All software
cerulean
A Python 3 library for talking to HPC clusters and supercomputers.
- High performance computing
- SFTP
- SLURM
- + 2
- Python
- Shell
- Dockerfile
Cesium-ncWMS
Web Application that visualizes data stored in the NetCDF format on a globe.
- Visualization
- JavaScript
- HTML
- CSS
- + 1
cffconvert GitHub Action
GitHub action to validate CITATION.cff files, and convert to other citation formats using the dockerized version of cffconvert
CHAMP-EU
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.
- Chemistry
- High performance computing
- Physics
- + 1
- C
- Fortran
- Nemerle
- + 16
check-deps
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.
- Dependency Hell
- python
- Workflow technologies
- Python
- CSS
- Awk
- + 1
Chemical Analytics Platform
Chemical Analytics Platform is a freely available Virtual Machine encompassing tools, databases, and KNIME workflows.
- Workflow technologies
- Shell
- Smarty
Cityblocks
Python utility to generate local climate zone (LCZ) tiles for rendering in 3D in QGIS
- QML
- Python
classmodel/form
Form component that renders a JSON schema using Solid UI components.
- TypeScript
- Jupyter Notebook
- JavaScript
- + 2
CLASS-web
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/.
- web service
- TypeScript
- Jupyter Notebook
- JavaScript
- + 2
cleanX
CleanX is an open-source python library for exploring, cleaning and augmenting large datasets of X-rays, or certain other types of radiological images.
- Image processing
- Machine learning
- Jupyter Notebook
- Python
- TeX
- + 3
Climate Rapid Evaluation Framework
Rapid Evaluation Framework for climate simulations
- Big data
- Climate modeling
- Python
- HTML
- TeX
- + 4
ClinDIG
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.
- clinical
- federated
- genomics
- + 1
- Python
- Shell
- Smarty
- + 5
clumped-processing
Clumped isotope measurement processing script for Thermo Fisher MAT 253 plus isotope ratio mass spectrometer with the Kiel IV
- clumped isotope
- Data Analysis
- mass spectrometry
- + 3
- HTML
- R
clumpedr
Clumpedr aims to facilitate analysis of clumped isotope data. It builds on isoreader which is used to import raw data files from the mass spectrometer, and most of the important data processing parts are based on Huntington et al. 2009 and Daëron et al. 2016.
- Data Analysis
- mass spectrometry
- R
- Makefile
- Rez
Code Auditor
A package and command-line utility to audit code quality and compliance to the best practices.
- code quality
- conformity assessment
- software development
- Python
CoeusAI
The CoeusAI QGIS plugin is designed for exploration of multiband geospatial datasets. It lets the user iteratively train and retrain segmentation models in seconds. A combination of Deep learning and traditional machine learning is used, leveraging the best of both methods.
- deep learning
- gis
- Machine learning
- + 2
- Python
Collens
Collens is a dynamic web-based tool designed for scholars to compare textual variants with annotations. Utilizing machine learning, it offers an efficient workflow for analyzing multiple versions of literary and scholarly documents.
- digital humanities
- Visualization
- Svelte
- TypeScript
- JavaScript
- + 2
Compass-school
This Python implementation tries to model school choice and resulting school segregation based on the work of Schelling (1971) and Stoica & Flache (2014).
- Agent-based modeling
- Python
- HTML
Compas Toolkit
The Compas Toolkit is a high-performance C++ library offering GPU-accelerated functions for use in quantitative MRI research.
- GPU
- High performance computing
- MRI
- Cuda
- C++
- Julia
- + 4
ConvolutionalNeuralOperators.jl
Julia package to implement Convolutional Neural Operators
- Julia Package
- Machine learning
- Scientific machine learning
- Julia
Cosimplat
Co-simulation framework made for RESCUE project
Cosmology.jl
Cosmology library for Julia
- astronomy
- Astrophysics
- cosmology
- + 1
- Julia
CoupledNODE
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.
- Julia Language
- Julia Package
- Machine learning
- + 1
- Julia
- Shell
rcrisp
rcrisp provides tools to automate the morphological delineation of riverside urban areas.
- Data Analysis
- geospatial
- R
- + 1
- R
- TeX
Cronian
Cronian is a Python package for building copper plate optimization models in Pyomo to optimize flexibility scheduling in multi-carrier integrated energy systems, which are specified through simple YAML and CSV files.
- Python
- Shell
CrowdED
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.
- Citizen Science
- Crowdsourcing
- Data Simulation
- Python
- R
- Dockerfile
cudawrappers
The cudawrappers library is a C++ wrapper for the Nvidia C libraries such as the CUDA driver, NVRTC, and cuFFT.
- accelerators
- CUDA
- GPU
- C++
- CMake
- Python
- + 2
cvasl
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.
- Jupyter Notebook
- Python
- R
- + 3
cwltool
The reference implementation of the Common Workflow Language standards
- CommonWL
- CWL
- SciWorkflows
- Python
- Common Workflow Language
- Shell
- + 4
CWRC-Writer
An in-browser text markup editor for collaborative editing of scholarly projects.
- LOD
- named entity linking
- named entity Recognition
- + 3
- JavaScript
- CSS
- Less
- + 2
Data Processing (What Works When for Whom)
Data processing scripts for the project What Works When for Whom
- Jupyter Notebook
- Python
- Shell
DataStream
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.
- Water quality
- watersheds
Democracy Datasets
Sentence-wise split datasets of country reports in CSV format
- CSV
- dataset
Democracy Scraping Tool
A scraping tool to scrape various sources of country reports.
- scraping
- Python
Democracy text classification
LLM transfer learning to classify country reports into democracy dimensions.
- fine-tuning
- llm
- transfer learning
- Jupyter Notebook
- Python
Democracy Topic Modelling
Various Jupyter notebooks for topic modelling on democracy texts including BERT and dictionary, keyword-based approaches.
- BERT
- dictionary
- Topic Modelling
- Jupyter Notebook
- Python
DG_RoomAcoustics
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.
- Acoustics
- High performance computing
- python
- Python
Discuit
Python package with the goal to split datasets (e.g. words defined by several variables) into subsets that are as comparable as possible.
- Data
- linguistics
- python
- + 1
- Python
- Shell
Distance explainer
Explainable AI tool for explaining models that create embeddings.
- Embedded spaces
- XAI
- Python
- Jupyter Notebook
- Shell
doc2sentences
A python library to split sentence-wise and convert various document formats to CSV format.
- CSV
- python
- + 1
- Rich Text Format
- Python
- Shell
Drug named entity recognition
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.
- Data Science
- Medical text
- Natural Language Processing
- + 1
- Jupyter Notebook
- Python
DTBase
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.
- Digital Twins
- Python
- HTML
- TypeScript
- + 3
DumME
Scikit-learn compatible version of Mixed-Effects Random Forests
- Python
e2e-Dutch
Coreference resolution for Dutch: automatically links references to the same entity in Dutch written texts.
- Machine learning
- Text analysis & natural language processing
- Python
- C++
- Shell
eEcology-SMS-reciever
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.
- Real time data analysis
- Python
- Perl
- Mako
- + 1
EEG_age_prediction
Deep learning for age prediction using EEG data
- deep learning
- EEG Signal
- Time Series
- Jupyter Notebook
- Python
- Shell
EEG epilepsy diagnosis
R package developed to extract features from multivariate time series from EEG data and feed them into a random forest classifier.
- Machine learning
- R
- Rebol
Effort Sharing
Analysis and plotting scripts for effort sharing, associated with the Carbon Budget Explorer
- Jupyter Notebook
- Python