Software | Research Software Directory

MATLAB scripts created during the work on "Design of experiments: a statistical tool for PIV uncertainty quantification"

Design of Experiement (DOE)
Particle Image Velocimetry
systematic uncertainty
+ 1

2

4

NetLogo model: "Agent-Based Simulation of Short-Term Peer-to-Peer Rentals: Evidence from the Amsterdam Housing Market"

agent-based modelling
Airbnb
Amsterdam
+ 4

2

4

SBSL

Data and code underlying the publication: Overcoming Selection Bias in Synthetic Lethality Prediction

anti-cancer therapeutics
computational prediction
gene dependency
+ 3

3

4

Source code for INCS (Iterative Nonlinear Contrast Source)

INCS
medical ultrasound
microbubbles
+ 1

Fortran
Other
Matlab
+ 5

2

4

Uncertainty Specification and Analysis for Thermosphere Observations

Accelerometer
GNSS tracking
Mass density
+ 2

Other
C
Matlab
+ 3

1

4

cffconvert

Command line tool to convert CITATION.cff files to various formats used by reference managers such as Zotero and JabRef.

Python
TeX
HTML
+ 1

5

4

cffinit

A web form to initialize CITATION.cff files which you can use to include citation information into your software repository.

Software Citation

TypeScript
Vue
JavaScript
+ 3

7

4

eAstroViz

This tool can convert and visualize radio astronomy measurement sets, as well as most LOFAR intermediate data products. It also performs RFI mitigation.

LOFAR
radio astronomy
RFI

Java
C++
Cuda
+ 3

1

4

evidence

doc2vec-based assisted close reading with support for abstract concept-based search and context-based search

Text analysis & natural language processing

TypeScript
Go
Jupyter Notebook
+ 5

9

4

howfairis

Command line tool to analyze a git repository's compliance with the fair-software.eu recommendations.

HTML
Python
Shell
+ 1

7

4

Lightning

Lightning: Fast data processing using GPUs on distributed platforms

Big data
GPU
High performance computing

Rust
C++
Python

2

4

LUE

LUE is software for storing and manipulating large amounts of information for large numbers of objects. The software is useful, and currently mainly used, in the context of environmental modelling of biological and physical systems, represented by agents and fields.

Agent-based modeling
environmental modelling
field based modelling
+ 6

C++
Python
CMake
+ 6

3

4

nanomesh

Python workflow tool for generating meshes from 2D and 3D microscopy image data

Image processing
Visualization
Workflow technologies

Jupyter Notebook
Python
Shell
+ 1

3

4

Noodles

Task-based parallel programming model in Python that offers the same intuitive interface when running complex workflows on your laptop or on large computer clusters.

High performance computing
Workflow technologies

Jupyter Notebook
Python
Shell
+ 2

9

4

Hercules

Retrieve recent tweets from certain users and classify them with machine learning

Machine learning
Text analysis & natural language processing

Python
Jupyter Notebook
Shell

1

4

PanVA

Variant Analysis within Pangenomes.

API
Data Analysis
pangenomics

Vue
TypeScript
Python
+ 6

2

4

PerfectFit

This is a virtual coach system that coaches users into being more physically active and stop smoking.

Big data
health

JavaScript
Gherkin
Shell

5

4

WEARDA

WEARDA: recording wearable sensor data for human activity monitoring.

embedded software
GPS
Human activity monitoring
+ 4

C
TeX

2

4

Xenon gRPC server

Run applications remotely via a gRPC interface.

High performance computing

Java

3

4

Network structures

A draft model with some useful code for creating different network structures using the Netlogo NW extension: small-world, preferential attachment, circular, star, wheel, lattice, random, nearest neighbours.

1

3

BrazilClim: script to gauge-calibrate the surfaces

Bioclimatic variables
Brazil
land surface temperatures
+ 4

5

3

Code for Detecting Anomalous Misconfigurations in AWS Identity and Access Management Policies

Identity and Access Management
Misconfiguration Detection
Security

Python
Markdown
Other

4

3

Code supporting the paper: Stability of a two-dimensional biomorphoelastic model for post-burn contraction

Burns
MATLAB
Morphoelasticity
+ 3

3

Code to produce the results of the publication: “Examining the Role of Intrinsic and Reflexive Contributions to Ankle Joint Hyper-Resistance Treated with Botulinum Toxin-A”

BoNT-A injections
Instrumented SPAT
Joint resistance
+ 2

1

3

Code underlying the publication: "RESTAD: Reconstruction and Similarity Transformer for time series Anomaly Detection"

