Software | Research Software Directory

Learning_on_SCs

Code underlying: Hodge-Aware Convolutional Learning on Simplicial Complexes

Hodge theorem
neural networks
simplicial complexes

(Markdown)
(Other)
(Python)
+ 1

1

6

MATLAB script and COMSOL models of the article "An efficient multiscale method for subwavelength transient analysis of acoustic metamaterials"

Equivalent fluid model
Homogenisation
Locally resonant acoustic metamaterials
+ 1

(Markdown)
(Matlab)
(Other)

4

6

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

6

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

6

eEcology Annotation Tool

Visualize and annotate GPS measurements of bird movements.

Inter-operability & linked data
Visualization

("API Blueprint")
(CSS)
(Dockerfile)
+ 5

1

6

Lightning

Lightning: Fast data processing using GPUs on distributed platforms

Big data
GPU
High performance computing

(C++)
(Python)
(Rust)

2

6

PSSMGen

Generates consistent PSSM and PDB files for protein-protein complexes

Big data
High performance computing
Optimized data handling

(Makefile)
(Python)

2

6

rWikiPathways

Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.

bioinformatics
WikiPathways

(HTML)
(R)
(TeX)

2

6

TulipaEnergyModel

This package provides an optimization model for the electricity market and its coupling with other energy sectors. The objective is to determine the optimal investment and operation decisions for different types of assets.

Energy system analysis
Energy system modelling
Integrated energy systems
+ 4

(Julia)
(Python)
(Ruby)
+ 2

9

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)
(C++)
(CMake)
+ 5

4

5

Automated xy calibration for 3D printers using a scanner

3D printer
calibration
FDM
+ 11

3

5

Code for the paper "Synergizing cycling and transit: Strategic placement of cycling infrastructure to enhance job accessibility"

code
cycling infrastructure
job accessibility

1

5

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

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

ColorIce: Automated in-plane ice thin section analysis tool

birefringence
crossed-polarization
grain boundary
+ 5

2

5

Inductive 3D printer XY calibration GUI

3D printer
calibration
FDM
+ 8

3

5

Sample dataset and software for FAST-EM array tomography

array tomography
FAST-EM
Image processing
+ 1

10

5

Script for: AID-PRIGSHARE: Automation of Indicator Development for Green Space Health Research in QGIS

buffer
gis
greenness
+ 2

(Markdown)
(Other)
(Python)

1

5

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

5

Summation of currents electromagnetic solver

Coil
FEM
Inductive
+ 6

3

5

Task-aware-connectivity-learning-for-incoming-nodes-over-growing-graphs

Code underlying the publication: Task-aware-connectivity-learning-for-incoming-nodes-over-growing-graphs

expanding graph
graph signal processing
incoming nodes
+ 2

(Matlab)

1

5

eEecology Classification

Automatic classification of accelerometer data using a supervised learning approach.

Machine learning

(Batchfile)
(CSS)
(HTML)
+ 3

1

5

MagnumPI - Potential Integrator

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

Inter-operability & linked data
Visualization

(C++)
(CMake)
(M4Sugar)
+ 2

6

5

mexca

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

Audio processing
Image processing
Machine learning
+ 1

(Dockerfile)
(Python)
(Shell)

5

PIQMIe

A web tool for mass spectrometry-based proteomics data analyses

Data Analysis
mass spectrometry
Optimized data handling
+ 2

(Dockerfile)
(HTML)
(JavaScript)
+ 3

1

5

sv-channels

Genome-wide detection of structural variants using deep learning

Machine learning

("Jupyter Notebook")
(Python)
(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

(C)
(R)

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

Livestock demography

This submodel simulates livestock herd demography and slaughter effects. Initially part of the ROMFARMS model for animal husbandry on the Dutch Roman frontier, it focused on cattle, sheep, and horses. However, the code is adaptable for various animals, regions, and historical periods.

2

4

Artefact of: JavaBIP meets VerCors: Towards the Safety of Concurrent Software Systems in Java

concurrent systems
Deductive verification
formal methods
+ 3

5

4

AutoEncodersDLSCA

Code underlying the publication: Autoencoder-enabled model portability for reducing hyperparameter tuning efforts in side-channel analysis

Autoencoders
Hyperparameter Tuning
Portability
+ 3

(Markdown)
(Other)
(Python)

1

4

Code and test data set underlying the publication: Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with a multiplexed magnetic tweezers

Dwell Time Analysis
magnetic tweezers
RdRP activity
+ 1

3

4

Code for Detecting Anomalous Misconfigurations in AWS Identity and Access Management Policies

Identity and Access Management
Misconfiguration Detection
Security

(Markdown)
(Other)
(Python)

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

Code to produce the results of the publication: “Neurophysiological Validation of Simultaneous Intrinsic and Reflexive Joint Impedance Estimates”

Electromyography
Joint resistance
Parallel-Cascade model
+ 2

1

4

Code underlying the publication: Maintenance Optimization for Multi-Component Systems with a Single Sensor

Condition-based maintenance
Inspection planning
Maintenance
+ 2

(Other)
(Python)

4

CoralModel: A Python-based model that resembles the biophysical interactions on a coral reef

biophysics
Coral Reef Ecology
hydrodynamics

1

4

Dataset of human gait in a domestic setup collected with an LFMCW MIMO radar

doppler signature
fmcw radar
gait
+ 4

4

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

characterization
fabrication
haptic display
+ 4

(Markdown)

3

4

endogenous-macrodynamics-in-algorithmic-recourse

Software and data underlying the publication: Endogenous Macrodynamics in Algorithmic Recourse

Algorithmic Recourse
Counterfactual Explanations
Dynamic Systems
+ 1

(CSS)
(HTML)
(JavaScript)
+ 8

3

4

etv_scheduling

Code underlying the publication: An environmentally-aware dynamic planning of electric vehicles for aircraft towing considering stochastic aircraft arrival and departure times

Dynamic scheduling
Electric towing vehicles
Stochastic scheduling
+ 2

(large-text-file)
(Markdown)
(Other)
+ 1

1

4

Matlab scripts and MuseScore scripts accompanying the book "The Perceptual Structure of Sound"

sound design

1

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

np_heating

Code for the modeling of heating around plasmonic core–shell nanoparticles

Heat transfer
Photothermal effect
Plasmonic nanoparticles
+ 1

(Markdown)
(Other)
(Python)

2

4

Script underlying the paper "On Robustly Convergent and Efficient Iterative Methods for Anisotropic Radiative Transfer"

acceleration
anisotropic
preconditioning
+ 3

3

4

scv_sparse_data

Code: Calculate Supply Chain Visibility with Sparse Data

sparse data
supply chain
supply chain visibility

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

1

4

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