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fsbrain

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.

Computational Neuroscience
Visualization

R
Dockerfile
Shell

3D-e-Chem Virtual Machine

A freely available Virtual Machine encompassing tools, databases, and workflows for cheminformaticians, including new resources developed for ligand binding site comparisons and GPCR research.

Inter-operability & linked data
Workflow technologies

Shell
Smarty

KLIFS KNIME nodes

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.

Workflow technologies

Java
Shell
Scala

KNIME Silicos-it nodes

A node for the KNIME workflow systems that allows you to use the Silicos-it software to filter or align molecules.

Workflow technologies

Java

KNIME node archetype

Want to write your own KNIME node Then use the KNIME node archetype to generate a node skeleton repository with sample code.

Workflow technologies

Java

KNIME GPCRdb nodes

A node for the KNIME workflow systems that allows you to retrieve data about your favorite G protein-coupled receptors from gpcrdb.org.

Workflow technologies

Java

KNIME node for Kripo

A node for the KNIME workflow systems that allows you to compare different binding sites in proteins with each other.

Workflow technologies

Java

KNIME Testflow

Allows you to test KNIME nodes automatically using JUnit.

Workflow technologies

Java

KNIME Pharmacophore

A plugin for the KNIME workflow system that adds a Pharmacophore data type and nodes to read, write, and align them.

Workflow technologies

Java

KNIME PLANTS

A node for the KNIME workflow system that allows you to use the PLANTS protein-ligand docking algorithm.

Workflow technologies

Java
Mustache

KNIME Python node archetype

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

Big data
Workflow technologies

Java
Python

KNIME Python wrapper

If you are developing a KNIME node which calls some Python code, then the KNIME Python wrapper can help you.

Workflow technologies

Java
Python

4CAT Capture & Analysis Toolkit

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.

Big data
python
Social media
+ 1

Python
JavaScript
HTML
+ 4

KNIME molecule viewer nodes

A 3D viewer for large molecules for the KNIME workflow system.

Visualization
Workflow technologies

Java
JavaScript
CSS

KNIME ss-TEA node

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.

Workflow technologies

Java

sv-callers

Highly portable parallel workflow to detect structural variants in cancer genomes.

Big data
High performance computing
Workflow technologies

Python
Shell

GSA report

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.

Explainable AI
Machine learning
python
+ 1

Python
HTML
CSS
+ 1

PanTools

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.

Data Analysis
Gene classification
pangenomics

Java
Snakemake
Python
+ 1

HyperCanny

Finds edges in high-dimensional data using the Canny algorithm.

Data Analysis
edge detection
High performance computing

C++
C
Python
+ 3

AHN2 pointcloud viewer

A web application able to visualize the AHN2 point cloud data of the Netherlands.

Big data
Real time data analysis
Visualization

JavaScript
HTML
CSS
+ 1

AMBER

A real-time pipeline to search for Fast Radio Bursts and other transient radio sources.

Big data
GPU
High performance computing
+ 1

C++
CMake

APE

A CLI, Java API and RESTful API for the automated generation of computational pipelines (scientific workflows) from large collections of computational tools.

Java
Program synthesis
Workflow technologies

Java
ANTLR

LitStudy

Explore scientific literature using Python from the comfort of a Jupyter notebook

Inter-operability & linked data
Text analysis & natural language processing
Visualization

Python
HTML

AHN point cloud viewer web service

A web service to serve large point cloud data efficiently using octrees.

Big data
Visualization

Java
Python

OMUSE

A Python environment to interface and couple oceanographic and other earth system model codes.

High performance computing
Multi-scale & multi model simulations

Fortran
Python
HTML
+ 10

laserchicken

Toolkit for preprocessing and feature calculation of point clouds created using airborne laser scanning

Big data
Machine learning

Python
Jupyter Notebook

MUSCLE3

MUSCLE3 is a coupling library for building multiscale simulations out of single-scale models.

High performance computing
Multi-scale & multi model simulations

Fortran
C++
Python
+ 4

swyft

swyft is the official implementation of Truncated Marginal Neural Ratio Estimation, a hyper-efficient, simulation-based inference technique for complex data and expensive simulators.

Bayesian Inference
Data Analysis

Jupyter Notebook
Python

talkr

{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.

conversation
talk
turn-taking
+ 1

Citation File Format

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.

FAIR
Inter-operability & linked data

Python

DIANNA

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.

Explainable AI
Image processing
Machine learning
+ 2

Jupyter Notebook
Python
TeX

Inseq

Interpretability for sequence generation models 🐛 🔍

deep learning
Explainable AI
generative models
+ 2

Python
Makefile
Dockerfile

BIAS

A toolbox for detecting structural bias in continuous optimization heuristics.

Bias
Metaheuristics
optimization
+ 1

Jupyter Notebook
Python
R

QTLTableMiner++

Extract gene-trait associations from scientific literature

Inter-operability & linked data
Text analysis & natural language processing

Java
Shell

Arena-Crowds

Arena-Crowds is Python scripts for the data analysis to estimate crowd density based on WiFi positioning.

Computer networks
Networks
Network Science

Jupyter Notebook
Python

DeepRank2

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.

Cancer vaccine
Convolutional Neural Network
Deep Learning Framework
+ 5

Python
Jupyter Notebook
TeX
+ 1

StoryTeller

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.

Visualization

JavaScript
HTML
CSS

Case Law App

Web application for exploring the citation network of Dutch court decisions.

Text analysis & natural language processing
Visualization

JavaScript
CSS
HTML

Dive

Interactively explore millions of 2D and 3D data points in your browser, without the need to install anything.

Big data
Machine learning
Visualization

HTML
JavaScript
CSS
+ 1

Foot Progression Angle Estimation

Use a single Accelerometer and Gyroscope on the foot to determine foot progression angle during walking.

FPA
IMU
Single sensor

MATLAB

pbg-ld

Access integrated data on genes and associated traits in plants

Data Analysis
genomics
Inter-operability & linked data

PLpgSQL
Shell
Python
+ 2

SLEPLET

SLEPLET is a Python package for the construction of Slepian wavelets in the spherical and manifold (via meshes) settings.

manifolds
python
slepian functions
+ 2

Python
TeX

Texcavator

Texcavator is a search engine and text mining application for creating word cloud and time line visualizations of large text corpora.

Text analysis & natural language processing
Visualization

JavaScript
Python
HTML
+ 1

COVID-19 Integrated Surveillance Data in Italy

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.

Clinical Data
Computational Epidemiology
COVID-19
+ 16

Julia
TeX
Python

Xenon

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.

batch-job
distributed computing
FTP
+ 11

Java
Shell
Batchfile

LinkAhead

Open Source Research Data Management Software

Data
ETL
Inter-operability & linked data
+ 4

Java
Shell
Python
+ 2

DALES

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.

Fortran
C
TeX
+ 8

DoE2Vec

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.

Machine learning
optimization
python

Python
R
Makefile