

65

MPI.jl

MPI wrappers for Julia

HPC
Julia Package
MPI

Julia
Python
Shell

4

65

QMflows

Construction and efficient execution of computational chemistry workflows.

Multi-scale & multi model simulations
Workflow technologies

Jupyter Notebook
Python
Shell

3

64

Vantage6

An open-source platform for supporting the development of federated learning projects

federated learning
healthcare
privacy preserving analysis
+ 1

Dockerfile
Go Template
HTML
+ 7

11

64

GSA report

GSAreport is an application to easily generate reports that describe the global sensitivities of your input parameters as best as possible. You can use the reporting application to inspect which features are important for a given real world function / simulator or model.

Explainable AI
Machine learning
python
+ 1

CSS
HTML
Jupyter Notebook
+ 1

2

63

open-DARTS

Open Delft Advanced Research Terra Simulator is a simulation framework for forward and inverse modelling and uncertainty quantification of multi-physics (thermo-hydro-mechanical-chemical) processes in geo-engineering applications as geothermal, CO2 sequestration, water pumping, and hydrogen storage.

energy transition
environmental modelling
geothermal
+ 3

C++
CMake
Cuda
+ 2

13

63

mcfly

Helps you find a suitable neural network configuration for deep learning on time series.

auto-ml
deep learning
Machine learning
+ 1

CSS
HTML
JavaScript
+ 1

12

61

Code and secondary data of analysis on pesticide transport during rainfall runoff events

erosion
particulate phase
Pesticides
+ 3

1

58

GreenspacePerception (Github) code repository: analysis underlying the publication "How well do NDVI and OpenStreetMap data capture people’s visual perceptions of urban greenspace?"

Crowdsourcing
NDVI
OpenStreetMap
+ 2

4

57

Software underlying the publication: Modelling communication-enabled traffic interactions

Human driver model
Interaction Models

1

57

Glotaran

Glotaran: A Java-Based Graphical User Interface for the R Package TIMP

global analysis
target analysis
time-resolved spectroscopy

HTML
Java

2

56

hyphe

A research-driven web-crawler aimed at building, curating and categorizing a corpus of web actors and the network graph of hyperlinks connecting them.

crawling
Networks
python
+ 1

CSS
Dockerfile
HTML
+ 3

4

56

Code underlying the publication: Integrity-based Explanations for Fostering Appropriate Trust in AI Agents

AI agent
appropriate trust
explanations
+ 1

4

51

MATLAB model of multiscale model for CO2 electrolysis

CO2 electrolysis
Multiscale model
Techno-economic analysis

5

49

[MegAWES] Matlab/Simulink model underlying the publication: Six Degrees-of-Freedom Simulation Model for Multi-Megawatt Airborne Wind Energy Systems

6 DoF rigid-body kite
Airborne Wind Energy (AWE)
Airborne wind energy power performance
+ 3

1

49

DUECA/DUSIME Middleware for Implementing Distributed Real-Time Simulations

Middleware framework
publish-subscribe communication
real-time simulation

4

48

fsbrain

The fsbrain package provides visualization of neuroimaging data in R. The plots produced by fsbrain can be integrated into R notebooks or written to high-quality bitmap image files, ready for publication.

Computational Neuroscience
Visualization

Dockerfile
R
Shell

1

48

Netherlands eScience Center Python Template

Generic template for Python packages, so you can spend less time setting up and configuring, and comply with the Netherlands eScience Center Software Development Guide from the start.

software development tools
software sustainability
template

Jinja
Python
Shell

23

48

Via Appia Visualization

A web application which visualizes the point clouds and additional data gathered in the Via Appia project with WebGL.

Visualization

CSS
HTML
JavaScript

8

48

LitStudy

Explore scientific literature using Python from the comfort of a Jupyter notebook

Inter-operability & linked data
Text analysis & natural language processing
Visualization

HTML
Python

7

46

InstaNovo

InstaNovo is a transformer neural network with the ability to translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s). InstaNovo+ is a multinomial diffusion model that further improves performance by iterative refinement of predicted sequences.

deep learning
Machine learning
mass spectrometry
+ 1

Makefile
Python

5

45

IUI2025_ConvXAI

User Interaction Dataset associated with IUI 2025 paper "Is Conversational XAI All You Need? Human-AI Decision Making With a Conversational XAI Assistant"

Appropriate Reliance
Conversational XAI Interface
Human-AI Decision Making

Jupyter Notebook
Markdown
Other
+ 1

3

44

compareMS2

compareMS2 is a tool for direct comparison of tandem mass spectrometry (MS/MS) datasets, typically from LC-MS/MS, in proteomics or metabolomics, defining a distance as a function of the share of similar spectra. Applications span biomedicine, phylogenetics, forensics, ecology and food science.

Ecology
Food Science
Forensics
+ 4

CSS
Go
HTML
+ 3

4

44

CorticalSim

Fast simulation of plant cortical microtubules.

C++
Meson
Python
+ 1

7

44

3D-e-Chem Virtual Machine

A freely available Virtual Machine encompassing tools, databases, and workflows for cheminformaticians, including new resources developed for ligand binding site comparisons and GPCR research.

Inter-operability & linked data
Workflow technologies

Shell
Smarty

2

42

KLIFS KNIME nodes

If you are working in the KNIME worflow platform and need data about your favorite kinase receptor ligand interaction, then these nodes are for you.

Workflow technologies

Java
Scala
Shell

2

42

Data and software supporting the publication "Telecom-band quantum interference of frequency-converted photons from remote detuned NV centers"

Quantum Frequency Conversion
quantum networks
Telecom wavelength
+ 1

4

41

simplicial_convolutions

Code underlying: Simplicial Convolutional Filters

convolution
neural networks
simplicial complex

large-text-file
Markdown
Matlab
+ 1

1

41

Supplementary materials for the article: Towards future pedestrian-vehicle interactions: Introducing theoretically-supported AR prototypes.

Augmented Reality
Automated vehicles
autonomous vehicles
+ 3

5

41

Supplementary Materials: When is variable importance estimation in species distribution modelling affected by spatial correlation?

empirical modelling
niche models
raster
+ 8

4

41