Software | Research Software Directory

LinkAhead

Open Source Research Data Management Software

Data
ETL
Inter-operability & linked data
+ 4

Java
Shell
Python
+ 2

6

13

Xenon

If you are using remote machines to do your computations, and don’t feel like learning and implementing many different APIs, Xenon is the tool for you.

batch-job
distributed computing
FTP
+ 11

Java
Shell
Batchfile

11

13

Code supporting the publication: Gromit: Benchmarking the performance and scalability of blockchain systems

Benchmarking
Blockchain
Performance
+ 1

Other
Python
JSON
+ 3

3

12

Data and Model of Scale Down Simulator for Industrial Syngas Fermentation

Fermentation
Process scale-up
Scale-down
+ 1

5

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

Software used in the publication "A Non-parametric Bayesian Network for multivariate probabilistic modelling of Weigh-in-Motion System Data”

axle load
Bayesian Networks (BN)
Weigh in motion

3

12

What does a Text Classifier Learn about Morality? An Explainable Method for Cross-Domain Comparison of Moral Rhetoric - code

Ethics
explainable artificial intelligence
Morality
+ 3

Python
Other
Markdown

7

12

nanopub

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

Inter-operability & linked data

Python
Shell
Batchfile

3

12

Code accompanying the paper "Modeling the effect of prior austenite grain size on bainite formation kinetics."

Bainite
Grain size
Nucleation
+ 2

3

11

Dataset for Nanowire solar cell above the radiative limit

nanowire
Shockley-Queisser limit
Solar cell devices

5

11

Gaussian FLORIDyn, Matlab implementation belonging to the paper: The revised FLORIDyn model: Implementation of heterogeneous flow and the Gaussian wake

FLOw Redirection and Induction Dynamics (FLORIDyn)
systems and control theory
wind currents
+ 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

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.

Fortran
C
TeX
+ 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

MATLAB
C
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
Makefile
+ 5

5

11

SIGA.py

Make genome annotations semantically interoperable

Inter-operability & linked data

Python

2

11

CIRRUS-HL-campaign-codes---Code-accompanying-dissertation

CIRRUS-HL campaign codes - Codes accompanying dissertation

Airborne measurements
Background aerosol
Backward trajectories
+ 7

Python
Markdown
YAML
+ 1

4

10

Code to incorporate entrapped air pocket dynamics into SWMM (AirSWMM2.0)

Air pocket dynamics
Intermittent water supply
Pipe-filling events
+ 1

C
Other
Markdown

4

10

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

IGBT modules
lifetime analysis
power electronic converters
+ 1

1

10

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

Python
Jupyter Notebook
Shell

3

10

MapReader

MapReader is an end-to-end computer vision (CV) pipeline for exploring and analyzing images at scale.

computer vision
digital humanities
geospatial
+ 4

Python
TeX
Dockerfile
+ 1

7

10

MDStudio

A tool to run molecular dynamics workflows.

High performance computing
Real time data analysis
Workflow technologies

Python
CSS
TypeScript
+ 5

4

10

A Public Ground-Truth Dataset for Handwritten Circuit Diagram Images

CGHD
Circuit Diagram
CircuitGraph
+ 4

XML
JSON
Python
+ 2

1

9

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

9

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

Other
Python
Markdown

5

9

Models and Optimization Tools for a Novel 3D Printed Capacitive Shear Stress Sensor

Capacitive Modeling
Capacitive Sensor
Mechanical Modeling
+ 2

4

9

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

COMSOL multiphysics software
Simulation

1

9

ChemSpaX: A Python tool for local chemical space exploration

ChemSpaX is a Python package that can be used for local chemical space exploration of any structure. This is done by placing substuents on a pre-defined skeleton. A substituent can be chosen from an existing library and can be attached to the skeleton.

catalysis
Chemistry
python

Python
Shell

3

9

gammalearn

Deep Learning for Imaging Cherenkov Telescopes Data Analysis

cta
deep learning
Gamma-ray telescopes
+ 1

Python
Dockerfile

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

Java
Common Workflow Language
Dockerfile
+ 2

2

9

AirSWMMv1.0

Code to incorporate entrapped air behaviour into SWMM (AirSWMM1.0)

Air–water interface interaction
Intermittent water supply
Stormwater management model (SWMM)
+ 1

C
Other

4

8

Bluesky software: underlying the publication “Distributed Conflict Resolution at High Traffic Densities with Reinforcement Learning”

Air traffic management (ATM)
BlueSky
Conflict detection and resolution
+ 3

1

8

eAC_charging_infra_optimization

Code underlying the publication: Optimizing the battery charging and swapping infrastructure for electric short-haul aircraft—The case of electric flight in Norway

Battery swapping systems
Commuter air transport
Electric aviation
+ 3

Other
Python
Markdown

1

8

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

8

Software underlying the publication: Modelling communication-enabled traffic interactions

Human driver model
Interaction Models

1

8

TraViA: a Traffic data Visualization and Annotation tool in Python

HighD
NGSIM
pNEUMA
+ 2

1

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

Python
Jupyter Notebook
TeX

7

8

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

Python
TeX
Makefile

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

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

Python
HTML
Jupyter Notebook
+ 2

2

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

7

Code underlying the publication: Forecasting estuarine salt intrusion in the Rhine-Meuse delta using an LSTM model

chloride
Delta
estuary
+ 7

4

7

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

7

ML-MoCap - Controller and Camera module Images

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

1

7

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

7

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

coastal waters
Infragravity waves
inland waters
+ 3

3

7

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