Software | Research Software Directory

DeepRank2

DeepRank2 is an open-source deep learning framework for data mining of protein-protein interfaces or single-residue missense variants. This package is an improved and unified version of three previously developed packages: DeepRank, DeepRank-GNN and DeepRank-Mut.

Cancer vaccine
Convolutional Neural Network
Deep Learning Framework
+ 5

Dockerfile
Jupyter Notebook
Python
+ 1

12

26

laserchicken

Toolkit for preprocessing and feature calculation of point clouds created using airborne laser scanning

Big data
Machine learning

Jupyter Notebook
Python

12

26

LinkAhead

Open Source Research Data Management Software

Data
Electronic Lab Notebook
ETL
+ 9

ANTLR
C++
CSS
+ 9

6

26

CIRRUS-HL-campaign-codes---Code-accompanying-dissertation

CIRRUS-HL campaign codes - Codes accompanying dissertation

Airborne measurements
Background aerosol
Backward trajectories
+ 7

Jupyter Notebook
Markdown
Python
+ 1

4

24

Code supporting the publication: Gromit: Benchmarking the performance and scalability of blockchain systems

Benchmarking
Blockchain
Performance
+ 1

JSON
Markdown
Other
+ 3

3

24

PyBanshee, Python-based open source of the MATLAB toolbox BANSHEE.

Bayesian network models
Gaussian copula
Python package

6

24

Visible vapor plumes in a tropical wet forest: R script

forest evaporation
lifting condensation layer
R script
+ 2

4

24

Arena-Crowds

Arena-Crowds is Python scripts for the data analysis to estimate crowd density based on WiFi positioning.

Computer networks
Networks
Network Science

Jupyter Notebook
Python

3

24

Measurements.jl

Error propagation calculator and library for physical measurements. It supports real and complex numbers with uncertainty, arbitrary precision calculations, operations with arrays, and numerical integration.

error propagation
Julia Package
Physics
+ 1

Julia

1

24

CHI2025_Plan-then-Execute_LLMAgent

User Interaction Dataset for CHI 2025 paper "Plan-Then-Execute: An Empirical Study of User Trust and Team Performance When Using LLM Agents As A Daily Assistant."

Daily Assistant
Human-AI Collaboration
large language models
+ 2

CSS
HTML
JavaScript
+ 7

3

23

Cross-Domain Classification of Moral Values - code

Cross-domain
Ethics
Morality
+ 3

Markdown
Other
Python

5

23

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

Jupyter Notebook
Markdown
Other
+ 2

4

23

Code used to generate the data underlying the publication: A monolithic Finite Element formulation for the hydroelastic analysis of Very Large Floating Structures

Finite Element
Fluid-structure interaction
hydroelasticity
+ 3

1

22

PolyR-CNN

Source code for “PolyR-CNN: R-CNN for End-to-End Polygonal Building Outline Extraction”

aerial imagery
building footprint extraction
instance segmentation
+ 4

Markdown
Other
Python
+ 1

3

22

Case Law App

Web application for exploring the citation network of Dutch court decisions.

Text analysis & natural language processing
Visualization

CSS
HTML
JavaScript

4

22

DIANNA

Deep Insight And Neural Network Analysis, DIANNA is the only Explainable AI, XAI library for scientists supporting Open Neural Network Exchange, ONNX - the de facto standard models format.

Explainable AI
Image processing
KD
+ 3

Jupyter Notebook
Python
TeX

12

22

PolarMorphism

PolarMorphism uses results from GWAS of multiple phenotypes to output statistics per SNP that describe its degree of 'sharedness' across the phenotypes of interest and its overall (multivariate) effect size, as well as p-values indicating significance for each statistic.

genomics
GWAS
pleiotropy

R

0

22

SLEPLET

SLEPLET is a Python package for the construction of Slepian wavelets in the spherical and manifold (via meshes) settings.

manifolds
python
slepian functions
+ 2

Python
TeX

1

22

etv_routing_assignment

Code underlying the publication: Dispatching a fleet of electric towing vehicles for aircraft taxiing with conflict avoidance and efficient battery charging

Electric aircraft taxiing
Electric towing vehicles
Partial battery recharging
+ 2

Markdown
Python

1

21

Machine learning-based classification model corresponding to the paper 'Machine learning to improve orientation estimation in sports situations challenging for inertial sensor use'

Inertial Measurement Unit
kinematics
Machine learning
+ 3

1

21

Matlab code for Full Range Adaptive Cruise Control with Integrated Collision Avoidance Strategy

Adaptive Cruise Control
collision avoidance algorithm
Full speed range ACC
+ 2

2

21

Model for the dynamic behaviour in magnetic nanoparticles: scripts and experimental data

Anisotropy
Brownian relaxation
Fokker-Planck equation
+ 5

1

21

Multistage-PINN

Code underlying the publication: Multistage physics informed neural network for solving coupled multiphysics problems in material degradation and fluid dynamics

Asphalt aging
Multiphysics modeling
Multistage learning
+ 2

Jupyter Notebook
Markdown
Other

4

21

qec-util

qec-util, supporting the publication: Neural network decoder for near-term surface-code experiments

python
Quantum Computing
quantum error correction
+ 1

Markdown
Other
Python

3

21

surface-sim

surface-sim, supporting the publication: Neural network decoder for near-term surface-code experiments

python
Quantum Computing
quantum error correction
+ 1

Markdown
Other
Python
+ 2

3

21

Citation File Format

The Citation File Format lets you provide citation metadata for software or datasets in plaintext files that are easy to read by both humans and machines.

