All software

Tilburg University Coding Café

Materials for Tilburg University's Coding Café

Tissue Simulation Toolkit

Tissue Simulation Toolkit (TST) 2.0 is an efficient C++ library for two-dimensional simulations of Glazier and Graner's Cellular Potts model (Glazier and Graner, 1993). It is suitable for simulations with live visualization as well as batch simulations on clusters.

TOPAS

The TOPAS toolkit aims to provide an intuitive Monte Carlo framework for medical physicists and researchers in related fields

TOPASopt

A toolkit for performing optimization with the TOPAS Monte Carlo simulation package. Includes tools for running simulations and analyzing results.

ToxTempAssistant

LLM-based web-app to assist users in drafting ToxTemp, a template for describing in-vitro toxicity test methods in compliance with GD211.

TrajectoryLog.NET

A Clibrary for reading and parsing Varian Eclipse trajectory log files. Provides a clear and simple API for accessing log data.

trex2champ

trex2champ is a tool that allows reading output files of quantum chemistry codes (GAMESS and trexio files) and writing input files for CHAMP in V3.0 format.

Trustchain

Trustchain is a decentralized approach to public key infrastructure designed for application to digital identity. Based on the W3C standards for decentralized identifiers (DID) and verifiable credentials (VC), it enables the creation of chains of trustworthy DIDs between recognizable legal entities.

tsdf

A package to read, modify and write TSDF data in Python.

TulipaClustering.jl

Cluster profiles into representative periods.

TulipaIO.jl

This package relies on DuckDB to tie a variety of data sources with Julia, and TulipaEnergyModel (TEM). It also enables a bidirectional capability to manipulate datasets from Julia and back to DuckDB.

Tweet_collector

This project is aimed to help researchers to use Academic Research product track to collect tweets of their interest and analyze them.

UCoMX

UCoMX (Universal Complexity Metrics Extractor) is a novel software package designed to extract complexity metrics from DICOM-RT plan files of radiotherapy treatment plans. The tool is platform-agnostic, engineered to seamlessly operate with DICOM-RT plan files created using diverse commercially…

UFEMISM2.0

The successor of UFEMISM, has all of its features (and more?), but is based on the distributed architecture introduced in minimism.

Unraphael

Unraphael is a computer vision tool for art history, designed to support the analysis of figure-outline similarities in images to study Renaissance copying practices. Its user-friendly interface lets researchers inspect structural patterns, revealing insights into artistic techniques.

UnrollingAverages.jl

A Julia package to deconvolve simple moving averages of time series.

UNSAT3D

Soil health is essential for infrastructure and plant growth. The UNSAT project aims to improve 3D soil image processing using machine learning and high-fidelity simulation data to study water transport and root-soil interactions during maize growth.

User-Defined Oceanographic Data Products

Allows researchers to access Oceans2.0 data products programmatically and also enable researchers to define, test, use and share processing code for user-defined data products in a custom-designed programming environment.

VarianESAPI-EQD2Converter

A Varian Eclipse scripting plugin for converting dose to EQD2 (equivalent dose in 2 Gy fractions). Automates the calculation of EQD2 for plans.

VarianESAPI-FieldEditor

A Varian Eclipse scripting plugin for editing treatment fields. Provides a graphical interface for modifying field shapes and parameters.

VarianESAPI-HalcyonGantryAngle

A Varian Eclipse scripting plugin for Halcyon gantry angle calculation. Automates the calculation of gantry angles for Halcyon plans.

Verbroken Verbinding NOA conversation survey

As part of our project Verbroken Verbinding we developed a conversation survey. This an AI-driven conversation with respondents. Contrary to conventional surveys, this method enables more detailed insights in the motivations behind answers to survey items.

Verticox+

Verticox+ is a Cox proportional hazards algorithm for vertically distributed data. The solution is based on the Verticox algorithm from Dai et al., 2022. It has been adapted to be used within the Vantage6 framework.

Virtual Health Gateway

The Virtual Health Gateway is a platform that facilitates direct, consistent, and standardized capture of diverse data types from research study participants in real-world settings.

Virus Seq

The VirusSeq Data Portal is an open-source and open-access data portal for all Canadian SARS-CoV-2 sequences and associated non-personal contextual data. It harmonizes, validates and automates submission to international databases.

visor

The goal of visor is to provide a set of tools for visibility analysis.

votca-xtp

VOTCA-XTP is a library which allows you to calculate the electronic properties of organic materials

vqls-prototype

Variational Quantum Linear Solver Library.

Web-enabled Awareness Research Network (WARN)

Web-enabled Awareness Research Network - Earthquake and Tsunami detection.

Winnow

Confidence control and FDR estimation for de novo peptide sequencing

wntr-quantum

wntr-quantum (pronounced winter-quantum) extends the capabilities of the popular wntr package for water network modelling and analysis to quantum computing routine.

xarray-regrid

An xarray plugin that adds regridding utilities for datasets and dataarrays.

Xenon Docker images

For your testing needs a collection of Docker images with different file systems and batch schedulers.

X-LAB Plotting Manager

The X-LAB Plotting Manager is a modular framework for turning raw data into plots. It offers a structured, scalable alternative. By enforcing modular components with clear responsibilities and a configurable UI, it replaces tangled plotting scripts with a robust and reproducible analysis pipeline.

xNoise

XrayTIFF2h5

This repository provides a workflow to transform X-rays data originally stored in .TIFF format, into .h5. Overall, this makes the data more compressed and easier to process in machine learning pipelines, such as unsat.

yatiml

Python library for YAML type inference, schema checking and syntactic sugar.

Yoda

A system for reliable, long-term storing and archiving large amounts of research data during all stages of a study.

zampy

Tool for downloading Land Surface Model input data

ZarrVis (Ruisdael)

Zarr files visualizer for the web. Ruisdael observatory (TU Delft)

Zeeschuimer

Zeeschuimer is a browser extension that monitors traffic while browsing social media, and collects seen posts/items for later systematic analysis. Its target audience is researchers who study content on social media platforms that resist conventional scraping or API-based data collection.