Software | Research Software Directory

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

PowerSensor3

PowerSensor is a low-cost, custom-built device that measures the instantaneous power consumption of GPUs and other devices at a high time resolution.

GPU
High performance computing

(C)
(C++)
(CMake)
+ 3

6

3

protein-quest

Python package to search/retrieve/filter proteins and protein structures

(Python)

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

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.

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

agda-core

Code underlying the publication: Building a Correct-By-Construction Type Checker for a Dependently Typed Core Language

core language
Dependent Types
type-checking
+ 2

(Haskell)
(Markdown)
(Other)
+ 1

2

Code supporting the paper: High-speed predictions of post-burn contraction using a neural network trained on 2D-finite element simulations

Feedforward neural network
Machine learning
Monte Carlo simulations
+ 2

3

2

Code to produce the results of the publication: “Reducing the Soleus Stretch Reflex with Conditioning: Exploring Game- and Impedance-based Biofeedback”

Electromyography (EMG)
Gamification
operant conditioning
+ 2

1

2

Code underlying the publication: Exploiting Learned Symmetries in Group Equivariant Convolutions

equivariance
equivariant convolutions
separable convolutions

(Markdown)
(Other)
(Python)

2

Code underlying the publication: "Humans disagree with the IoU for measuring object detector localization error."

Human preference
Intersection over Union (IoU)
Object detection

("Jupyter Notebook")
(Markdown)
(Other)

3

2

Dynamic-Graph-Decomposition

Code underlying the publication: Tensor Graph Decomposition for Temporal Networks

decomposition
dynamic graphs
graph signal processing
+ 1

(Matlab)
(Other)

2

hybrid-vehicle-platoon

Software for publication: A comparison benchmark for distributed hybrid MPC control methods: Distributed vehicle platooning

autonomous vehicles
distributed model predictive control
Hybrid Systems
+ 2

(Markdown)
(Other)
(Python)

1

2

MC_RB_EM_1D

Data and scripts underlying the publication: Estimation of electrical conductivity models using multi-coil rigid-boom electromagnetic induction measurements

electromagnetic induction
frequency domain electromagnetics
inversion

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

3

2

mml_nbh_class_paper

Code underlying the paper "The Spatio-Temporal Evolution of Social Inequalities in Cities: A Multidimensional, Multiscalar and Longitudinal Approach for Neighbourhood Classification"

Cluster Analysis
code
geodemographics
+ 6

(Markdown)
(Other)
(R)

2

OFF framework, code underlying the publication A dynamic open-source model to investigate wake dynamics in response to wind farm flow control strategies

dynamic parametric wake model
surrogate wake model
wind farm flow control
+ 1

(CSS)
(HTML)
(JavaScript)
+ 7

2

oraqle

Oraqle: A Depth-Aware Secure Computation Compiler

arithmetization
compiler
cryptography
+ 1

(C++)
("Jupyter Notebook")
(Markdown)
+ 4

1

2

PETsChallenge

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

Anomaly detection
cryptography
elliptic curves
+ 4

(HTML)
(Markdown)
(Other)
+ 4

8

2

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++)
(Markdown)
(Other)
+ 1

1

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

stable-dmpc-pwa

Software underlying publication: Distributed model predictive control for piecewise affine systems based on switching ADMM

Alternating direction method of multipliers (ADMM)
distributed model predictive control (MPC)
networked systems
+ 1

(Markdown)
(Matlab)
(Other)
+ 1

1

2

TU/e Microscopic Energy Consumption PRediction tOol 0.1 (TU/e MECPRO 0.1)

Automotive Engineering
Battery Electric Vehicle
Electric Vehicle (EV)
+ 3

4

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

("Common Workflow Language")
(Java)
("Jupyter Notebook")
+ 1

2

Data Storytelling

Developing consistent, structured ways to present data across projects. Using LLMs and interactive tools to turn results into clear, engaging stories. Applying this approach to selected eScience projects, especially those in the upcoming center-wide evaluation.

application
llm
storytelling
+ 1

(CSS)
(HTML)
(JavaScript)
+ 3

3

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

(CSS)
(JavaScript)
(Makefile)
+ 5

1

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

(Dockerfile)
(Python)

10

2

FAIRSECO

FAIRSECO provides a way to quickly analyse a variety of data and metrics of your software, and it allows you to explore the impact of your software on the academic world. Metadata is gathered from many different sources, which is then analysed and compiled into a clear overview.

Data Analysis
FAIR
Inter-operability & linked data
+ 2

(EJS)
(JavaScript)
(TypeScript)

3

2

fairtally

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

(Dockerfile)
(Python)
(Shell)

4

2

fairworkflows

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

("Common Workflow Language")
(HTML)
(Python)
+ 1

5

2

FlexRL

A Flexible Model For Record Linkage

latent variable model
partially identifying variables
record linkage
+ 1

(C++)
(R)

1

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

(CSS)
(HTML)
(JavaScript)

1

2

GridFormat

Header-only C++ Library for grid file I/O

Grid-based PDE methods
grid file I/O
mesh file I/O
+ 3

(C++)
(CMake)
(Dockerfile)
+ 1

2