CodeMeta overview
This page gives a succinct overview of all software pages that export to CodeMeta.
Warning: this feature is still in development, so the generated CodeMeta data might still
change.
A freely available Virtual Machine encompassing tools, databases, and workflows for cheminformaticians, including new resources developed for ligand binding site comparisons and GPCR research.
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.
The 4CAT Capture and Analysis Toolkit provides modular data capture & analysis for a variety of social media platforms.
Its goal is to make the capture and analysis of data from these platforms accessible to people through a web interface, without requiring any programming or web scraping skills.
Abinit is a software package based on density functional theory for calculating the properties of solids.
Use adhtools for analyzing Arabic corpora.
Estimate age-depth models in geology and use them to transform various types of data (fossil ages, phylogenetic trees, trait evolution of lineages) between the time domain and the stratigraphic domain.
A web application able to visualize the AHN2 point cloud data of the Netherlands.
A web service to serve large point cloud data efficiently using octrees.
The aiida-champ plugin to handle the CHAMP workflow using AiiDA.
Generate and compare deep learning models for generating synthetic mass spectral libraries
If you are studying how single nucleotide polymorphisms are clustered in genomic samples, then the Allelic Variation Explorer can help you visualize them.
A real-time pipeline to search for Fast Radio Bursts and other transient radio sources.
Combine existing numerical codes in an easy to use Python framework. With AMUSE you can simulate objects such as star clusters, proto-planetary disks and galaxies.
Analizo is a free, multi-language, extensible source code analysis. It supports the extraction and calculation of a fair number of source code metrics, generation of dependency graphs, and software evolution analysis.
ANNUBeS is a deep learning framework meant to generate synthetic data and train on them neural networks aimed at developing and evaluating animals' training protocols in neuroscience.
Python package to replace identifiable strings in multiple files and folders at once
A CLI, Java API and RESTful API for the automated generation of computational pipelines (scientific workflows) from large collections of computational tools.
ArcticConnect is a network-enabled platform for realizing geospatial referencing of information about the arctic system derived from research, education, and private sector activities in the arctic and subarctic.
Arctic Web Map (AWM) is an Arctic-specific web mapping tool allowing researchers to customize map projections for scientifically accurate visualization and analysis, a function that is critical for arctic research but missing in existing web mapping platforms.
Arena-Crowds is Python scripts for the data analysis to estimate crowd density based on WiFi positioning.
Argopy is a python library dedicated to Argo data access, manipulation and visualisation for standard users as well as Argo experts.
The Biocloud is the underlying digital back-end infrastructure of the ARISE program.
Arpra is a C library for analyzing the propagation of numerical error in arbitrary precision IEEE-754 floating-point computations.
Command line interface to simulate an ASReview analysis using a variety of prior sampling strategies, classifiers, feature extractors, queriers, balancers, and stopping rules, all of which can be configured to run with custom parameterizations.
A tool written in rmarkdown for assessing the level of agreement between two raters following screening in ASReview. Users only need the two .csv files downloaded from ASReview, and the tool will automatically compile a summary report as an HTML file, viewable in your web browser.
The ASTRA Toolbox is a Python and MATLAB library of flexible, high-performance GPU-accelerated primitives for 2D and 3D tomography.
An interactive dashboard for visualisation, integration and classification of data using Active Learning.
Atlascine is an open-source, online mapping platform dedicated to bringing stories and maps closer together. This tool combines multimedia storytelling with digital mapping technologies to enable researchers to create, interact with and study spatial relationships within and between stories.
The atlas demonstrates outputs from the probabilistic projection methods developed or assessed in the European Climate Projection system EUCP Horizon2020 project.
Implements the Attention mechanism in Julia as a modular Lux layer
Bacting is an open-source platform for chemo- and bioinformatics based on Bioclipse that defines a number of common domain objects and wraps common functionality, providing a toolkit independent, scriptable solution to handle data from the life sciences.
Deploys a Kubernetes cluster and big data services on the cloud.
This project simulates Landsat data and evaluates the performance of recovery indicators with respect to data and disturbance characteristics.
BestieTemplate.jl is a template focused on best practices for package development in Julia.
Measure the number of contributions to Wikipedia entries from individuals from different counties as a measure of cultural bias.
A toolbox for detecting structural bias in continuous optimization heuristics.
a scalable and extensible image analysis framework
BIRCH is a powerful framework for organizing and using bioinformatics. BIRCH comes with hundreds of commonly-used tools, and allows you to customize your BIRCH site by adding new ones.
bird-cloud-gnn is a Python package that helps generate a graph representation from point cloud data and fits graph neural networks for classification problem
A library of numeric, geometric and XML routines
Boatswain is a simple build system for docker images. It is especially useful when you have multiple docker images that depend on each other.
BrainBrowser is an open source JavaScript library exposing a set of web-based 3D visualization tools primarily targetting neuroimaging
a minimalist workflow system in Python
Java library for identifier mapping
R package for the BridgeDb Java library making identifier mapping functionality available in the R environment.
REST API for identifier mapping
Parser library for reading custom binary files from Python.
Web Processing Service for Climate Data Analysis in the MAGIC project.
The Canadian Advanced Network for Astronomy Research (CANFAR) is a consortium that serves data-intensive storage, access, and processing needs of university groups and centers engaged in astronomy research.
CWRC aims to make digital research methods broadly accessible, and to develop an active community of researchers engaged in exploring the potential of collaboration online.
CHORD is a project to build a federated, Canadian, national data service for privacy- sensitive genomic and related health data. It allows the technologies and services being built by CanDIG and its international partners to be made available to the Canadian health research community more broadly.
The goal of this project is to provide a web service providing inland waterbodies initially available on GeoBase and updated using the most recent Landsat-8 imagery.
CanWIN (Canadian Watershed Information Network) is the data centre for the Centre for Earth Observation Science (CEOS). We support research and education, and inform management, policy and evidence based decision-making from the Nelson River Watershed to the Arctic.
Web application to visualize countries' carbon emission pathways under various views on fairness.
Web application for exploring the citation network of Dutch court decisions.
Caselawnet constructs citation networks from collections of Dutch case law.
CAT is a collection of tools designed for the construction of various chemical compounds.
CBRAIN is a flexible Ruby on Rails framework for accessing and processing of large data on high-performance computing infrastructures.
The Complex CUDA GEMM Library (ccglib) provides mixed-precision matrix-matrix multiplication kernels for complex data.
The CDF2Medmij-Mapping-tool facilitates the seamless transformation of cohort data into MedMij-compliant FHIR formats, enabling the harmonization of diverse datasets within a federated learning infrastructure.
