Software | Research Software Directory

swiftmhc

SwiftMHC is a deep learning algorithm for predicting pMHC structure and binding affinity at the same time.

deep learning
Protein-Protein Interaction
Transformer

Python
Mask
Shell

2

1

TaxoTagger

DNA barcode identification, powered by semantic searching.

Fungi
Machine learning
semantic search
+ 3

Python
Makefile
Mustache

1

Umple

Umple allows generation of code in Java, PHP and other languages from a textual representation of UML state machines, associations and other modeling constructs, thus saving coding effort

Code Generation
Software Modeling
State Machines
+ 1

Java
JavaScript
GAP
+ 17

14

1

ValidSense

The ValidSense toolbox aims to assess the agreement between two quantitative methods using the Limits of Agreement analysis, aka the Bland-Altman analysis. Four existing variants are available. Moreover, a Longitudinal analysis is developed to assess agreement over time.

Agreement Analysis
Bland-Altman
Limits of Agreement
+ 1

Python

4

1

WAM2layers

WAM2layers is an atmospheric moisture-tracking model that can be used to determine where precipitation originally evaporated (backtracking), or where evaporated moisture eventually ends up (forward tracking).

atmospheric rivers
ERA5
hydrological cycle
+ 4

Python
Jupyter Notebook
Shell

4

1

Workflomics

Web platform for workflow exploration and benchmarking in bioinformatics

Inter-operability & linked data
Workflow technologies

TypeScript
CSS
HTML
+ 1

7

1

WRF-runner

Simple shell script to run a complete WPS/WRF experiment in one go

climate
Forecasting
workflow
+ 1

Shell

2

1

Angle-and-step random walk

An Python implementation of random walk in 2D space based on agent angle orientation and step distance. It defines an agent class `Walker` capable of random walk movement based on random angle and movement step distance in a continuous 2D space.

1

0

Random walk in data frames

Collection of methods for producing random walks in two-dimensional space outputting position coordinates in data frames, including alternatives for grid and non-grid space. In R, it uses tidyverse "tibble" to construct the data frames that store trajectories.

2

0

Resource exploitation procedure

This module takes an agent and lets it decide which resources to target and exploit. The agent moves to the patch to be harvested, takes the resources and returns home

1

0

Absorption Coefficient Estimator using Domain Adaptation

Code underlying the research project: Extracting absorption coefficients from a room impulse response using a convolutional neural network with domain adaptation

Absorption Coefficient
domain adaptation
Machine learning
+ 3

Other
Python
Markdown
+ 1

1

0

ACDC-OpFlow

ACDC-OpFlow, Unified, Cross-Language Framework for AC/DC Optimal Power Flow Solutions

AC/DC power systems
Optimal Power Flow
power electronic converters

4

0

A demand management and frequency settings model for complying to the COVID-19 capacity limits in public transport operations

COVID-19
demand management
frequency settings
+ 3

1

0

AeoLiS v2.1.0

advection
aeolian sediment transport
coastal dunes
+ 5

9

0

Agent-based model software written for the master thesis Scaling Up, Staying Secure

Agent based modelling and simulation (ABMS)
CYBER SECURITY
Distributed energy resources (DER)
+ 2

1

0

A high spatial resolution Extended Spring Indices database over American and European regions

Citizen Science
Climate change
Cloud computing
+ 4

Python
Markdown
Other

2

0

AircraftDuctedFanOptimisation

The Unified Ducted Fan Code and Ducted Fan Optimisation Framework

Aircraft
Aircraft performance
Conceptual aircraft design
+ 7

Python
Other
Markdown

1

0

Air Traffic Control Reinforcement Learning Environment

Air Traffic Control (ATC)
Air traffic management (ATM)
Reinforcement Learning (RL)

4

0

A model for modifying the public transport service patterns to account for the imposed COVID-19 capacity

capacity
coronavirus
COVID-19
+ 7

1

0

ANNESI: An open-source artificial neural network for estuarine salt intrusion

estuary
Neural Network
salt intrusion

1

0

Application of SDDTMPC to control a unicycle

MPC
nonlinear control
robotics
+ 2

Matlab
Markdown

1

0

ApPlyWood: a calculation tool supporting the design of plywood-based seismic retrofitting interventions on existing timber floors

Architectural conservation
Design tools
Earthquake engineering
+ 4

1

0

APS

APS: Asses Pedestrian model Speed framework

Computational Complexity
Model assessment framework
Pedestrian models
+ 1

Python
Other
Markdown
+ 1

1

0

Argon Laser-Plasma Thruster - Design and Test of a Laboratory Model - Processing and Analysis Code

argon
laser
laser-sustained plasma
+ 4

Other
TeX
Jupyter Notebook
+ 5

1

0

Artifact for paper (Alpinist: an Annotation-Aware GPU Program Optimizer)

