Software | Research Software Directory

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

10

Global analysis of DNA methylation in hepatocellular carcinoma via a whole-genome bisulfite sequencing approach

DNA methylation analyses
prognosis model
WGBS (Whole Genome Bisulfite Sequencing)

1

10

HCOMP2022_ARCHIE

Analogy-based explanation evaluation dataset for HCOMP 2022 paper "It Is Like Finding a Polar Bear in the Savannah! Concept-level AI Explanations with Analogical Inference from Commonsense Knowledge."

Analogy
Commonsense Knowledge
Concept-level Explanation
+ 1

(Markdown)
(Other)
(Python)

5

10

ML-MoCap - Controller and Camera module Images

human movement
markerless
MarkerLess Motion Capture (ML-MoCap)
+ 1

1

10

MDStudio

A tool to run molecular dynamics workflows.

High performance computing
Real time data analysis
Workflow technologies

(CSS)
(Dockerfile)
(HTML)
+ 5

4

10

Blade Element Momentum Theory Code for Positive and Negative Thrust Propellers

BEM
BEMT
Blade Element Momentum Theory
+ 2

1

9

petcluster

Petrochemical cluster analysis tool

complex networks
Industrial cluster
industrial ecology
+ 2

(Markdown)
(Other)
(Python)

4

9

Scripts and data accompanying publication: "Manure matters: Prospects for regional banana-livestock integration for sustainable intensification in South-West Uganda"

cattle
crop-livestock integration
East African Highland Banana
+ 5

1

9

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

9

gammalearn

Deep Learning for Imaging Cherenkov Telescopes Data Analysis

cta
deep learning
Gamma-ray telescopes
+ 1

(Dockerfile)
(Python)

4

9

orbitN

Symplectic integrator for near-Keplerian planetary systems

astronomical solution
astronomy
N-body
+ 2

1

9

pdb2sql

Fast and versatile Python package that leverages SQL queries to parse, manipulate and process biomolecular structure files. The structure files should be in the PDB format and are available on www.rcsb.org.

Big data
Optimized data handling

(Makefile)
(Python)
(TeX)

2

9

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

(Dockerfile)
(Jinja)
(Python)
+ 3

29

9

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

9

Xenon command line interface

A command line interface for the Xenon library that allows you to use remote machines to do your computations.

High performance computing

(Batchfile)
("Common Workflow Language")
(Dockerfile)
+ 2

2

9

Code supporting the paper: A Bayesian finite-element trained machine learning approach for predicting post-burn contraction

Feed-forward neural network
Machine learning
MATLAB
+ 5

3

8

Code underlying the publication: "PATE: Proximity-Aware Time series anomaly Evaluation"

Anomaly detection
Evaluation Metrics
Precision
+ 2

(Markdown)
(Other)
(Python)
+ 1

3

8

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

Hanson's model
Propeller Aeroacoustics
Propeller Noise
+ 1

1

8

Hydrodynamic Analysis of Marine Structures-Marine Renewable Energies Lab (HAMS-MREL)

BIEM
HAMS
HAMS-MREL
+ 4

5

8

MATLAB scripts created during the work on "Multi-Δt approach for peak-locking error correction and uncertainty quantification in PIV"

PIV (Particle Image Velocimetry)
Uncertainty Quantification

3

8

mpcrl-for-ramp-metering

Source code for the publication: Reinforcement Learning with Model Predictive Control for Highway Ramp Metering

Model predictive control
Ramp Metering
Reinforcement learning

(Markdown)
(Other)
(Python)
+ 1

1

8

Multistage-PINN

Code underlying the publication: Multistage physics informed neural network for solving coupled multiphysics problems in material degradation and fluid dynamics

Asphalt aging
Multiphysics modeling
Multistage learning
+ 2

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

4

8

Shoreline Evolution Model and Appendix A - Supplementary data to the manuscript Challenges and new strategies in assessing multidecadal shore platform sandy beach evolution from aerial imagery

beach change
beach toe
beach volume
+ 4

4

8

Clustering Geo-data Cubes

Tool to perform cluster analysis of multi-dimensional geospatial data, running on local or distributed systems.

Big data
geospatial
Machine learning
+ 1

("Jupyter Notebook")
(Python)
(TeX)

7

8

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

("Common Workflow Language")
(Dockerfile)
(Python)

2

8

COVID-19 Piedmont

COVID-19 Surveillance Data Modelling and Management Pipeline in Piedmont.

Computational Epidemiology
COVID-19
COVID-19 Data
+ 14

(Julia)

2

8

PuReGoMe

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

Machine learning
Social media

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

3

8

pypfilt

A Sequential Monte Carlo (SMC, or "particle filter") Python package for online model estimation and probabilistic forecasting.

Bayesian Inference
Forecasting
Sequential Monte Carlo

1

8

recipy

Effortless provenance tracking in Python

Inter-operability & linked data
Optimized data handling

(CSS)
(Gherkin)
(HTML)
+ 2

2

8

Virtual Human Platform

The Virtual Human Platform (VHP) was developed through the VHP4Safety project to support chemical and pharmaceutical safety testing. VHP provides you with human-relevant tools and models for precision safety evaluation, helping you reduce reliance on laboratory animals.

toxicology

(CSS)
(Dockerfile)
(HTML)
+ 4

0

8

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

Design
Digitalization
Shape optimization
+ 1

(Automake)
(C)
(C++)
+ 3

3

7

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

Burns
Feasibility
MATLAB
+ 4

3

7

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

Ammonia
Atmospheric ammonia
blending distance
+ 7

4

7

SBSL

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

anti-cancer therapeutics
computational prediction
gene dependency
+ 3

3

7

Source code of the SWAN model: Free Infragravity Waves in the North Sea

coastal waters
Infragravity waves
inland waters
+ 3

3

7

Uncertainty Specification and Analysis for Thermosphere Observations

Accelerometer
GNSS tracking
Mass density
+ 2

(C)
(C++)
(Fortran)
+ 3

1

7

ece2cmor3

Process EC-Earth output to publish for CMIP6

Big data
High performance computing
Optimized data handling

(Python)
(Shell)

2

7

jaspProcess

A JASP implementation of the PROCESS macro for SPSS

Data Analysis
Statistics
Visualization

(QML)
(R)

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

PanVA

Variant Analysis within Pangenomes.

API
Data Analysis
pangenomics

(CSS)
(Dockerfile)
(HTML)
+ 6

2

7

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

(CSS)
(Dockerfile)
(JavaScript)
+ 2

7

xtas

the eXtensible Text Analysis Suite

Text analysis & natural language processing

(Java)
(Python)
(Shell)

2

7

[Artifact] Deductive Verification of Parameterized Embedded Systems modeled in SystemC

Deductive verification
embedded systems
parameterized systems
+ 2

6

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

Clutch
Electroadhesion
self-reinforcement
+ 2

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

dmpcrl-concept

Software for publication: Multi-agent reinforcement learning via distributed MPC as a function approximator

ADMM
alternating direction method of multipliers
distributed model predictive control
+ 2

(Markdown)
(Other)
(Python)

1

6

fedKMeans

Code supporting chapter 4 of the PhD thesis: Federated K-Means Clustering.

Big data
Clustering
federated learning
+ 3

2

6

FedvsCent

Code supporting chapter 3 of the PhD thesis: "A comprehensive experimental comparison between federated and centralized learning Open Access"

benchmark
complex models
Distributed data
+ 3

3

6

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