Ceiba and its command-line interface Ceiba-cli solve the problem of computing, storing, and securely sharing computationally expensive simulation results.
command line interface to interact to interact with the ceiba web server
Cerise is a service for running CWL workflows on HPC resources. You add software, tool descriptions, and connection information, then your user runs workflows whenever they want.
A Python 3 library for talking to HPC clusters and supercomputers.
Web Application that visualizes data stored in the NetCDF format on a globe.
Command line tool to convert CITATION.cff files to various formats used by reference managers such as Zotero and JabRef.
GitHub action to validate CITATION.cff files, and convert to other citation formats using the dockerized version of cffconvert
A web form to initialize CITATION.cff files which you can use to include citation information into your software repository.
The Cornell-Holland Ab-initio Materials Package (CHAMP) is a quantum Monte Carlo suite of programs for electronic structure calculations. The code is developed by Claudia Filippi and Saverio Moroni, with significant contributions by Ravindra Shinde, N. Renaud, V. Azizi, E. Landinez, and S. Shepard.
This Python script checks whether a given set of software dependencies is met. This script itself is completely stand-alone and depends only on Python being installed. You may include this script along with a `dependencies.ini` in a project that has a diverse set of dependencies.
Chemical Analytics Platform is a freely available Virtual Machine encompassing tools, databases, and KNIME workflows.
Open Source cheminformatics library.
ChemSpaX is a Python package that can be used for local chemical space exploration of any structure. This is done by placing substuents on a pre-defined skeleton. A substituent can be chosen from an existing library and can be attached to the skeleton.
ChemTools is a free and open source Python library for interpreting the results of quantum chemistry calculations.
The Python package `junglesounds` is a machine learning pipeline for classifying bioacoustic data using machine learning. The pipeline is reusable for other settings and species or vocalization types as long as a certain amount of labeled data has been collected.
The Citation File Format lets you provide citation metadata for software or datasets in plaintext files that are easy to read by both humans and machines.
Citation.js converts formats like BibTeX, Wikidata JSON and BibJSON to CSL-JSON to convert to other formats like APA, Vancouver, RIS and back to BibTeX.
Python utility to generate local climate zone (LCZ) tiles for rendering in 3D in QGIS
Implementation of the Chemistry Land-surface Atmosphere Soil Slab (CLASS) model that runs entirely in the browser.
For more information on CLASS, see https://classmodel.github.io/.
CleanX is an open-source python library for exploring, cleaning and augmenting large datasets of X-rays, or certain other types of radiological images.
ClinDIG provides a federated data management and analysis solution for clinical and genomic data while to provide opportunity for distributed analysis centred on protecting patient privacy.
Tool to perform cluster analysis of multi-dimensional geospatial data, running on local or distributed systems.
Java library for working with Chemical Markup Language files.
compareMS2 is a tool for direct comparison of tandem mass spectrometry datasets, typically from liquid chromatography-tandem mass spectrometry (LC-MS/MS), defining a distance as a function of the share of similar spectra. Applications span biomedicine, phylogenetics, forensics and food science.
This Python implementation tries to model school choice and resulting school segregation based on the work of Schelling (1971) and Stoica & Flache (2014).
The Compas Toolkit is a high-performance C++ library offering GPU-accelerated functions for use in quantitative MRI research.
React components used by analyse command of haddock3 and haddock3 web application.
Julia package to implement Convolutional Neural Operators
COPASI is an open source software for simulation and analysis of biochemical networks and their dynamics. It provides simulations using ODEs, SDEs, or Gillespie's stochastic simulation algorithm, with optional discrete events. COPASI provides several analyses, optimization, and parameter estimation.
CoupledNODE.jl is a SciML repository that extends NODEs (Neural Ordinary Differential Equations) to C-NODEs (Coupled Neural ODEs), providing a data-driven approach to modelling solutions for multiscale systems when exact solutions are not feasible.
COVID-19 integrated surveillance data provided by the Italian National Institute of Health and processed via UnrollingAverages.jl to deconvolve the weekly simple moving averages.
COVID-19 Surveillance Data Modelling and Management Pipeline in Piedmont.
CRiSp (City River Spaces) provides tools to automate the morphological delineation of riverside urban areas.
An application that uses cross-perspective topic modeling to extract topics and opinions from text and provides insight into how they change over time.
CrowdED is a two-staged statistical guideline for optimal crowdsourcing experimental design in order to a-priori estimate optimal workers and tasks' assignment to obtain maximum accuracy on all tasks.
The cudawrappers library is a C++ wrapper for the Nvidia C libraries such as the CUDA driver, NVRTC, and cuFFT.
This library allows exploration and analyses of neuroimaging datsets. The software was developed to allow implementation of multiple large data harmonization and machine learning algorithms over neuroradiology datasets. The core algorithms are implemented in Python.
The reference implementation of the Common Workflow Language standards
An in-browser text markup editor for collaborative editing of scholarly projects.
DALES is a large-eddy simulation code designed for studies of the
physics of the atmospheric boundary layer, including convective and stable boundary layers as well as cloudy boundary layers.
Data processing scripts for the project What Works When for Whom
DataStream is a powerful online platform for sharing information about freshwater health. It is open access and built with communities, policy-makers and researchers in mind.
This package contains a Modern Fortran implementation of the Davidson diagonalization algorithms to compute several eigenvalue-eigenvector pairs of a symmetric matrix
Python file-system interface for dCache storages.
Deep learning framework for data mining protein-protein interactions using CNN
DeepRank2 is an open-source deep learning framework for data mining of protein-protein interfaces or single-residue missense variants. This package is an improved and unified version of three previously developed packages: DeepRank, DeepRank-GNN and DeepRank-Mut.
DeepRank-GNN is the graph neural network of our DeepRank package. DeepRank GNN allows to train graph neural networks to classify protein-protein interface
Sentence-wise split datasets of country reports in CSV format
A scraping tool to scrape various sources of country reports.
LLM transfer learning to classify country reports into democracy dimensions.
Various Jupyter notebooks for topic modelling on democracy texts including BERT and dictionary, keyword-based approaches.
DG_RoomAcoustics is an open-source python-based software for room acoustics using the time-domain wave-based method. It implements the nodal discontinuous Galerkin method for spatial discretization of the linear acoustic equations, integrated over time with explicit schemes.
A photohypsometric Python library to estimate glacier elevation change via optical remote sensing imagery
Deep Insight And Neural Network Analysis, DIANNA is the only Explainable AI, XAI library for scientists supporting Open Neural Network Exchange, ONNX - the de facto standard models format.
