Software | Research Software Directory

howfairis

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

HTML
Python
Shell
+ 1

7

4

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

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

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 and data underlying the publication: Symmetrization of 2D Polygonal Shapes Using Mixed-Integer Programming

Design
Digitalization
Shape optimization
+ 1

C
C++
Other
+ 3

3

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

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: “Neurophysiological Validation of Simultaneous Intrinsic and Reflexive Joint Impedance Estimates”

Electromyography
Joint resistance
Parallel-Cascade model
+ 2

1

3

ColorIce: Automated in-plane ice thin section analysis tool

birefringence
crossed-polarization
grain boundary
+ 5

2

3

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

Ammonia
Atmospheric ammonia
blending distance
+ 7

4

3

Fast Rotor Loss Calculations in Fractional-Slot Permanent Magnet Machines

COMSOL multiphysics software
Eddy current losses
Permanent magnet machine

1

3

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

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

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

bandwidth
Computer simulation
replication
+ 2

2

3

Uncertainty Specification and Analysis for Thermosphere Observations

Accelerometer
GNSS tracking
Mass density
+ 2

Other
C
Matlab
+ 3

1

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

PanVA

Variant Analysis within Pangenomes.

API
Data Analysis
pangenomics

Vue
TypeScript
Python
+ 6

2

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

Importing a Roman Transport network

Use open Roman datasets via and import them into a NetLogo model, using the ORBIS dataset (http://orbis.stanford.edu/) to create a set of Roman settlements and major routes between them.

1

2

Out of Africa - Conditional isotropic diffusion

A reimplementation of the classical study by Young and Bettinger (1992) investigating the possible drivers behind the Out of Africa dispersal of modern humans.

4

2

Landscape and Land Cover Generation

This algorithm generates landscapes and landcovers in contiguous zones. Users can define different landscape types, landcovers and rules for settlement placement in the setup procedure. It is designed to allow flexible configuration of environmental and social parameters.

1

2

SyGMa

SyGMa provides fast and lightweight predictions of human metabolites to support discovery scientists design better and safer drugs

Workflow technologies

Python

2

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

Identity and Access Management
Misconfiguration Detection
Security

Python
Markdown
Other

4

2

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

2

Code underlying the publication: Maintenance Optimization for Multi-Component Systems with a Single Sensor

Condition-based maintenance
Inspection planning
Maintenance
+ 2

Python
Other

4

2

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

2

Code underlying the publication: "Self-Supervised PPG Representation Learning Shows High Inter-Subject Variability"

Autoencoder
Human Activity Recognition
Inter-Subject Variability
+ 3

Python
Other
Markdown
+ 1

3

2

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

biophysics
Coral Reef Ecology
hydrodynamics

1

2

Data underlying the publication: Fabrication and Characterization of Pneumatic Unit Cell Actuators

characterization
fabrication
haptic display
+ 4

Markdown

3

2

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