Annotation-aware
Deductive verification
GPU
+ 2

4

0

Artifact for the paper "A Formally Verified IEEE 754 Floating-Point Implementation of Interval Iteration for MDPs"

Correct-by-construction
Floating-point
IEEE 754
+ 6

Other
C
JSON
+ 5

5

0

Artifact for the paper "Efficient Formally Verified Maximal End Component Decomposition for MDPs"

Correct-by-construction
Interactive Theorem Proving
Maximal End Components
+ 3

Other
XML
JSON
+ 6

3

0

Artifact of Knor: reactive synthesis using Oink

binary decision diagrams
parity games
reactive synthesis

Other
C
HTML
+ 15

1

0

Artifact to the paper "A Fast and Verified Probabilistic Model Checking Pipeline for Minimal Reachability Probabilities"

Correct-by-construction
Interactive Theorem Proving
Markov decision process
+ 1

Other
C
C++
+ 4

1

0

Assets for JOAN: a framework for human-automated vehicle interaction experiments in a virtual reality driving simulator

Carla simulator
Driving simulation
JOAN simulator
+ 1

5

0

Attitudes Toward a Virtual Smoking Cessation Coach: Analysis Code

Acceptance
Behavior change support systems
Chatbot
+ 7

6

0

auction-tas

Truck Appointment Systems - Auction Based

Auction
competition
Scheduling
+ 2

Other
Jupyter Notebook
Python
+ 2

1

0

Axies: Identifying and Evaluating Context Specific Values - code

Context
Ethics
NLP
+ 1

4

0

bachelor-thesis

Code underlying the BSc thesis: Creating Robust Train Unit Shunting Plans using Probabilistic Programming

inference
Probabilistic modelling
railroad
+ 12

JSON
Other
Julia
+ 2

1

0

Bayesian Ensembles for Exploration in Deep Reinforcement Learning; Code underlying the dissertation "Bayesian Model-Free Deep Reinforcement Learning"

Bayesian modelling
Deep Reinforcement Learning (DRL)
Ensemble model
+ 2

Python
Markdown

1

0

Bluesky software: underlying the publication “Improving Algorithm Conflict Resolution Manoeuvres with Reinforcement Learning”

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

1

0

Boundary-Layer-Program underlying the master thesis: Simulation of Two-Dimensional Steady State Boundary Layers Applied to Nonideal Gas Flows

algebraic turbulence model
boundary layer method
CS-model
+ 6

1

0

bounded-private-cycle-detection

Source code underlying the publication: Privacy-Preserving Peer-to-Peer Cycle Detection

cycle detection
multi-party computation
privacy-preserving
+ 1

C++
C
Other
+ 2

2

0

CEConv

Code underlying the publication: Color Equivariant Convolutional Networks

color equivariance
color robustness
equivariance
+ 1

Python
Markdown
Other

5

0

ChildsPlayAccessibility (Github) code repository: spatial analysis underlying the conference paper "Easy as child’s play? Co-designing a network-based metric for children’s access to play space"

Accessibility
Children
Co-design
+ 2

2

0

Cities for Citizens: Identification of Public Value Conflicts in Urban Spaces - Accompanying Code

Natural Language Processing
spatial analysis
Structural Topic Modelling
+ 1

1

0

Cluster Analysis of Temporal Patterns of Travel Production

The codes associated with the publication: A Cluster Analysis of Temporal Patterns of Travel Production in the Netherlands: Dominant within-day and day-to-day patterns and their association with Urbanization Levels

demand pattern
land-use feature
temporal pattern
+ 2

Jupyter Notebook
Python
Markdown
+ 1

3

0

Code Accompanying the Doctoral Dissertation: Theory of Chirality Induced Spin Selectivity in Two Terminal Transport

Magneto-transport
Onsager reciprocity, Büttiker reciprocity, Voltage probes, Coulomb interactions, Mean-field theory, (non-)collinear Hubbard one approximation, Vibrational modes, Spin-orbit coupling, Stray fields, Chirality Induced Spin Selectivity

1

0

Code accompanying the paper on aircraft path planning in continuous environments with deep reinforcement learning

BlueSky
Deep Reinforcement Learning
Path Planning
+ 1

1

0

Code accompanying the paper "Validating human driver models for interaction-aware automated vehicle controllers: A human approach”

automated driving
driver model validation
interaction-aware controllers
+ 1

3

0

Code and data accompanying the paper entitled "Seismic fault slip behaviour predicted from internal microphysical processes"

Earthquake simulation
high velocity friction
microphysical model
+ 1

1

0

Codebase Underlying the BSc Thesis: Type-Checking Modules and Imports using Scope Graphs

glob imports
haskell
lm
+ 5

Other
Haskell
Python
+ 1

3

0

Code belonging to the publication: Closed-loop model-predictive wind farm flow control under time-varying inflow using FLORIDyn

dynamic engineering wake model
FLORIDyn
MATLAB
+ 5

Other
Matlab
Markdown
+ 1

1

0

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