Software | Research Software Directory

SNAPWF

Code underlying the publication: Automated Python workflow for generating Sentinel-1 PSI and SBAS interferometric stacks using SNAP on Geospatial Computing Platform

InSAR
Interferometric Stacks
Open-Source Tools
+ 2

("Jupyter Notebook")
(Markdown)
(Python)
+ 1

7

4

Source code for INCS (Iterative Nonlinear Contrast Source)

INCS
medical ultrasound
microbubbles
+ 1

(Automake)
(C)
(Fortran)
+ 5

2

4

cffconvert

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

(Dockerfile)
(HTML)
(Python)
+ 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

(CSS)
(HTML)
(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

(C)
(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

(CSS)
(Dockerfile)
(Go)
+ 5

9

4

howfairis

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

(Dockerfile)
(HTML)
(Python)
+ 1

7

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

(Batchfile)
(C)
(C++)
+ 6

3

4

nanomesh

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

Image processing
Visualization
Workflow technologies

("Jupyter Notebook")
(PowerShell)
(Python)
+ 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

(HTML)
("Jupyter Notebook")
(Lua)
+ 2

9

4

Hercules

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

Machine learning
Text analysis & natural language processing

("Jupyter Notebook")
(Python)
(Shell)

1

4

PerfectFit

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

Big data
health

(Gherkin)
(JavaScript)
(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

Artifact for the Paper "Fast Verified SCCs for Probabilistic Model Checking"

Correct-by-construction
Gabow
IRF
+ 13

3

BrazilClim: script to gauge-calibrate the surfaces

Bioclimatic variables
Brazil
land surface temperatures
+ 4

5

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: "Self-Supervised PPG Representation Learning Shows High Inter-Subject Variability"

Autoencoder
Human Activity Recognition
Inter-Subject Variability
+ 3

(JSON)
(Markdown)
(Other)
+ 1

3

Combining-Deeb-Learning-with-Uncertinity

Code and results underlying the publication: Combining Deep Neural Networks and Gaussian Processes for Asphalt Rheological Insights

Asphalt binder
Asphalt mastic
Gaussian process
+ 3

("Jupyter Notebook")
(Markdown)
(Other)
+ 1

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

Fast Rotor Loss Calculations in Fractional-Slot Permanent Magnet Machines

COMSOL multiphysics software
Eddy current losses
Permanent magnet machine

1

3

Generics library for datatype-generic programming in Agda

Agda
Dependent Types
Generic Programming
+ 2

2

3

group-trip-planning

Code underlying the publication: When in Doubt! Understanding the Role of Task Characteristics on Peer Decision-Making with AI Assistance

Empirical Studies
Group Decision-Making
Human-AI Decision-Making
+ 5

(CSS)
(HTML)
(JavaScript)
+ 4

2

3

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

(Markdown)
(Other)
(Python)

1

3

Supplementary data for the paper 'From A to B with Ease: User-Centric Interfaces for Shuttle Buses'

Micro-mobility
Shuttle bus
User Interface
+ 1

5

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

(CSS)
(HTML)
(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

Climate Rapid Evaluation Framework

Rapid Evaluation Framework for climate simulations

Big data
Climate modeling

(Dockerfile)
("Go Template")
(HTML)
+ 6

10

3

Emma

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

Big data

(Python)
(R)
(Scala)
+ 1

4

3

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

(C)
(C++)
(Jinja)
+ 3

5

3

eOSSR

The eOSSR is the Python library to programmatically manage the ESCAPE OSSR.

jupyter-notebook
repository
research software
+ 2

(Dockerfile)
(Python)

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

(Blade)
(Dockerfile)
(HTML)
+ 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

(JavaScript)
(SCSS)
(TypeScript)
+ 1

3

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

(CSS)
(HTML)
(JavaScript)
+ 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")
(Makefile)
(Python)

2

3

SedTRAILS

SedTRAILS is a Lagrangian particle-tracking model for simulating and visualizing coastal sediment pathways and connectivity. Initial public release forthcoming ~February 2026.

Coastal Engineering
coastal processes
connectivity
+ 5

(Python)

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)
(C++)
(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

(CSS)
(HTML)
(JavaScript)
+ 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

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