Python package with the goal to split datasets (e.g. words defined by several variables) into subsets that are as comparable as possible.
Explainable AI tool for explaining models that create embeddings.
Interactively explore millions of 2D and 3D data points in your browser, without the need to install anything.
A python library to split sentence-wise and convert various document formats to CSV format.
DoE2Vec is a self-supervised approach to learn exploratory landscape analysis features from design of experiments. The model can be used for downstream meta-learning tasks such as learninig which optimizer works best on a given optimization landscape.
A lightweight Python library for finding drug names in a string, otherwise known as named entity recognition (NER) and named entity linking. This library finds only high confidence drugs and doesn't support misspellings at present.
DTBase is a starter kit for making your own digital twin. Forking it will get you started with a database, a backend API, infrastructure for data ingress and running models, a basic web frontend, etc. You can then start building the more bespoke features of your digital twin on this foundation.
A Python package to load raw Distributed Temperature Sensing (DTS) files, perform a calibration, and plot the result.
Scikit-learn compatible version of Mixed-Effects Random Forests
DuMux - DUNE for Multi-{Phase, Component, Scale, Physics, …} flow and transport in porous media and more. The swiss army knife of porous media research. Open-source simulator in modern C++.
DUNE, the Distributed and Unified Numerics Environment, is a modular toolbox for solving partial differential equations (PDEs) with grid-based methods. It supports the easy, flexible, and efficient implementation of finite element and volume methods. DUNE is C++ code and also has a Python interface.
Duqtools is a tool for Dynamic Uncertainty Quantification for Tokamak reactor simulations modelling.
Coreference resolution for Dutch: automatically links references to the same entity in Dutch written texts.
This tool can convert and visualize radio astronomy measurement sets, as well as most LOFAR intermediate data products. It also performs RFI mitigation.
Process EC-Earth output to publish for CMIP6
A European community Earth-System Model
Visualize and annotate GPS measurements of bird movements.
If you have birds flying around carrying UvA-BiTS trackers, then this software can save the SMS messages containing the bird's last known positions which are sent by the tracker to the UvA Bird tracking system's central database.
Calendar overview with daily statistics of GPS-trackers used to track bird movements.
Automatic classification of accelerometer data using a supervised learning approach.
Deep learning for age prediction using EEG data
R package developed to extract features from multivariate time series from EEG data and feed them into a random forest classifier.
Offload Eigen matrix-matrix multiplications to an Nvidia GPU
eitprocessing is an open source collaborative python library for the processing and analysis of electrical impedance tomography for clinical use.
Emma is a project to create a platform for development of application for Spark and DockerSwarm clusters.
Interactive visualization and exploration of multi modal time-series data and video
A Python package for computing emotion expression-related features from speech signals.
Entangled makes literate programming easier. It keeps markdown and program source in sync. This makes it more convenient to extend and debug your literate code.
The eOSSR is the Python library to programmatically manage the ESCAPE OSSR.
A command line interface to download ERA5 data from the Copernicus Climate Data Store
The Ersilia Model Hub is an open source platform to serve AI/ML models for infectious disease drug discovery.
ESMValTool Core: core functionalities and driver for ESMValTool, a community diagnostic and performance metrics tool for routine evaluation of Earth System Models in CMIP.
The Earth System Model eValuation Tool is a community diagnostics and performance metrics tool for the evaluation of Earth System Models that allows for routine comparison of models and observations.
doc2vec-based assisted close reading with support for abstract concept-based search and context-based search
The eWaterCycle package makes it easier to use hydrological models without having intimate knowledge about how to install and run the models.
eWatercycle plugin for HYPE hydrological model
eWatercycle plugin for LISFLOOD hydrological model
eWatercycle plugin for MARRMoT hydrological model
eWaterCycle plugin for PCRGlobWB hydrological model
Codified instructions for deploying the eWaterCycle platform on the SURF Research Cloud.
eWaterCycle plugin for wflow hydrological model
If you have large amounts of Geospatial grid-based data you would like to explore quickly, eWaterLeaf could be the visualisation for you.
A utility to assist in managing FHIR resources in spreadsheets.
An open workflow for creating machine learning models for estimating the global biospheric CO2 exchange.
Generate and launch Jupyter notebooks for your users.
Experiments with regard to explanation of embedded spaces and multi modal models.
ExploreASL is a pipeline and toolbox for image processing and statistics of arterial spin labeling perfusion MR images. It is designed as a multi-OS, open-source, collaborative framework that facilitates cross-pollination between image processing method developers and clinical investigators.
RESTful web service that enables data owners to expose their data sets using rich machine-readable metadata.
fairdatapoint-client is a simple and elegant library to interact with FAIR Data Point resources from Python, e.g. read and write catalogs, datasets and distributions in an FDP server.
FAIRSECO provides a way to quickly analyse a variety of data and metrics of your software, and it allows you to explore the impact of your software on the academic world. Metadata is gathered from many different sources, which is then analysed and compiled into a clear overview.
Create comprehensive reports on compliance with the fair-software.nl recommendations.
A python library for constructing, annotating and publishing scientific workflows described using semantic technologies.
Detect clusters in for example large collections of DNA or protein sequences, and visualize the results in a web browser.
Retrieves and converts patient records from a FHIR endpoint and uploads it to a CAPACITY registry.
A Python package for regression testing simulation results. Compare field data supporting various structured formats such as CSV and VTK file formats, through Python API or the command-line interface.
FLAME GPU is a GPU accelerated simulator for domain independent complex systems simulations. FLAME GPU provides a mapping between a simple description of an agent and its interactions into optimised GPU code. The software abstracts the details and complexity of the GPU away from modellers.
Compute and filter molecular properties for quantum dot ligands
A python library to write ascii based fm128_radar files to be used in WRFDA
Use a single Accelerometer and Gyroscope on the foot to determine foot progression angle during walking.
A workflow to produce emission factor forecasts for the electricity mix of the Netherlands, up to 7 days ahead.
A database to store a catalog of Fast Radio Bursts and expose them as Virtual Observation Events.
Provides an easy to-use web frontend to browse and filter the Fast Radio Burst Catalogue.
The fsbrain package provides visualization of neuroimaging data in R. The plots produced by fsbrain can be integrated into R notebooks or written to high-quality bitmap image files, ready for publication.
