Software | Research Software Directory

DeepCASE

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

Event Analysis
Security

(JSON)
(large-text-file)
(Markdown)
+ 2

10

80

DeepLog

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

Event Analysis
Security

(large-text-file)
(Markdown)
(Other)
+ 1

1

80

Ersilia Model Hub

The Ersilia Model Hub is an open source platform to serve AI/ML models for infectious disease drug discovery.

AI
Chemistry
Drug discovery
+ 1

(Dockerfile)
("Jupyter Notebook")
(Python)

3

77

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

openAVEM (Open Aviation Emissions)

aircraft emissions
air pollution
aviation
+ 1

4

74

powerfit

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

cryo-electron microscopy
macromolecular structure
map fitting

(C)
(Cuda)
(Cython)
+ 2

6

70

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

68

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

65

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

64

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

dlr
fiber placement
inspection

2

63

MPI.jl

MPI wrappers for Julia

HPC
Julia Package
MPI

(Julia)
(Shell)

4

63

QMflows

Construction and efficient execution of computational chemistry workflows.

Multi-scale & multi model simulations
Workflow technologies

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

3

63

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

63

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

Artificial Intelligence
chemical engineering
chemical process development
+ 2

4

59

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

58

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

57

Software underlying the publication: Modelling communication-enabled traffic interactions

Human driver model
Interaction Models

1

56

Glotaran

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

global analysis
target analysis
time-resolved spectroscopy

(HTML)
(Java)

2

56

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

55

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

55

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

53

DUECA/DUSIME Middleware for Implementing Distributed Real-Time Simulations

Middleware framework
publish-subscribe communication
real-time simulation

4

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

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

47

[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

46

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

45

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

erosion
particulate phase
Pesticides
+ 3

1

43

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

CODaN

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

color invariants
computer vision
day-night
+ 2

(Markdown)
(Other)
(Python)

4

42

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

42

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)
(HTML)
(JavaScript)
+ 1

4

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

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

AI agent
appropriate trust
explanations
+ 1

4

41

Research Software Directory

A content management system for research software, which promotes the visibility, reuse, and impact of research software.

FAIR
Research Software Impact
Software Citation

(CSS)
(Dockerfile)
(Go)
+ 9

26

41

KNIME Silicos-it nodes

A node for the KNIME workflow systems that allows you to use the Silicos-it software to filter or align molecules.

Workflow technologies

(Java)

2

40

KNIME node archetype

Want to write your own KNIME node Then use the KNIME node archetype to generate a node skeleton repository with sample code.

Workflow technologies

(Java)

1

40

KNIME GPCRdb nodes

A node for the KNIME workflow systems that allows you to retrieve data about your favorite G protein-coupled receptors from gpcrdb.org.

Workflow technologies

(Java)

2

40

KNIME node for Kripo

A node for the KNIME workflow systems that allows you to compare different binding sites in proteins with each other.

Workflow technologies

(Java)

1

40

KNIME Testflow

Allows you to test KNIME nodes automatically using JUnit.

Workflow technologies

(Java)

1

40

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

40

KNIME Pharmacophore

A plugin for the KNIME workflow system that adds a Pharmacophore data type and nodes to read, write, and align them.

Workflow technologies

(Java)

1

39

KNIME PLANTS

A node for the KNIME workflow system that allows you to use the PLANTS protein-ligand docking algorithm.

Workflow technologies

(Java)
(Mustache)

1

39

KNIME Python node archetype

Want to write your own KNIME node wrapping a Python library. Then use the KNIME Python node archetype to generate a node skeleton repository with sample code

Big data
Workflow technologies

(Java)
(Python)

1

39

KNIME Python wrapper

If you are developing a KNIME node which calls some Python code, then the KNIME Python wrapper can help you.

Workflow technologies

(Java)
(Python)

1

39

BlueObelisk Euclid

A library of numeric, geometric and XML routines

(HTML)
(Java)

1

39

CMLXOM

Java library for working with Chemical Markup Language files.

Chemical Markup Language
Chemistry
XML

(Batchfile)
(HTML)
(Java)
+ 1

2

39

KNIME molecule viewer nodes

A 3D viewer for large molecules for the KNIME workflow system.

Visualization
Workflow technologies

(CSS)
(Java)
(JavaScript)

2

39