Software | Research Software Directory

PETsChallenge

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

Anomaly detection
cryptography
elliptic curves
+ 4

Rust
Markdown
Python
+ 4

8

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

sse-akf-directional-waves-pem

Code underlying the publication: Unidirectional and multi-directional wave estimation from ship motions using an Adaptive Kalman Filter with the inclusion of varying forward speed

Adaptive Kalman filter
Sea state estimation
Ship motion responses
+ 1

Python
Markdown
Other

1

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

Jupyter Notebook
Python
Common Workflow Language
+ 1

2

Climate Rapid Evaluation Framework

Rapid Evaluation Framework for climate simulations

Big data
Climate modeling

Python
HTML
TeX
+ 4

10

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

Python
Makefile
JavaScript
+ 5

1

2

Entangled

Entangled makes literate programming easier. It keeps markdown and program source in sync. This makes it more convenient to extend and debug your literate code.

Literate Programming
open science
python
+ 2

Python
Makefile
C++
+ 2

5

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

Python
Dockerfile

10

2

fairtally

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

Python
Shell
Dockerfile

4

2

fairworkflows

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

Python
HTML
Common Workflow Language
+ 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

JavaScript
CSS
HTML

1

2

MOTrainer

Measurement Operator Trainer for data assimilation purposes.

Data assimilation
High performance computing
Machine learning
+ 2

Jupyter Notebook
Python
TeX
+ 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

Jupyter Notebook
Python
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
Jupyter Notebook
Python
+ 2

1

2

PathVisio

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

bioinformatics
PathVisio
Systems Biology
+ 2

Java
HTML
JavaScript
+ 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

PyChelator

PyChelator is a Python-based Colab and web application for metal chelator calculations, taking into account pH, temperature, and ionic strength. The build-in constants can be used for EGTA and ATP as chelators, together with Calcium and Magnesium as metals. User-defined constants can be used.

application
calcium
chelator
+ 7

Jupyter Notebook
JavaScript
HTML
+ 2

3

2

pyglotaran

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

biophysics
global analysis
glotaran
+ 3

Python
Nix

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

Python
Makefile
Shell
+ 5

1

2

sfb-annotator

Annotate field books of natural history collections

Inter-operability & linked data

JavaScript
Java
CSS
+ 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

Python
JavaScript
HTML
+ 3

1

2

tortellini

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

TypeScript
JavaScript

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

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

3D-CNN
Action recognition
BagNet
+ 2

Python
Markdown
XML
+ 1

4

1

CounterfactualExplanations.jl

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

Algorithmic Recourse
Counterfactual Explanations
explainable artificial intelligence
+ 1

Other
Julia
TeX
+ 7

3

1

Data and code underlying the publication: Deep learning reveals key predictor of thermal conductivity of covalent organic frameworks

Covalent organic frameworks
deep learning
Thermal conductivity
+ 1

5

1

Dataset-NonDimensionalisationQMOM

Data to reproduce the paper: "Non-dimensionalization of quadrature method of moments for wet granulation"

10th granulation conference Sheffield
Buckingham Theorem
non-dimensionalization
+ 3

Other
Matlab
Markdown
+ 1

3

1

det2d-read

Python package to read 2D human poses from json files

2D pose detection
Data loading
Multiprocessing
+ 1

Python
Markdown
Other
+ 2

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

Hodge-Edge-GP

Code underlying: Hodge-Compositional Edge Gaussian Processes

edge space
forex
Gaussian process
+ 2

Jupyter Notebook
Python
Other
+ 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
Python
Other
+ 2

3

1

mo-tas

Truck Appointment Systems - Multi-Objective model

Collaboration
Multi-Agent Systems
prioritized planning
+ 2

Python
Markdown

1

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

agent-based simulation
Beirut
econometrics
+ 3

2

1

np_heating

Code for the modeling of heating around plasmonic core–shell nanoparticles

Heat transfer
Photothermal effect
Plasmonic nanoparticles
+ 1

Python
Markdown
Other

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
Other
Markdown
+ 1

3

1

ProbabilisticValidation

Source code underlying the publication: Privacy-Preserving Data Aggregation with Probabilistic Range Validation

privacy-preserving summation
range validation
secure multi-party computation
+ 1

Matlab
Markdown

2

1

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++
Other
Shell
+ 1

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 underlying the article: Modelling the cross-sectional dynamics of tidal sandbanks in sediment-scarce conditions

Asymmetry
Coastal Engineering
Equilibrium shape
+ 12

3

1

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