Software | Research Software Directory

ece2cmor3

Process EC-Earth output to publish for CMIP6

Big data
High performance computing
Optimized data handling

Shell
Python

2

7

jaspProcess

A JASP implementation of the PROCESS macro for SPSS

Data Analysis
Statistics
Visualization

R
QML

2

7

MultilayerGraphs.jl

A Julia package for the creation, manipulation and analysis of the structure, dynamics and functions of multilayer graphs.

Graphs
Graph Theory
Hierarchical Graphs
+ 10

Julia

2

7

nlppln

A flexible solution to build text mining workflows that allows you to quickly combine Natural Language Processing tools from different sources.

Text analysis & natural language processing

Python
Common Workflow Language
Dockerfile

2

7

Turing Data Safe Haven

Data Safe Haven is an open-source framework for creating Trusted Research Environments (TREs) to analyse sensitive data. It provides a set of scripts that will allow you to deploy, administer and use your own TRE on Microsoft Azure cloud.

Cloud
cloud storage
Infrastructure as code
+ 3

Python
Shell
Jinja
+ 3

29

7

WRFpy

WRFpy is a python application that provides an easy way to set up, run, and monitor Weather Research and Forecasting simulations

Data Simulation
python

Python

4

7

xtas

the eXtensible Text Analysis Suite

Text analysis & natural language processing

Python
Shell
Java

2

7

Code supporting the paper: Sensitivity and feasibility of a one-dimensional morphoelastic model for post-burn contraction

Burns
Feasibility
MATLAB
+ 4

3

6

Data/software underlying the publication: Robust quantum-network memory based on spin qubits in isotopically engineered diamond

distributed quantum computation
entanglement distillation

12

6

Framework for the publication: MirrorLabs – creating similar learning environments for students all over Europe for human-robot coproduction

Augmented Reality
Interactive Visualization
robotics
+ 2

2

6

Microscopy data, code and analysis underlying the publication "Optical STEM detection for scanning electron microscopy"

Electron Detection
Instrumentation Development
Scanning Electron Microscopy
+ 2

Other
Markdown
Jupyter Notebook
+ 2

6

eEcology Annotation Tool

Visualize and annotate GPS measurements of bird movements.

Inter-operability & linked data
Visualization

HTML
Python
Mako
+ 5

1

6

orbitN

Symplectic integrator for near-Keplerian planetary systems

astronomical solution
astronomy
N-body
+ 2

1

6

PSSMGen

Generates consistent PSSM and PDB files for protein-protein complexes

Big data
High performance computing
Optimized data handling

Python
Makefile

2

6

PuReGoMe

Analyzes social media messages for polarity and stance towards governmental COVID-19 measures

Machine learning
Social media

Jupyter Notebook
Python
Shell

3

6

SPOT

SPOT is an interactive visualization tool for multi-dimensional data. It allows quick analysis of complex datasets and easy identification of correlations between variables.

Big data
Visualization

JavaScript
Pug
Stylus
+ 2

7

6

Reference evapotranspiration (FAO-56)

Calculate a daily value of reference evapotranspiration, useful for vegetation (incl. crop) models. The module code is based on FAO-56 Penman-Monteith method.

1

5

3D Slicer

3D Slicer is a free, open source software for visualization, processing, segmentation, registration, and analysis of medical, biomedical, and other 3D images and meshes; and planning and navigating image-guided procedures.

