Software | Research Software Directory

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

swiftmhc

SwiftMHC is a deep learning algorithm for predicting pMHC structure and binding affinity at the same time.

deep learning
Protein-Protein Interaction
Transformer

Jupyter Notebook
Mask
Python
+ 1

3

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

Barter

A simple algorithm of barter with two interexchangeble goods.

4

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

AnisoVision

Data accompanying the publication: Characterization of the 3D-optical properties of van der Waals materials with deep learning based coherent Fourier scatterometry

anisotropic thin films
coherent Fourier scatterometry
deep learning metrology
+ 2

Jupyter Notebook
Markdown
Other

9

1

auction-tas

Truck Appointment Systems - Auction Based

Auction
competition
Scheduling
+ 2

Jupyter Notebook
large-text-file
Markdown
+ 2

1

Code and dataset supporting the publication "STARVESPAM: Mitigating Spam with Local Reputation in Permissionless Blockchains"

Blockchain
Decentralized reputation
Peer-to-Peer
+ 2

large-text-file
Markdown
Other
+ 2

4

1

CounterfactualExplanations.jl

Software and data underlying the publication: Explaining Black-Box Models through Counterfactuals

Algorithmic Recourse
Counterfactual Explanations
explainable artificial intelligence
+ 1

CSS
JavaScript
JSON
+ 7

3

1

Data and Code for "Same Signal, Different Story: Demystifying Receiver Effects in Wi-Fi Channel State Information"

Channel state information
CSI
Human Activity Recognition (HAR)
+ 3

4

1

Effects of PLU Polling Interval

The codes associated with the publication: The Effects of PLU Polling Interval on the Reconstructed OD Matrix: A Dutch Case Study Using a Data-Driven Method

Bayesian
GSM
OD matrix
+ 2

Jupyter Notebook
Markdown
Other

3

1

epistemic-bellman-operators

Epistemic Bellman Operators; code underlying the dissertation ‘Bayesian Model-Free Deep Reinforcement Learning’

Bayesian modelling
Deep Reinforcement Learning (DRL)
dynamic programming
+ 2

Jupyter Notebook
Markdown
Python

1

Filtering-explanding-graph-signals

Code underlying the publication: Online graph filter design over expanding graphs

expanding graphs
graph filters
graph signal processing
+ 2

Matlab
Other

1

ghc

GHC with stream fusion, used as benchmark in the publication: Higher Order Patterns for Rewrite Rules

compiler
fusion
higher order matching
+ 2

Automake
C
C++
+ 16

1

Hodge-Edge-GP

Code underlying: Hodge-Compositional Edge Gaussian Processes

edge space
forex
Gaussian process
+ 2

JSON
Jupyter Notebook
Markdown
+ 3

1

IntervalMDPAbstractions.jl_ReproducibilityPackage

Data and code underlying the publication: Scalable control synthesis for stochastic systems via structural IMDP abstractions

embedded systems
Markov processes
Stochastic control and optimization

C
C++
HTML
+ 10

3

1

longterm_datasets

Code underlying the publication: "Are current long-term video understanding datasets long-term?"

computer vision
deep learning
Long-term action recognition

HTML
Markdown
Other
+ 2

3

1

mean-field-quantum-networks

Code underlying the publication: Service-the-Longest-Queue Among d Choices Policy for Quantum Entanglement Switching

entanglement generation switch
load-balancing.
mean-field analysis
+ 1

JSON
Julia
Markdown
+ 2

1

mpcrl-cbf

Source code for the publication: Probabilistically safe and efficient model-based Reinforcement Learning

Control Barrier Function
Model predictive control
Reinforcement learning
+ 1

Markdown
Matlab
Other
+ 2

1

mpcrl-vehicle-gears

Software underlying publications: Learning-based MPC for fuel efficient control of autonomous vehicles with discrete gear selection and Reinforcement Learning with Distributed MPC for Fuel-Efficient Platoon Control with Discrete Gear Transitions

autonomous driving
Model predictive control
Reinforcement learning
+ 1

Markdown
Other
Python

1

NCS_SedimentAnalysis

Code and data underlying the publication: "Subsurface Sediment Properties and Potential Impacts of Marine Sand Extraction on Sand Wave Occurrence on the Netherlands Continental Shelf"