Enable FHIR service for GameBus and beyond
Deep Learning for Imaging Cherenkov Telescopes Data Analysis
a Generalized Molecular Dynamics Analysis Tool
Genetics and Genomics Analysis Platform (GenAP)
Geodisy is a research data discovery tool that harvests information from existing research data repositories and displays applicable records onto a map-based search interface.
Visualizes any type of flow between countries. Takes a CSV as input, applies filtering and aggregation (danfojs) to show relations and data in a number of visualizations (d3.js)
Converts raw data from wearables into insightful reports for researchers investigating human daily physical activity and sleep.
GitHub action for setting up apptainer in a Continous Integration job
To compile C Plus code against gRPC in a GitHub action workflow you need to install it first. This GitHub action compiles or downloads it for you.
To use Singularity containers in a GitHub action workflow you need to install it first. This GitHub Action downloads, compiles and installs it for you.
Glotaran: A Java-Based Graphical User Interface for the R Package TIMP
Unsure about the parameters of your grains in a computer simulation? Use Iterative Bayesian Filtering to learn parameter distributions from limited data. Is your model running slowly? Speed up your simulations with machine-learning surrogates. All these features are integrated within GrainLearning.
Interface for Graphviz in Julia. This module helps to create graph visualizations programatically in Julia, with Graphviz as a back-end.
Header-only C++ Library for grid file I/O
Builds a web API from SPARQL queries hosted on GitHub to accessing triple store data.
Run, read and write model state of a numerical simulation written in a variety of languages remotely from Python
GSAreport is an application to easily generate reports that describe the global sensitivities of your input parameters as best as possible. You can use the reporting application to inspect which features are important for a given real world function / simulator or model.
Haddock3 (High Ambiguity Driven protein-protein DOCKing) is a modular software for for the integrative modeling and refinement of biomolecular complexes.
The haddock3 web application had several components that could be used outside of the web application. This software contains those components.
Web app to build haddock3 configuration and run it.
Scripts that transform cultural heritage relational databases into linked data by using cultural heritage ontologies.
Making harmonisation simple. Social scientists often have to compare items from different questionnaires or datasets. Harmony is a tool that uses natural language processing and generative AI models to help researchers harmonise questionnaire items quickly, even in different languages.
Radioastronomy calibration pipeline of the HERA telescope ported on quantum computers
Retrieve recent tweets from certain users and classify them with machine learning
This tool analyzes the transmission of political ideas during the American Revolution. It enables users to track shifts in concepts in letter correspondence networks, using semi-supervised topic modeling and temporal social network modeling to reveal ideological shifts and identify key influencers.
The HHL prototype allows to use the HHL algorithm to solve linear system of equations
A command-line tool written in shell script to simplify the creation of LXC Linux containers.
HORTON is a Helpful Open-source Research Tool for N-fermion systems, written primarily in the Python programming language. The ultimate goal of HORTON is to provide a platform for testing new ideas on the quantum many-body problem at a reasonable computational cost.
Command line tool to analyze a git repository's compliance with the fair-software.eu recommendations.
hpGEM is a C++ partial differential equation solver. It is intended for Discontinuous Galerkin Finite Element Methods, but can also do normal (conforming) Finite Element Methods and Finite Volume.
A package to determine the quality of a a digitized text, from a handwritten script or scanned print (HTR/OCR output).
Finds edges in high-dimensional data using the Canny algorithm.
A research-driven web-crawler aimed at building, curating and categorizing a corpus of web actors and the network graph of hyperlinks connecting them.
A wrapper around the python-irodsclient to allow for easy interaction with iRODS servers for research software engineers to integrate compute wokflows and data management.
A graphical user interface to iRODS employing the iBridges python package.
A Julia package that allows to translate ICD-9 into ICD-10 codes and viceversa via the General Equivalence Mappings (GEMs) of the International Classification of Diseases (ICD).
Harmonising world-wide efforts to reduce the global burden of cancer
This package, available at pip as icoscp, allows you to have direct access to data objects from the ICOS Carbon Portal where a "Preview" is available. It provides easy access to data objects hosted at the ICOS Carbon Portal. By using this library you can load data files directly into memory.
The ICOS Portal app is a FAIR linked data repository for metadata and data. In first instance primarily targeted at hosting the high quality data from ICOS. The repository is optimized for machine to machine communication. Instances in production now for ICOS, Swedish SITES and ICOS Cities networks.
An Implicit Earth system Model of Intermediate Complexity
iEnvironment is a web-based, extensible and distributed data management platform and user gateway for integrated environmental monitoring and modelling (IEMM).
This is a free and open source software (FOSS) Python version of the simulation model IMAGE-land, the land cover change model from the IMAGE 3.1 Integrated Assessment Model (IAM). Most, but not all, capabilities of the original model are included.
Imas2xarray is a python library for reading IMAS data in hdf5 format into xarray.
A tool for visualising and analysing Institutional Statements
This package implements energy-conserving solvers for the incompressible Navier-Stokes equations on a staggered Cartesian grid. It is based on the Matlab package INS2D/INS3D. The simulations can be run on the single/multithreaded CPUs or Nvidia GPUs.
Set-up and run STEMMUS-SCOPE on SURF research cloud (SRC)
Interpretability for sequence generation models 🐛 🔍
The Internet Archive scraper is a workflow for collecting webpages archived in Internet Archive's Wayback Machine. It is designed to run serverless on Amazon's AWS infrastructure.
This lesson gives an introduction to deep learning.
This lesson material shows how practical geospatial data analysis tasks can be carried out using Python
A Distributed Data Management System and Scientific Gateway for Mining Next Generation Sequence Data from Immune Responses.
Integrated Rapid Infectious Disease Analysis (IRIDA) platform is a user-friendly, distributed, open source bioinformatics and analytical web platform that was developed to support real-time infectious disease outbreak investigations using whole genome sequencing data.
Chrome Web Extension for support of the NWO ISAAC platform. This extension is not endorsed or developed by the NWO.
A framework and predictor based on support vector machine and random walk graph kernel for scoring protein-protein interfaces.
Islandora is an open-source software framework designed to help institutions and organizations and their audiences collaboratively manage, and discover digital assets using a best-practices framework.
Bartender is a middleware web service to schedule jobs on various infrastructures.
Jupter Lab extension to create/edit haddock3 configuration file.
Need to write a complex config file then the i-VRESSE workflow builder might be the tool for you.
A JASP implementation of the PROCESS macro for SPSS
JUBE is a generic, lightweight, configurable environment to run, monitor and analyse application execution in a systematic way. This software is commonly used to execute benchmarks and complex workflows on High Performance Computers, but is not limited to these systems.