FAIR
Inter-operability & linked data

Python

2

21

Foot Progression Angle Estimation

Use a single Accelerometer and Gyroscope on the foot to determine foot progression angle during walking.

FPA
IMU
Single sensor

MATLAB

0

21

Bluesky software: underlying the publication “Distributed Conflict Resolution at High Traffic Densities with Reinforcement Learning”

Air traffic management (ATM)
BlueSky
Conflict detection and resolution
+ 3

1

20

Data and Optimisation model for space heating and committed emissions for the built environment

Carbon lock-in
Committed carbon emissions
Electrification of heating
+ 4

5

20

ReconUS

ReconUS v1.0 - Matlab toolbox for 2D, 3D and multi-probe ultrasound simulation, reconstruction and signal processing.

2d reconstructions
3D reconstruction
Beamforming
+ 4

C++
JSON
Markdown
+ 2

13

20

QTLTableMiner++

Extract gene-trait associations from scientific literature

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

Java
Shell

3

20

Code to incorporate entrapped air pocket dynamics into SWMM (AirSWMM2.0)

Air pocket dynamics
Intermittent water supply
Pipe-filling events
+ 1

C
Markdown
Other

4

19

Code underlying the publication: "PATE: Proximity-Aware Time series anomaly Evaluation"

Anomaly detection
Evaluation Metrics
Precision
+ 2

Markdown
Other
Python
+ 1

3

19

Software related to "Impact of optical aberrations on axial position determination by photometry"

Axial position
Gaussian fitting
Optical aberrations
+ 6

6

19

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

19

StoryTeller

StoryTeller is a web application for visual analysis of textual data which can show you the connections between storylines, participants and other entities in complex humanities data.

Visualization

CSS
HTML
JavaScript

2

19

A Public Ground-Truth Dataset for Handwritten Circuit Diagram Images

CGHD
Circuit Diagram
CircuitGraph
+ 4

JSON
Markdown
Other
+ 2

1

18

Data and Model of Scale Down Simulator for Industrial Syngas Fermentation

Fermentation
Process scale-up
Scale-down
+ 1

5

18

FedvsCent

Code supporting chapter 3 of the PhD thesis: "A comprehensive experimental comparison between federated and centralized learning Open Access"

benchmark
complex models
Distributed data
+ 3

3

18

FAIR Data Station

A web application for creating, validating and managing research metadata using the ISA framework, turning it into FAIR RDF linked data ready for reuse and submission to public repositories.

FAIR
metadata
Metadata Management
+ 1

CSS
HTML
Java
+ 2

1

18

AirSWMMv1.0

Code to incorporate entrapped air behaviour into SWMM (AirSWMM1.0)

Air–water interface interaction
Intermittent water supply
Stormwater management model (SWMM)
+ 1

C
Other

4

17

Software used in the publication "A Non-parametric Bayesian Network for multivariate probabilistic modelling of Weigh-in-Motion System Data”

axle load
Bayesian Networks (BN)
Weigh in motion

3

17

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

automation
chemoinformatics
Computational Chemistry
+ 6

Automake
Chemical XYZ
HTML
+ 5

2

17

citation.js

Citation.js converts formats like BibTeX, Wikidata JSON and BibJSON to CSL-JSON to convert to other formats like APA, Vancouver, RIS and back to BibTeX.

Bibliography
BibTeX
Data Citation
+ 2

Go Template
JavaScript
TeX
+ 1

6

17

FAME_AMR_model

Data and code underlying Chapter 3 of the PhD thesis "Advanced Magnetocaloric Regenerators for Heat Pump Applications"

layered AMR
layering strategies
magnetocaloric heat pump
+ 5

Other
Python

3

16

fltk

FLTK toolkit supporting the publication: Aergia: leveraging heterogeneity in federated learning systems

federated learning
resource heterogeneity
Stragglers
+ 1

Markdown
Other
Python
+ 2

2

16

Models and Optimization Tools for a Novel 3D Printed Capacitive Shear Stress Sensor

Capacitive Modeling
Capacitive Sensor
Mechanical Modeling
+ 2

4

16

mpcrl-for-ramp-metering

Source code for the publication: Reinforcement Learning with Model Predictive Control for Highway Ramp Metering

Model predictive control
Ramp Metering
Reinforcement learning

Markdown
Other
Python
+ 1

1

16