Software

Check out all the research software, including tools and libraries, that the eScience Center has contributed to over the years. Click on the entries to get a full description, the source code, related projects and tools, citation information and much more.

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PyTorch Performance Analysis

Lessons on PyTorch Performance Analysis: from Profiling to Optimization

• deep learning
• GPU
• High performance computing
• Machine learning
• Profiling
• PyTorch

• 1 contributors
• 0 mentions

python-mock-precommit-hook

precommit hook to prevent monkeypatching in Python

• 1 contributors
• 0 mentions

hipDecomp

hipDecomp is an Adaptive Pencil Decomposition Library for AMD GPUs.

• GPU
• High performance computing
• HIP

• 1 contributors
• 0 mentions

CaNS

Canonical Navier-Stokes is a library for massively-parallel numerical simulations of fluid flows.

• Computational Fluid Dynamics (CFD)
• GPU
• Numerical analysis

• 3 contributors
• 134 mentions

pdbwords

Render text as protein structures

• 1 contributors
• 0 mentions

docker sandbox templates

Enhanced docker sandbox templates for using AI agents in a secure vm-based sandbox

• AI agent
• docker
• LLM security
• sandbox
• Security

• 1 contributors
• 0 mentions

devcontainer

CLI to create devcontainer template for running AI agents in a container

• AI agent
• containers
• docker
• sandbox
• Security

• 1 contributors
• 0 mentions

LARA Lab Automation

Open source toolset for lab automation

• laboratory automatization

• 6 contributors
• 4 mentions

duckdb-mmcif

Read/write protein structure mmCIF files using SQL with DuckDB

• Data
• Data Analysis
• Optimized data handling

• 1 contributors
• 0 mentions

CorticalSim

Fast simulation of plant cortical microtubules.

• 7 contributors
• 44 mentions

prfmodel

A modern Python implementation for population receptive field modelling.

• GPU
• neuroimaging
• Neuroscience
• optimization
• python

• 3 contributors
• 0 mentions

rcrisp

rcrisp provides tools to automate the morphological delineation of riverside urban areas.

• Data Analysis
• geospatial
• R
• Urban rivers

• 4 contributors
• 0 mentions

VU-Lab

This is the configuration and documentation page of the LARA lab automation setup at the VU. It i...

• Dynamic scheduling
• laboratory automatization
• orchestration

• 4 contributors
• 0 mentions

snakemake-storage-plugin-rucio

A Snakemake storage plugin that handles files available through [Rucio](https://rucio.cern.ch/).

• rucio
• snakemake

• 3 contributors
• 0 mentions

Pure3D

A web platform for exploring 3D digital collections and editions in cultural heritage.

• 2 contributors
• 0 mentions

Climate Rapid Evaluation Framework

Rapid Evaluation Framework for climate simulations

• Big data
• Climate modeling

• 12 contributors
• 8 mentions

jaspKinematics

A trajectory analyzer for JASP

• Biology
• kinematics
• Physics

• 1 contributors
• 0 mentions

jaspModuleTemplate

Template to create a JASP module.

• Data Analysis
• Statistics

• 0 contributors
• 0 mentions

JASP modules app

A web application that allows you to search/filter all the available JASP modules and install them.

• 3 contributors
• 0 mentions

Streetscapes explorer frontend

Web application to review and edit segmented street view images.

• 4 contributors
• 0 mentions

rocrate-action-recorder

Python package to record calls of Python CLI commands into a Research Object Crate (RO-Crate). S...

• Inter-operability & linked data
• Workflow technologies

• 1 contributors
• 1 mentions

swiftmhc

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

• deep learning
• Protein-Protein Interaction
• Transformer

• 3 contributors
• 2 mentions

QANS

QANS (Questionnaire And Nomination Software) is a collection of software components to enable lon...

• Peer Nomination
• questionnaire
• sociology
• Sociometry
• survey

• 7 contributors
• 0 mentions

ModuleMixins.jl

Make your Julia modules composable! With ModuleMixins you can design larger programs in Julia, bu...

• Entity Component System
• Julia Package
• Metaprogramming
• Software Architecture
• Software Design

• 1 contributors
• 0 mentions

CAExplorer.jl

A widget that lets you explore the dynamics of a particular cellular automaton that operates on a...

• Agent-based modeling
• Interactive Visualization
• Julia Language

• 1 contributors
• 0 mentions

CarboKitten.jl

A toolkit for forward modelling of stratigraphic record of carbonate platforms, written in Julia.