A Dask cluster and a Jupyter server on a SLURM system
A browser that allows you to include NetCDF data stored in THREDDS catalog into a Jupyter Notebook.
JURI (Jülich Reporting Interface) provides a template-driven fully client-based web framework to visualise data lists and associated data graphs.
Dynamically compile GPU kernels and launch them easily and safely using C++ magic. Tight integration with Kernel Tuner results in blazing fast CUDA code that is maintainable and performance portable.
Kernel Tuner greatly simplifies the development of highly-optimized and auto-tuned CUDA, OpenCL, and C code, supporting many advanced use-cases and optimization strategies that speed up the auto-tuning process.
If you are working in the KNIME worflow platform and need data about your favorite kinase receptor ligand interaction, then these nodes are for you.
KMM is a lightweight C++ middleware for accelerated computing.
A node for the KNIME workflow systems that allows you to retrieve data about your favorite G protein-coupled receptors from gpcrdb.org.
A 3D viewer for large molecules for the KNIME workflow system.
Want to write your own KNIME node Then use the KNIME node archetype to generate a node skeleton repository with sample code.
A node for the KNIME workflow systems that allows you to compare different binding sites in proteins with each other.
A plugin for the KNIME workflow system that adds a Pharmacophore data type and nodes to read, write, and align them.
A node for the KNIME workflow system that allows you to use the PLANTS protein-ligand docking algorithm.
Want to write your own KNIME node wrapping a Python library. Then use the KNIME Python node archetype to generate a node skeleton repository with sample code
If you are developing a KNIME node which calls some Python code, then the KNIME Python wrapper can help you.
A node for the KNIME workflow systems that allows you to use the Silicos-it software to filter or align molecules.
A node for the KNIME workflow systems that allows you to identify which residue position in a big protein sequence alignment is specific to ligand binding.
Allows you to test KNIME nodes automatically using JUnit.
A Python package that helps users run containerized applications on HPC systems
LARA (Laboratory Automation Robotic Assistant) is an open source Research Data Management Suite and 2nd generation Electronic Lab Notebook with that provides a rich infrastructure for lab communication, orchestration, data/metadata storage, evaluation and exchange.
Toolkit for preprocessing and feature calculation of point clouds created using airborne laser scanning
Laserfarm: Laserchicken Framework for Applications in Research in Macroecology. Leverage Laserchicken in distributed fashion to use continental scale point cloud datasets for research.
Workflow and participant registration support
A Python BMI leaky bucket model 🪣
This tool converts Lifelines cohort study data from CSV to CDF/JSON, a format used in the MyDigiTwin project. Lifelines tracks health data over time, but variables are often scattered across files, making analysis difficult. CDF organizes data per participant, enabling FHIR/MedMij-compliant analysis
Lightning: Fast data processing using GPUs on distributed platforms
A Python package for generating calendars to resample timeseries into training and target data for machine learning. Named after the inventor of the Gregorian Calendar.
Open Source Research Data Management Software
Explore scientific literature using Python from the comfort of a Jupyter notebook
LLview is a set of software components to monitor clusters that are controlled by a resource manager and a scheduler system.
Publish LOFAR catalog as Linked Data.
Software tool to cluster outputs of different baselines within a specific observation. There are often over 1500 baselines in a single observation which takes a lot of time to inspect. This tool makes inspecting output of baselines more productive.
Deploy GlusterFS, Docker, Spark and JupyterHub services on bare-metal cluster.
Longitudinal Online Research and Imaging System (LORIS) is a web-based data and project management software for neuroimaging research studies. It is an OPEN SOURCE framework for storing and processing behavioural, clinical, neuroimaging and genetic data.
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.
An open-access website for collecting, displaying, and downloading electron and ion scattering cross sections for modeling low temperature plasmas.
Type, JSON schema and validator for cross section set used in low-temperature plasma community.
Find people on Twitter given a small initial set of interesting people.
An R package containing C++ implementations to speed up the simulation and parameter estimation of the Predictive Pedestrian model.
Magic Castle aims to recreate the HPC user experience in public clouds.
MAGMa is an online application for the automatic chemical annotation of mass spectrometry data.
A package for the calculation of scattering angles and cross sections.
A prototype for a federated, distributed data sharing and processing system.
MapReader is an end-to-end computer vision (CV) pipeline for exploring and analyzing images at scale.
Deploying clusters of VMs on bare metal using OpenNebula, provisioning, and running services made easy by fully configurable scalable automation
Use parallel processing to quickly convert large point cloud data sets to the format used by the Potree viewer.
A user-friendly, fully extensible framework for mass spectrometry analysis.
A fusion of the popular OpenMS suite of functionality with the powerful Mass Spec Studio. Users have access to OpenDIA and OpenPRM to support large scale processing of clinical proteomics data sets.
Python library for fuzzy comparison of mass spectrum data and other Python objects
Helps you find a suitable neural network configuration for deep learning on time series.
A tool to run molecular dynamics workflows.
This lesson introduces some specifics of medical image processing with popular Python libraries such as SimpleITK, Pydicom and NiBabel. Reconstruction algorithms, image and DICOM anonymization, registration, segmentation, data augmentation and generative AI are covered.
Capture emotion expressions from video, audio, and text with a single pipeline.
MiBiReMo (Microbiome Bioremediation Reaction Module) is a Python interface to the PhreeqcRM library. The package is designed to be coupled with transport models to simulate reactive transport in porous media, with applications in environmental and geochemical engineering.
Data handling and screening package of the Microbiome based remediation Prediction Tool
A collection of analytical and semi-semianalytical solutions for hydrogeological transport phenomena
A minimal distributed MPI port from UFEMISM, used as a basis for UFEMISM2.0
MINTED (Making Identifiers Necessary for Tracking Evolving Data) aims to apply dataset citation Digital Object Identifiers (DOIs) and researcher ORCIDs into ONC's Oceans 3.0 digital infrastructure.
This software generates the SBML version of the Mixed Meal Model, for predicting the glucose level evolution after the intake of a meal.
MATLAB toolbox for global optimization and state estimation of dynamic models using distributed computing.
Measurement Operator Trainer for data assimilation purposes.
The Motus Wildlife Tracking System (Motus) is an international collaborative research network that uses coordinated automated radio telemetry to facilitate research and education on the ecology and conservation of migratory animals.
This software is designed to run simulations of batteries with porous electrodes using porous electrode theory, which is a volume-averaged, multiscale approach to capture the coupled behavior of electrolyte and active material within electrodes
Deep learning based similarity measure of mass spectrometry data.
