Software | Research Software Directory

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
TeX
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++
Python
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 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

Inductive 3D printer XY calibration GUI

3D printer
calibration
FDM
+ 8

3

5

petcluster

Petrochemical cluster analysis tool

complex networks
Industrial cluster
industrial ecology
+ 2

Python
Other
Markdown

4

5

Sample dataset and software for FAST-EM array tomography

array tomography
FAST-EM
Image processing
+ 1

10

5

SBSL

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

anti-cancer therapeutics
computational prediction
gene dependency
+ 3

3

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

TeX
Other
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

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

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

Python
Other
Markdown

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

Python
Markdown
Other

4

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

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

Python
Other

4

ColorIce: Automated in-plane ice thin section analysis tool

birefringence
crossed-polarization
grain boundary
+ 5

2

4

endogenous-macrodynamics-in-algorithmic-recourse

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

Algorithmic Recourse
Counterfactual Explanations
Dynamic Systems
+ 1

Other
HTML
JSON
+ 8

3

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

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

buffer
gis
greenness
+ 2

Other
Python
Markdown

1

4

SNAPWF

Code underlying the publication: Automated Python workflow for generating Sentinel-1 PSI and SBAS interferometric stacks using SNAP on Geospatial Computing Platform

InSAR
Interferometric Stacks
Open-Source Tools
+ 2

Jupyter Notebook
XML
Python
+ 1

7

4

Source code for INCS (Iterative Nonlinear Contrast Source)

INCS
medical ultrasound
microbubbles
+ 1

Fortran
Other
Matlab
+ 5

2

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

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

howfairis

Command line tool to analyze a git repository's compliance with the fair-software.eu recommendations.

HTML
Python
Shell
+ 1

7

4

LUE

LUE is software for storing and manipulating large amounts of information for large numbers of objects. The software is useful, and currently mainly used, in the context of environmental modelling of biological and physical systems, represented by agents and fields.

Agent-based modeling
environmental modelling
field based modelling
+ 6

C++
Python
CMake
+ 6

3

4

nanomesh

Python workflow tool for generating meshes from 2D and 3D microscopy image data

Image processing
Visualization
Workflow technologies

Jupyter Notebook
Python
Shell
+ 1

3

4

Noodles

Task-based parallel programming model in Python that offers the same intuitive interface when running complex workflows on your laptop or on large computer clusters.

High performance computing
Workflow technologies

Jupyter Notebook
Python
Shell
+ 2

9

4

Hercules

Retrieve recent tweets from certain users and classify them with machine learning

Machine learning
Text analysis & natural language processing

Python
Jupyter Notebook
Shell

1

4

PerfectFit

This is a virtual coach system that coaches users into being more physically active and stop smoking.

Big data
health

JavaScript
Gherkin
Shell

5

4

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