3D
3DSlicer
Extension
+ 7

C++
Python
CMake
+ 5

4

5

Blade Element Momentum Theory Code for Positive and Negative Thrust Propellers

BEM
BEMT
Blade Element Momentum Theory
+ 2

1

5

Code complementing the paper "Feasibility Analysis of a Self-Reinforcing Electroadhesive Rotational Clutch"

Clutch
Electroadhesion
self-reinforcement
+ 2

3

5

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

burn
cell proliferation
MATLAB
+ 4

4

5

Code supporting the paper: Stability of a one-dimensional morphoelastic model for post-burn contraction

Burns
MATLAB
Morphoelasticity
+ 3

3

5

Learning_on_SCs

Code underlying: Hodge-Aware Convolutional Learning on Simplicial Complexes

Hodge theorem
neural networks
simplicial complexes

Other
Python
Markdown
+ 1

1

5

Source, documentation, tests: MACE: Automated Assessment of Stereochemistry of Transition Metal Complexes and its Applications in Computational Catalysis

automation
chemoinformatics
Computational Chemistry
+ 6

Chemical XYZ
Other
Jupyter Notebook
+ 5

2

5

eEecology Classification

Automatic classification of accelerometer data using a supervised learning approach.

Machine learning

Java
JavaScript
HTML
+ 3

1

5

MagnumPI - Potential Integrator

A package for the calculation of scattering angles and cross sections.

Inter-operability & linked data
Visualization

C++
Mathematica
Python
+ 2

6

5

mexca

Capture emotion expressions from video, audio, and text with a single pipeline.

Audio processing
Image processing
Machine learning
+ 1

Python
Dockerfile
Shell

5

PIQMIe

A web tool for mass spectrometry-based proteomics data analyses

Data Analysis
mass spectrometry
Optimized data handling
+ 2

HTML
JavaScript
Python
+ 3

1

5

sv-channels

Genome-wide detection of structural variants using deep learning

Machine learning

Python
Jupyter Notebook
R
+ 1

4

5

TIMP

TIMP is an R package for fitting superposition models that implements the partitioned variable projection algorithm. The package has been extensively applied to modeling spectroscopy and Fluorescence Lifetime Imaging Microscopy (FLIM) datasets. It serves as the backend for the Glotaran software.

global analysis
target analysis
time-resolved spectroscopy

R
C

2

5

Get fertility rates (females, 5-year cohort)

This NetLogo code snippet provides fertility estimates of females for use in demographic simulations. The figures used are based on two different sources, and will be assigned per 5-year age cohort.

1

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 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

finite-strain-inverse-designed-spinodoids

Data and Code underlying publication: Experiment-informed finite-strain inverse design of spinodal metamaterials

In situ characterization
Inverse design
Machine learning
+ 2

Other
Python
Matlab

5

4

Hanson's Model in Frequency Domain - Tonal Noise of Rotors in Uniform Inflow

Hanson's model
Propeller Aeroacoustics
Propeller Noise
+ 1

1

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

SBSL

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

anti-cancer therapeutics
computational prediction
gene dependency
+ 3

3

4

Software supporting the publication: Background Electromagnetic Noise Received via Ionospheric Propagation in a Remote Rural Location in Spain (set 1)

ambient noise
electromagnetic noise
ionosphere
+ 3

4

Source code for INCS (Iterative Nonlinear Contrast Source)

INCS
medical ultrasound
microbubbles
+ 1

Fortran
Other
Matlab
+ 5

2

4

SWMM_GNN_Repository_Paper_version

SWMM GNN metamodel – Code for paper: Transferable and Data Efficient Metamodeling of Storm Water System Nodal Depths Using Auto-Regressive Graph Neural Networks

GNN
Graph neural networks
Machine learning
+ 5

Other
Python
Jupyter Notebook
+ 2

4

Bacting

Bacting is an open-source platform for chemo- and bioinformatics based on Bioclipse that defines a number of common domain objects and wraps common functionality, providing a toolkit independent, scriptable solution to handle data from the life sciences.

bioinformatics
Cheminformatics

Java
TeX

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

citation.js

Citation.js converts formats like BibTeX, Wikidata JSON and BibJSON to CSL-JSON to convert to other formats like APA, Vancouver, RIS and back to BibTeX.

Bibliography
BibTeX
Data Citation
+ 2

JavaScript
TeX
Roff

6

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

All software