An Integrative Modeling Platform
A Julia package for the creation, manipulation and analysis of the structure, dynamics and functions of multilayer graphs.
MUSCLE3 is a coupling library for building multiscale simulations out of single-scale models.
mzRecal recalibrates mass spectrometry (MS1) data in mzML format, using peptide identifications in mzIdentML.
Python workflow tool for generating meshes from 2D and 3D microscopy image data
The nanopub library provides a high-level, user-friendly python interface for searching, publishing and retracting nanopublications.
JupyterLab extension to aid in searching and publishing of Nanopublications in a python notebook
The NatureCounts platform allows users to collect, archive, interpret and access wildlife data to advance the understanding of bird populations across the Western Hemisphere.
The NEBULA (Nuxt & eScience Based Universal Learning Application) framework can be used to create an easily maintainable, version-controllable, web-based lesson collection. It uses Nuxt.js and Vue.js.
nedextract is a python library that helps you to extract information on person names and organisations mentioned in Dutch (annual report) PDF files.
An application to convert NetCDF files to the Little-R format
Generic template for Python packages, so you can spend less time setting up and configuring, and comply with the Netherlands eScience Center Software Development Guide from the start.
NeuroAnalyzer is a Julia toolbox for analyzing neurophysiological data.
NeuroGym is a curated collection of neuroscience tasks with a common interface. The goal is to facilitate the training of neural network models on neuroscience tasks.
Software for running the online platform of the NEWSGAC project for running explainable machine learning models on textual data
A flexible solution to build text mining workflows that allows you to quickly combine Natural Language Processing tools from different sources.
Fitting proton substructure to observation data using neural networks
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.
Microbial natural products data mining by integrating genomics and metabolomics data
These materials were used as a part of the NPLinker eScience Workshop on Natural Product Genome & Metabolome Mining: https://www.wur.nl/en/research-results/chair-groups/plant-sciences/bioinformatics/teaching/nplinker_workshop.htm
Most materials are available in a format facilitating its reuse.
The Nunaliit Atlas Framework aims to make it easy to tell stories and highlight relationships between many different forms of information from a variety of sources, using maps as a central way to connect and interact with the data.
Agate is a web application that offers users related services to the OBiBa software stack.
Mica is OBiBa's software application that is used to create data web portals for large-scale epidemiological studies or multiple-study consortia.
Opal is OBiBa's core data repository application for epidemiological studies.
By bringing data to the surface, ONC provides ocean intelligence to scientists, governments, organizations, and citizens. Ocean data are archived, processed and made freely available via ONC’s data management system, Oceans 3.0.
A tool to clean up text generated by OCR using individual words as well as their context.
Analyze retinal optical coherence tomography images.
A Python environment to interface and couple oceanographic and other earth system model codes.
Web application for running a CWL workflow on a bunch of files.
OpenChrom is a vendor independent open source software for chromatography, spectrometry and spectroscopy.
OpenCMP is a computational multiphysics software package based on the finite element method
Open data assimilation toolbox. OpenDA is an open interface standard for a set of tools to quickly implement data-assimilation and calibration for arbitrary numerical models.
Open Delft Advanced Research Terra Simulator is a simulation framework for forward and inverse modelling and uncertainty quantification of multi-physics (thermo-hydro-mechanical-chemical) processes in geo-engineering applications as geothermal, CO2 sequestration, water pumping, and hydrogen storage.
OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS, and Linux.
OpenPNM is an open source project aiming to provide porous media researchers with a ready-made framework for performing a wide range of pore network simulations.
openPSTD is a Python-based research software that allows efficient and detailed calculation of sound propagation in a 2D built environment. It is especially useful as a reference tool for other developed software on acoustic sound propagation.
A UI for building OpenSim models
This open-source Python package facilitates the processing, analysis, and visualization of argument corpora. Additionally, It offers user-friendly GUIs integrated into the Orange3 scientific workflow platform, enabling non-programmers to utilize its capabilities.
Add-on providing quantitative textual story analysis based on principles in narrative psychology
Orange modules for text processing in the project What Works When for Whom
Start, stop and monitor applications remotely via a HTTP interface.
oTree demo experiment: Public goods game
A Docker environment for programming against multiple oTree server
A load balancer for oTree servers.
Data can be messy, let Arranger organize it for you.
Overture is a collection of open-source, extendable solutions for big-data genomic science that research institutions and individual researchers can use to support their work.
A stateless authorization and user management service.
Organizing your distributed data into one index.
Transfer data quickly and easily to and from any cloud-based storage system.
Quickly and reliably track genome metadata scattered across multiple Cloud storage systems.
A Collaborative Electronic Text Annotation Platform
If you do metabolomics experiments with mass spectra and have sequenced the genomes of the samples, then the platform can help you link them.
PanTools is a pangenomic toolkit for comparative analysis of large number of genomes. It is developed in the Bioinformatics Group of Wageningen University, the Netherlands. Please cite the relevant publication(s) from the list of publications if you use PanTools in your research.
General purpose Snakemake pipeline for PanTools v4.
Variant Analysis within Pangenomes.
A toolbox to calculate digital biomarkers for wearable sensors in Parkinson's disease.
An open-source modelling framework for ice sheets and glaciers
This package runs the parareal algorithm on a black-box simulator. Parallelisation is managed through Dask.
Parcels (Probably A Really Computationally Efficient Lagrangian Simulator) is a set of Python classes and methods to create customisable particle tracking simulations using output from Ocean Circulation models. Parcels can be used to track passive and active particulates such as plastic and fish.
PathVisio is a free open-source software to curate biological pathway models.
Library for aligning and scaling one point cloud to an other.
PAVICS is a virtual laboratory facilitating the analysis of climate data. It provides access to several data collections ranging from observations, climate projections and reanalyses. It also provides a Python programming environment to analyze this data without the need to download it.
Access integrated data on genes and associated traits in plants
An open-source python package to identify breakthrough innovations within patents.
Fast and versatile Python package that leverages SQL queries to parse, manipulate and process biomolecular structure files. The structure files should be in the PDB format and are available on www.rcsb.org.
Want to parse Protein Data Bank files in JavaScript
This is a virtual coach system that coaches users into being more physically active and stop smoking.
Decentralized coordination of multi-domain workflows using Hyperledger Fabric blockchain and Petri nets.
PhenoTips is a software tool that makes it easy for clinicians and researchers to draw pedigrees and collect structured phenotype data for patients with genetic disorders.
Showcases a diachronic analysis of the Dutch Royal Library's newspaper archive.