Anomaly detection
Radial Basis Function (RBF) kernel
Time Series
+ 1

Python
YAML
Markdown
+ 1

3

ColorIce: Automated in-plane ice thin section analysis tool

birefringence
crossed-polarization
grain boundary
+ 5

2

3

CoralModel: A Python-based model that resembles the biophysical interactions on a coral reef

biophysics
Coral Reef Ecology
hydrodynamics

1

3

DALES v4.2 modified for ammonia plume dispersion and blending-distance estimations

Ammonia
Atmospheric ammonia
blending distance
+ 7

4

3

Data and code underlying Chapter 4 of the PhD thesis "Advanced Magnetocaloric Regenerators for Heat Pump Applications"

active magnetocaloric regenerator
layered AMR
magnetocaloric heat pump
+ 5

Other
Python

4

3

endogenous-macrodynamics-in-algorithmic-recourse

Software and data underlying the publication: Endogenous Macrodynamics in Algorithmic Recourse

Algorithmic Recourse
Counterfactual Explanations
Dynamic Systems
+ 1

Other
HTML
JSON
+ 8

3

Fast Rotor Loss Calculations in Fractional-Slot Permanent Magnet Machines

COMSOL multiphysics software
Eddy current losses
Permanent magnet machine

1

3

Matlab scripts and MuseScore scripts accompanying the book "The Perceptual Structure of Sound"

sound design

1

3

Script for: AID-PRIGSHARE: Automation of Indicator Development for Green Space Health Research in QGIS

buffer
gis
greenness
+ 2

Other
Python
Markdown

1

3

Script underlying the paper "On Robustly Convergent and Efficient Iterative Methods for Anisotropic Radiative Transfer"

acceleration
anisotropic
preconditioning
+ 3

3

Supplementary materials for the paper: On Senders’s Models of Visual Sampling Behavior

bandwidth
Computer simulation
replication
+ 2

2

3

AstronomicAL

An interactive dashboard for visualisation, integration and classification of data using Active Learning.

Active Learning
Classification
Data Analysis
+ 11

Python
TeX

1

3

Beyond the book

Measure the number of contributions to Wikipedia entries from individuals from different counties as a measure of cultural bias.

Text analysis & natural language processing

Jupyter Notebook
Python
JavaScript
+ 2

2

3

chimp-classifier

The Python package `junglesounds` is a machine learning pipeline for classifying bioacoustic data using machine learning. The pipeline is reusable for other settings and species or vocalization types as long as a certain amount of labeled data has been collected.

audio
Audio processing
bioacoustics
+ 2

Jupyter Notebook
Python
Shell

2

3

Emma

Emma is a project to create a platform for development of application for Spark and DockerSwarm clusters.

Big data

Shell
Scala
Python
+ 1

4

3

Introduction to Geospatial Raster and Vector Data with Python

This lesson material shows how practical geospatial data analysis tasks can be carried out using Python

Data Analysis
geospatial
Image processing
+ 4

3

iReceptor Gateway

A Distributed Data Management System and Scientific Gateway for Mining Next Generation Sequence Data from Immune Responses.

immunogenomics
Immunology
iReceptor

PHP
Shell
Blade
+ 7

12

3

Lilio

A Python package for generating calendars to resample timeseries into training and target data for machine learning. Named after the inventor of the Gregorian Calendar.

AI
Preprocessing
S2S

Python
Shell

5

3

NEBULA

The NEBULA (Nuxt & eScience Based Universal Learning Application) framework can be used to create an easily maintainable, version-controllable, web-based lesson collection. It uses Nuxt.js and Vue.js.

teaching
web

Vue
TypeScript
SCSS
+ 1

3

s2spy

A high-level python package integrating expert knowledge and artificial intelligence to boost sub-seasonal to seasonal (S2S) forecasting.

AI
S2S

Python
Shell

6

3

SalientDetector-matlab

If you want to automate object detection or image photo-identification tasks in an easy way with open MATLAB software, the SalientDetector-MATLAB is right for you

Image processing

MATLAB

1

3

SalientDetector-python

If you want to automate your object detection or photo-identification image tasks in an easy way with free open-source software, the SalientDetector-Python is the tool for you

Image processing

Jupyter Notebook
Python
Makefile

2

3

SlicerRT

SlicerRT allows users to analyze spatio-temporal accumulation of the therapeutic dosage (radiation, thermal, etc.). Tools include dose visualization, quantitative metrics computation, comparison, and import/export to DICOM format.

C++
Python
CMake
+ 1

3

Revisited Via Appia

Create visual storylines that involve media like images and videos embedded in a 3D environment with efficient Pointcloud data directly from the web browser.

cultural heritage
Digital Twins
gis
+ 2

JavaScript
HTML
Vue
+ 3

2

3

All software