Software | Research Software Directory

Livestock demography

This submodel simulates livestock herd demography and slaughter effects. Initially part of the ROMFARMS model for animal husbandry on the Dutch Roman frontier, it focused on cattle, sheep, and horses. However, the code is adaptable for various animals, regions, and historical periods.

2

4

Artefact of: JavaBIP meets VerCors: Towards the Safety of Concurrent Software Systems in Java

concurrent systems
Deductive verification
formal methods
+ 3

5

4

Code and test data set underlying the publication: Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with a multiplexed magnetic tweezers

Dwell Time Analysis
magnetic tweezers
RdRP activity
+ 1

3

4

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

Identity and Access Management
Misconfiguration Detection
Security

Python
Markdown
Other

4

Code for the paper "Synergizing cycling and transit: Strategic placement of cycling infrastructure to enhance job accessibility"

code
cycling infrastructure
job accessibility

1

4

Code to produce the results of the publication: “Disentangling acceleration-, velocity- and duration-dependency of the short- and medium-latency stretch reflexes in the ankle plantarflexors”

Group Ia afferents
M1-M2 stretch reflex
Motoneuron pool
+ 1

1

4

Code to produce the results of the publication: “Neurophysiological Validation of Simultaneous Intrinsic and Reflexive Joint Impedance Estimates”

Electromyography
Joint resistance
Parallel-Cascade model
+ 2

1

4

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

4

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

Ammonia
Atmospheric ammonia
blending distance
+ 7

4

MATLAB script and COMSOL models of the article "An efficient multiscale method for subwavelength transient analysis of acoustic metamaterials"

Equivalent fluid model
Homogenisation
Locally resonant acoustic metamaterials
+ 1

Other
Matlab
Markdown

4

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

Source code for INCS (Iterative Nonlinear Contrast Source)

INCS
medical ultrasound
microbubbles
+ 1

Fortran
Other
Matlab
+ 5

2

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 the publication: Vibration-induced friction modulation for a general frequency of excitation

Average friction
Mechanical vibration
Method of direct separation of motion
+ 1

1

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

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

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

petcluster

Petrochemical cluster analysis tool

complex networks
Industrial cluster
industrial ecology
+ 2

Python
Other
Markdown

4

3

Sample dataset and software for FAST-EM array tomography

array tomography
FAST-EM
Image processing
+ 1

10

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

Software and data underlying the publication: Faithful Model Explanations through Energy-Constrained Conformal Counterfactuals

Classification and Regression
Deep Generative Models & Autoencoders
Humanities & Computational Social Science
+ 1

TeX
Other
Julia
+ 6

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

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