Software | Research Software Directory

Dataset for Nanowire solar cell above the radiative limit

nanowire
Shockley-Queisser limit
Solar cell devices

5

12

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

12

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

Hanson's model
Propeller Aeroacoustics
Propeller Noise
+ 1

1

12

petcluster

Petrochemical cluster analysis tool

complex networks
Industrial cluster
industrial ecology
+ 2

(Markdown)
(Other)
(Python)

4

12

Python notebook to generate Figure 3 Panel C from: "Adaptability and evolution of the cell polarization machinery in budding yeast"

death ratios
jupyter notebook
microscopy
+ 1

1

12

Python notebook to generate the cell sizes changes across yeast mutants (Figure 3 Panel D from paper: "Adaptability and evolution of the cell polarization machinery in budding yeast")

cell sizes averages
jupyter notebook
microscopy
+ 1

1

12

TraViA: a Traffic data Visualization and Annotation tool in Python

HighD
NGSIM
pNEUMA
+ 2

1

12

nanopub

The nanopub library provides a high-level, user-friendly python interface for searching, publishing and retracting nanopublications.

Inter-operability & linked data

(JavaScript)
(Python)
(Shell)

3

12

Blade Element Momentum Theory Code for Positive and Negative Thrust Propellers

BEM
BEMT
Blade Element Momentum Theory
+ 2

1

11

Code and data belonging to the publication "Closed-loop Aspects of Data-Enabled Predictive Control"

closed loop identification
Data-driven control
Data-enabled Predictive Control
+ 2

(Markdown)
(Matlab)
(Other)

4

11

Code for the publication: Vibration-induced friction modulation for a general frequency of excitation

Average friction
Mechanical vibration
Method of direct separation of motion
+ 1

1

11

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

11

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

11

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

11

Numerical models and datasets concerning the publication:"Electrocatalytic reaction-driven flow"

COMSOL multiphysics software
Simulation

1

11

SIMULINK model for Lifetime Analysis of IGBT Power Modules in Passively Cooled Tidal Turbine Converters

IGBT modules
lifetime analysis
power electronic converters
+ 1

1

11

Software supporting the publication: Background Electromagnetic Noise Received via Ionospheric Propagation in a Remote Rural Location in Spain (set 2)

ambient noise
electromagnetic noise
ionosphere
+ 3

4

11

Cross-perspective Topic Modeling

An application that uses cross-perspective topic modeling to extract topics and opinions from text and provides insight into how they change over time.

Text analysis & natural language processing

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

3

11

DALES

DALES is a large-eddy simulation code designed for studies of the physics of the atmospheric boundary layer, including convective and stable boundary layers as well as cloudy boundary layers.

(C)
(CMake)
(Fortran)
+ 8

24

11

ExploreASL

ExploreASL is a pipeline and toolbox for image processing and statistics of arterial spin labeling perfusion MR images. It is designed as a multi-OS, open-source, collaborative framework that facilitates cross-pollination between image processing method developers and clinical investigators.

ASL
Image processing
MRI

(C)
(MATLAB)
(Python)

7

11

FastMLC

Detect clusters in for example large collections of DNA or protein sequences, and visualize the results in a web browser.

Big data
Machine learning
Visualization

(C)
(C++)
(CMake)
+ 5

5

11

SIGA.py

Make genome annotations semantically interoperable

Inter-operability & linked data

(Python)

2

11

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

11

fedKMeans

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

Big data
Clustering
federated learning
+ 3

2

10

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

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

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

BIEM
HAMS
HAMS-MREL
+ 4

5

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

scv_sparse_data

Code: Calculate Supply Chain Visibility with Sparse Data

sparse data
supply chain
supply chain visibility

("Jupyter Notebook")
(Other)
(Python)

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

ENCORE

Enhancing Computational Reproducibility

Communication and replication
Computational science
computer science
+ 2

(HTML)
(Python)
(TeX)

2

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

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

Deductive verification
embedded systems
parameterized systems
+ 2

6

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

8

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: Maintenance Optimization for Multi-Component Systems with a Single Sensor

Condition-based maintenance
Inspection planning
Maintenance
+ 2

(Other)
(Python)

4

8

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

characterization
fabrication
haptic display
+ 4

(Markdown)

3

8

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

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

Sample dataset and software for FAST-EM array tomography

array tomography
FAST-EM
Image processing
+ 1

10

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

Software and data underlying the publication: Faithful Model Explanations through Energy-Constrained Conformal Counterfactuals

Classification and Regression
Deep Generative Models & Autoencoders
Humanities & Computational Social Science
+ 1

(JavaScript)
(JSON)
(Julia)
+ 6

3

8