Median grain size
Mud content
Netherlands Continental Shelft
+ 1

Chemical XYZ
Matlab
Other
+ 1

4

1

NetLogo model: "Urbanism and Geographic Crises: A Micro-Simulation Lens on Beirut"

agent-based simulation
Beirut
econometrics
+ 3

2

1

Online COP heuristic learning code: "Online Learning of Variable Ordering Heuristics for Constraint Optimisation Problems"

constraint optimisation problem
Gecode
Machine learning
+ 3

2

1

P1-data-combination-code

Code to paper "Changing Sea Level, Changing Shorelines: Integration of Remote Sensing Observations at the Terschelling Barrier Island"

coastline
Remote sensing
sea level
+ 1

Jupyter Notebook
large-text-file
Markdown
+ 1

3

1

patient-interaction-detection

Python code to detect interaction of medical personnel with the operating table from surveillance videos

2D human poses
Action recognition
Operating table interaction
+ 3

JSON
large-text-file
Markdown
+ 2

1

Pbox Code, supporting the publication: Macro-element refinement schemes for THB-splines: Applications to Bézier projection and structure-preserving discretizations

adaptive refinement
finite element method
isogeometric analysis
+ 1

Markdown
Matlab
Other
+ 2

1

propeller_airspeed_sensor

Data and Code for Unmanned Aerial Vehicles airspeed estimation using propeller feedback.

BEM
ESC feedback
flight data
+ 4

Julia
Markdown
Matlab
+ 1

3

1

reference_set_selection_benchmark

Code underlying the publication: "Benchmarking the impact of reference genome selection on taxonomic profiling accuracy"

Genome Selection
Lineage Abundance Estimation
Sequence Clustering
+ 2

Jupyter Notebook
Markdown
Other
+ 3

3

1

Software accompanying the publication: Surrogate DC Microgrid Models for Optimization of Charging Electric Vehicles under Partial Observability

DC microgrid
Electric vehicles (EV),
Optimization Algorithms

3

1

Software supporting the article: Community Detection for Temporal Weighted Bipartite Networks

Bipartite Network
Bipartite Networks
Community Detection
+ 4

Jupyter Notebook
Markdown
Other
+ 1

4

1

Soil suitability maps for agriculture for the province Noord-Brabant (Netherlands) created with WaterVissionAgriculture and scripts to generate input data and to run the model WWL-tabel

Agriculture
crop production
soil suitability
+ 2

2

1

Source code for: Assessing the Validity of a Calcifying Oral Biofilm Model as a Suitable Proxy for Dental Calculus

dental calculus
Fourier-transform infrared spectroscopy (FTIR)
metagenomics
+ 2

5

1

supervised-learning-pwa-mpc

Software underlying the publication: Learning-based model predictive control for piecewise affine systems with feasibility guarantees

Feasibility
Hybrid Systems
Machine learning
+ 1

Markdown
Matlab
Other
+ 1

1

Analizo

Analizo is a free, multi-language, extensible source code analysis. It supports the extraction and calculation of a fair number of source code metrics, generation of dependency graphs, and software evolution analysis.

Software Evolution
Source Code Metrics
Static Analysis

C
C#
C++
+ 7

2

1

anonymoUUs

Python package to replace identifiable strings in multiple files and folders at once

de-identification
python
text

Jupyter Notebook
Python

3

1

Baklava

Deploys a Kubernetes cluster and big data services on the cloud.

Big data
High performance computing
Optimized data handling

Dockerfile
HCL
Python
+ 2

1

BenchmarkRecovery

This project simulates Landsat data and evaluates the performance of recovery indicators with respect to data and disturbance characteristics.

R

2

1

BestieTemplate.jl

BestieTemplate.jl is a template focused on best practices for package development in Julia.

best practices
julia
template

Julia
Python

9

1

BIRCH

BIRCH is a powerful framework for organizing and using bioinformatics. BIRCH comes with hundreds of commonly-used tools, and allows you to customize your BIRCH site by adding new ones.

bioinformatics
BLAST
genomics
+ 3

1

BrainBrowser

BrainBrowser is an open source JavaScript library exposing a set of web-based 3D visualization tools primarily targetting neuroimaging

3D
brainbrowser
neurology
+ 2

CSS
HTML
JavaScript
+ 1

5

1

byteparsing

Parser library for reading custom binary files from Python.

Big data
Multi-scale & multi model simulations
Optimized data handling

Batchfile
C++
CSS
+ 5

2

1

CBRAIN

CBRAIN is a flexible Ruby on Rails framework for accessing and processing of large data on high-performance computing infrastructures.

CBRAIN
cluster
Data Analysis
+ 6

CSS
HTML
JavaScript
+ 3

14

1

ChemTools

ChemTools is a free and open source Python library for interpreting the results of quantum chemistry calculations.

atoms in molecules
conceptual dft
density matrices kinetic energy density
+ 2

Python

1