A web tool for mass spectrometry-based proteomics data analyses
Platalea contains deep neural network architectures for modeling spoken language from multiple sources at once: audio, and simultaneously images, text or video. This can be used to learn about what different context sources add to the language acquisition process.
Toolkit for data acquisition, pre-processing, calibration, and real-time streaming of imaging, position tracking, and other sensor data for medical applications.
PoreSpy is a collection of image analysis tools used to extract information from 3D images of porous materials (typically obtained from X-ray tomography).
Rigid body fitting of atomic strucures in cryo-electron microscopy density maps
PowerSensor is a low-cost, custom-built device that measures the instantaneous power consumption of GPUs and other devices at a high time resolution.
PROTEUS is a Python framework that simulates the coupled evolution of the atmospheres and interiors of rocky planets.
If you want to do astrophysics in python, this could come in handy. Connect to a radiotelescope and process data in real-time.
Generates consistent PSSM and PDB files for protein-protein complexes
Analyzes social media messages for polarity and stance towards governmental COVID-19 measures
PyChelator is a Python-based Colab and web application for metal chelator calculations, taking into account pH, temperature, and ionic strength. The build-in constants can be used for EGTA and ATP as chelators, together with Calcium and Magnesium as metals. User-defined constants can be used.
Python wrapper for ELSEPA, a numeric code for computing elastic scattering cross-sections for electrons and positrons off neutral atoms.
A Python library for Global and Target Analysis of time-resolved spectroscopy data
A Sequential Monte Carlo (SMC, or "particle filter") Python package for online model estimation and probabilistic forecasting.
Pyspextools is a collection of python tools for the SPEX X-ray spectral fitting package.
A python package for running the STEMMUS-SCOPE model
A physics-agnostic implementation of the Trajectory-Adataptive Multilevel Splitting (TAMS) algorithm for predicting transition probability in bi-stable dynamic problems.
Use the industry-standard Point Cloud Library from within Python.
Python wrapper for the Xenon programming interface to various compute and storage resources.
A Python library to handle Kinetic Monte Carlo codes.
Core Library of the Quantum Application Lab
Quantum Computing for Quantum Chemistry
QMCBlip allows to couple Quantum Monte Carlo Simulations with Machine Learning Force Fields to accelerate Molecular Dynamics simulations
Use and design neural network ansatz wave function for real-space quantum Monte Carlo simulations of molecular systems.
Construction and efficient execution of computational chemistry workflows.
Extract gene-trait associations from scientific literature
Questionnaire analysis using Fisher Information Non-Parametric Embedding. Explore high-dimensional continuous and discrete questionnaire data sets.
The Quantum Newton Raphson package allows to leverage quantum computing routines to accelerate the Newton-Raphson algorithm.
qubols allows to solve linear system using a QUBO approach that can be deployed on quantum annealers
qubops allows to solve polynomial system of equations using a QUBO approach that can be deployed on quantum annealers
QUICKLB is a very efficient library that sacrifices optimality for speed. It shines in distributed applications that have unpredictable unbalanced computational peaks in their domains.
Scripts and files related to ML training for the QUMIA project
Radiam helps researchers keep track of their data, regardless of where it is stored. There are multiple components working together, and most of them run within Docker containers.
Identify continuous lines in a spatial network.
This application ontology is dedicated to the ReaxPro framework for the multi-scale modeling of catalytic materials.
This repository is a collection of wrappers used in the ReaxPro project. It holds wrappers for the Amsterdam Modeling Suite (AMS) and Zacros.
Effortless provenance tracking in Python
Software developed in the project REE-HDSC (Recognizing Extracted Entities for the Historical Database Suriname Curacao, 2023-2024) of the Radboud University Nijmegen and the Netherlands eScience Center.
Remote BMI allows you to communicate with Basic Model Interface enabled numerical models using a RESTful API
Islandora 8 is an open-source software framework designed to help organizations collaboratively manage and discover digital assets using a best-practices, standards-based preservation framework.
A Research Portal that can address these different usage models, while serving as website and gateway for authorized researchers to capture, query, and visualize patient data; communicate, collaborate and share datasets; and access support and training resources. platforms.
A content management system for research software, which promotes the visibility, reuse, and impact of research software.
RESTfull API for the APE (Automated Pipeline Explorer) library.
ReSurfEMG is an open source collaborative python library for analysis of respiratory electromyography (EMG). The library includes functions for pre-processing, analysis and machine learning.
A dashboard for visualizing and analyzing respiratory EMG signal, making use of the ReSurfEMG library
This package contains a scalable pipeline to perform argument reasoning on a dataset of product reviews, to identify the highest quality ones. By tuning both lossy and lossless parameters, it is possible to tune the pipeline to foster the accuracy of the computation or its speed.
Create visual storylines that involve media like images and videos embedded in a 3D environment with efficient Pointcloud data directly from the web browser.
With Ricgraph (Research in context graph), you can create a graph from research information that is stored in various source systems. You can explore this graph and discover relations you were not aware of.
Robust Optimization by Iterative Scenario Sampling and Statistical Testing
Rocket is a framework for efficient execution of all-pair applications on heterogeneous platforms.
An open-source data analysis framework used by high energy physics and others.
Rosemary is a plugin for YASGUI (Yet Another SPARQL GUI), facilitating creation of SPARQL queries without requiring knowledge of SPARQL.
This repository contains the Rucio deployment for KM3NeT. It can be used as an example of how to deploy Rucio.
Package with custom policies for the Rucio instance of KM3NeT.
A high-level python package integrating expert knowledge and artificial intelligence to boost sub-seasonal to seasonal (S2S) forecasting.
Fast, memory efficient and GPU accelerated radio interferometric calibration program
If you need to automate your image matching tasks for the purposes of object detection or photo-identification in an easy way, the SalientDescriptor-matlab is right for you
If you want to automate object detection or image photo-identification tasks in an easy way with open MATLAB software, the SalientDetector-MATLAB is right for you
If you want to automate your object detection or photo-identification image tasks in an easy way with free open-source software, the SalientDetector-Python is the tool for you
An Xarray extension to process coregistered Single Look Complex (SLC) image stacks acquired by Synthetic Aperture Radar (SAR).
A Python library for land use classification based in satellite images.
Graphical User Interface around Wikidata that uses SPARQL to collect data
Scikit-talk is an open-source toolkit for processing collections of
real-world conversational speech in Python. The toolkit aims to facilitate the
exploration of large collections of transcriptions and annotations of
conversational interaction.
Create CWL workflows by writing a simple Python script.