• Geosciences
• Julia Language
• modelling

• 2 contributors
• 0 mentions

document-segementation

Tool for identifying document boundaries and categories from VoC inventories.

• AI
• deep learning
• Machine learning
• python
• Text analysis & natural language processing

• 1 contributors
• 0 mentions

Introduction to deep learning lesson

This lesson gives an introduction to deep learning.

• deep learning
• lesson
• python

• 13 contributors
• 0 mentions

Enriching Digital Heritage (pre-workshop)

Software related to the startup phase of the project Enriching Digital Heritage

• cultural heritage
• large language models
• named entity linking
• named entity Recognition

• 1 contributors
• 0 mentions

The Cultural Heritage AI Cookbook: Notebooks

Google Colab notebook that uses large language models for analyzing and expanding text metadata r...

• cultural heritage
• large language models
• named entity linking
• named entity Recognition
• relation finding

• 3 contributors
• 0 mentions

Containers for the KM3NeT Rucio deployment

This repository contains configuration files and scripts to build KM3NeT-specific container image...

• Big data
• High performance computing

• 2 contributors
• 0 mentions

Rucio policy package for KM3NeT

Package with custom policies for the Rucio instance of KM3NeT.

• Big data
• Data management

• 2 contributors
• 0 mentions

Rucio deployment for KM3NeT

This repository contains the Rucio deployment for KM3NeT. It can be used as an example of how to ...

• Big data
• High performance computing

• 3 contributors
• 1 mentions

powerfit

Rigid body fitting of atomic strucures in cryo-electron microscopy density maps

• cryo-electron microscopy
• macromolecular structure
• map fitting

• 6 contributors
• 72 mentions

protein-detective

Python package to detect proteins in EM density maps.

• 3 contributors
• 0 mentions

REE-HDSC

Software developed in the project REE-HDSC (Recognizing Extracted Entities for the Historical Dat...

• hand-written text recognition
• named entity Recognition

• 1 contributors
• 0 mentions

Annular

Annular is a setup for running coupled energy system models with the aim of modeling flexibility ...

• 3 contributors
• 0 mentions

cudawrappers

The cudawrappers library is a C++ wrapper for the Nvidia C libraries such as the CUDA driver, NVR...

• accelerators
• CUDA
• GPU

• 13 contributors
• 0 mentions

PlanEO Dashboard

Provides an interactive interface for visualizing geographical data relevant to the MINE-DD proje...

• Data Analysis
• Demographic Analysis
• Geographic Visualization
• gis
• Interactive Dashboard
• Life Sciences
• Pathogen Distribution
• Point Data
• Raster Overlays
• Risk Factors
• Spatial Data Analysis

• 3 contributors
• 0 mentions

TulipaClustering.jl

Cluster profiles into representative periods.

• Clustering
• Energy system analysis
• Energy system modelling
• Open source tool

• 6 contributors
• 0 mentions

TulipaIO.jl

This package relies on DuckDB to tie a variety of data sources with Julia, and TulipaEnergyModel ...

• 4 contributors
• 0 mentions

TulipaEnergyModel

This package provides an optimization model for the electricity market and its coupling with othe...

• Energy system analysis
• Energy system modelling
• Integrated energy systems
• Investment planning
• Open source tool
• optimization
• Sector coupling

• 9 contributors
• 6 mentions

RESTful APE

RESTful API for the APE (Automated Pipeline Explorer) library.

• Java
• Program synthesis
• REST API
• Workflow technologies

• 3 contributors
• 0 mentions

mkdocs rich argparse

An MkDocs plugin to generate documentation for a rich argparse parser. It renders commands, sub c...

• python

• 1 contributors
• 0 mentions

Effort Sharing

Analysis and plotting scripts for effort sharing, associated with the Carbon Budget Explorer

• 4 contributors
• 0 mentions

Open Matrices Stimulus Set (omss)

omss is a Python package for generating matrix reasoning puzzles, inspired by Raven's Progressive...

• Intelligence
• Matrices
• python
• Stimuli

• 4 contributors
• 0 mentions

Cosimplat

Co-simulation framework made for RESCUE project

• 4 contributors
• 0 mentions

KMM

KMM is a lightweight C++ middleware for accelerated computing.

• GPU
• High performance computing

• 2 contributors
• 0 mentions

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