Collection of resources to set up GitHub runners on self-hosted infrastructure
Annotate field books of natural history collections
grpc4bmi wrapper around Delteras/sfincs BMI for use with eWaterCycle
Share Trait web application is a web application that allows users to deposit trait data in the Share Trait database.
A visualization that shows how the meaning we attach to a given concept shifts over time.
Make genome annotations semantically interoperable
The only fully open source software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis.
Sirup is an open-source Python package that makes it easy to connect to, and rotate across, VPN servers provided by services such as ProtonVPN and Surfshark.
SLEPLET is a Python package for the construction of Slepian wavelets in the spherical and manifold (via meshes) settings.
Software toolkit for rapid development of image-guided therapy systems - for minimally invasive medical procedures, where operators rely on computer-generated images rather than direct sight of the target organs.
SlicerRT allows users to analyze spatio-temporal accumulation of the therapeutic dosage (radiation, thermal, etc.). Tools include dose visualization, quantitative metrics computation, comparison, and import/export to DICOM format.
SLURM CLI-API Proxy client is a tool designed to bridge existing applications and scripts that rely on the SLURM CLI. The tool mimics traditional SLURM CLI commands, translating them into REST API calls, enabling seamless integration of existing tools with external SLURM workload managers.
A package to download slurm usage from a supercomputer and upload it to MongoDB
Display Slurm job remaining time in Jupyter top bar
Android OS Wear Application to measure children's activity when playing.
SMP decision tree is a questionnaire for creating a Software Management Plan (SMP).
A snakemake workflow to run WRF, including pre- and postprocessing. See our blog post for a detailed description.
spec2vec is a novel similarity measure for comparing mass spectrometry data, which learns peak representations using Word2Vec.
SpeckleCn2Profiler revolutionizes satellite communication, combining SCIDAR and AI. By accurately estimating turbulence strength and refining signals, it ensures reliable performance in any environment. Dive into our repository and join the quest to transform optical links.
SPEX is a software package for fitting high-resolution astrophysical X-ray and UV spectra.
Estimates split-half reliabilities for scoring algorithms of cognitive tasks and questionnaires.
SPOT is an interactive visualization tool for multi-dimensional data. It allows quick analysis of complex datasets and easy identification of correlations between variables.
Spatiotemporal phenology research with interpretable models
Software developed in the project Automation of the Cognitive Mapping Text-analysis Technique
STAC2dCache is a Python tool to create and manipulate STAC catalogs on a dCache storage system.
Integrated code of SCOPE and STEMMUS
Xarray extension for Space-Time Matrix.
The storyboards application allows you to host a collection of stories using an intuitive layout.
StoryTeller is a web application for visual analysis of textual data which can show you the connections between storylines, participants and other entities in complex humanities data.
R package for modeling pipelines in stratigraphic paleobiology
Streetscapes is a package for code for downloading, segmenting and analysing images from Mapillary and KartaView.
Perform semantic segmentation on images, using Facebook's Mask2Former models.
Semantic Role labeling for Dutch. Understanding who does what, where, to whom.
Construct 3D pointclouds from a set of 2D images
Highly portable parallel workflow to detect structural variants in cancer genomes.
Genome-wide detection of structural variants using deep learning
Highly portable parallel workflow to generate artificial genomes with structural variants.
Swan is a Python package to create statistical models to predict molecular properties
swyft is the official implementation of Truncated Marginal Neural Ratio Estimation, a hyper-efficient, simulation-based inference technique for complex data and expensive simulators.
SyGMa provides fast and lightweight predictions of human metabolites to support discovery scientists design better and safer drugs
{talkr} is an R package that offers a set of convenience functions for quality control, visualisation and analysis of conversational data. Most notably it provides a range of plotting functions that play well with ggplot and the tidyverse.
DNA barcode identification, powered by semantic searching.
Webapp for DNA barcode identification, powered by semantic searching.
An entry for testing the connection with a BitBucket repo
Texcavator is a search engine and text mining application for creating word cloud and time line visualizations of large text corpora.
A web browser extension to evaluate Digital Object FAIRness developed at Maastricht University Library.
An open source, open science approach to the design of, and research with conversational agents.
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.
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.
GitHub action to check whether any licensing issues exist for given software.
The LOFAR Transients Pipeline (or "TraP") is a Python and SQL based system for detecting and responding to transient and variable sources in a stream of astronomical images.
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 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.
A package to read, modify and write TSDF data in Python.
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.
Data Safe Haven is an open-source framework for creating Trusted Research Environments (TREs) to analyse sensitive data.
It provides a set of scripts that will allow you to deploy, administer and use your own TRE on Microsoft Azure cloud.
This project is aimed to help researchers to use Academic Research product track to collect tweets of their interest and analyze them.
Software behind the web server twiqs.nl, which has provided free access to statistics about Dutch tweets since 2010
The successor of UFEMISM, has all of its features (and more?), but is based on the distributed architecture introduced in minimism.
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
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.
A Julia package to deconvolve simple moving averages of time series.
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.
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.
An open-source platform for supporting the development of federated learning projects
A web application which visualizes the point clouds and additional data gathered in the Via Appia project with WebGL.
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.
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.
The goal of visor is to provide a set of tools for visibility analysis.
VOTCA-XTP is a library which allows you to calculate the electronic properties of organic materials
Variational Quantum Linear Solver Library.
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).
WEARDA: recording wearable sensor data for human activity monitoring.
Web-enabled Awareness Research Network - Earthquake and Tsunami detection.
wntr-quantum (pronounced winter-quantum) extends the capabilities of the popular wntr package for water network modelling and analysis to quantum computing routine.
Web platform for workflow exploration and benchmarking in bioinformatics
WRFpy is a python application that provides an easy way to set up, run, and monitor Weather Research and Forecasting simulations
Simple shell script to run a complete WPS/WRF experiment in one go
An xarray plugin that adds regridding utilities for datasets and dataarrays.
If you are using remote machines to do your computations, and don’t feel like learning and implementing many different APIs, Xenon is the tool for you.
A command line interface for the Xenon library that allows you to use remote machines to do your computations.
For your testing needs a collection of Docker images with different file systems and batch schedulers.
Run applications remotely via a gRPC interface.
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.
the eXtensible Text Analysis Suite
Python library for YAML type inference, schema checking and syntactic sugar.
A system for reliable, long-term storing and archiving large amounts of research data during all stages of a study.
Tool for downloading Land Surface Model input data
Zarr files visualizer for the web. Ruisdael observatory (TU Delft)
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.