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ExploreASL

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.

ASL
Image processing
MRI

MATLAB
C
Python

FastMLC

Detect clusters in for example large collections of DNA or protein sequences, and visualize the results in a web browser.

Big data
Machine learning
Visualization

C++
C
Makefile
+ 5

SIGA.py

Make genome annotations semantically interoperable

Inter-operability & linked data

Python

Cross-perspective Topic Modeling

An application that uses cross-perspective topic modeling to extract topics and opinions from text and provides insight into how they change over time.

Text analysis & natural language processing

Python
Jupyter Notebook
Shell

MDStudio

A tool to run molecular dynamics workflows.

High performance computing
Real time data analysis
Workflow technologies

Python
CSS
TypeScript
+ 5

MapReader

MapReader is an end-to-end computer vision (CV) pipeline for exploring and analyzing images at scale.

computer vision
digital humanities
geospatial
+ 4

Python
TeX
Dockerfile
+ 1

Xenon command line interface

A command line interface for the Xenon library that allows you to use remote machines to do your computations.

High performance computing

Java
Common Workflow Language
Dockerfile
+ 2

Clustering Geo-data Cubes

Tool to perform cluster analysis of multi-dimensional geospatial data, running on local or distributed systems.

Big data
geospatial
Machine learning
+ 1

Python
Jupyter Notebook
TeX

ChemSpaX: A Python tool for local chemical space exploration

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.

catalysis
Chemistry
python

Python
Shell

pdb2sql

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.

Big data
Optimized data handling

Python
TeX
Makefile

COVID-19 Piedmont

COVID-19 Surveillance Data Modelling and Management Pipeline in Piedmont.

Computational Epidemiology
COVID-19
COVID-19 Data
+ 14

Julia

pypfilt

A Sequential Monte Carlo (SMC, or "particle filter") Python package for online model estimation and probabilistic forecasting.

Bayesian Inference
Forecasting
Sequential Monte Carlo

recipy

Effortless provenance tracking in Python

Inter-operability & linked data
Optimized data handling

Python
HTML
Jupyter Notebook
+ 2

ece2cmor3

Process EC-Earth output to publish for CMIP6

Big data
High performance computing
Optimized data handling

Shell
Python

jaspProcess

A JASP implementation of the PROCESS macro for SPSS

Data Analysis
Statistics
Visualization

MultilayerGraphs.jl

A Julia package for the creation, manipulation and analysis of the structure, dynamics and functions of multilayer graphs.

Graphs
Graph Theory
Hierarchical Graphs
+ 10

Julia

nlppln

A flexible solution to build text mining workflows that allows you to quickly combine Natural Language Processing tools from different sources.

Text analysis & natural language processing

Python
Common Workflow Language
Dockerfile

Turing Data Safe Haven

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.

Cloud
cloud storage
Infrastructure as code
+ 3

Python
Shell
Jinja
+ 3

WRFpy

WRFpy is a python application that provides an easy way to set up, run, and monitor Weather Research and Forecasting simulations

Data Simulation
python

Python

xtas

the eXtensible Text Analysis Suite

Text analysis & natural language processing

Python
Shell
Java

eEcology Annotation Tool

Visualize and annotate GPS measurements of bird movements.

Inter-operability & linked data
Visualization

HTML
Python
Mako
+ 5

PSSMGen

Generates consistent PSSM and PDB files for protein-protein complexes

Big data
High performance computing
Optimized data handling

Python
Makefile

PuReGoMe

Analyzes social media messages for polarity and stance towards governmental COVID-19 measures

Machine learning
Social media

Jupyter Notebook
Python
Shell

SPOT

SPOT is an interactive visualization tool for multi-dimensional data. It allows quick analysis of complex datasets and easy identification of correlations between variables.

Big data
Visualization

JavaScript
Pug
Stylus
+ 2

3D Slicer

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.

3D
3DSlicer
Extension
+ 7

C++
Python
CMake
+ 5

eEecology Classification

Automatic classification of accelerometer data using a supervised learning approach.

Machine learning

Java
JavaScript
HTML
+ 3

MagnumPI - Potential Integrator

A package for the calculation of scattering angles and cross sections.

Inter-operability & linked data
Visualization

C++
Mathematica
Python
+ 2

mexca

Capture emotion expressions from video, audio, and text with a single pipeline.

Audio processing
Image processing
Machine learning
+ 1

Python
Dockerfile
Shell

PIQMIe

A web tool for mass spectrometry-based proteomics data analyses

Data Analysis
mass spectrometry
Optimized data handling
+ 2

HTML
JavaScript
Python
+ 3

TIMP

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.

global analysis
target analysis
time-resolved spectroscopy

Bacting

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.

bioinformatics
Cheminformatics

Java
TeX

cffconvert

Command line tool to convert CITATION.cff files to various formats used by reference managers such as Zotero and JabRef.

Python
TeX
HTML
+ 1

cffinit

A web form to initialize CITATION.cff files which you can use to include citation information into your software repository.

Software Citation

TypeScript
Vue
JavaScript
+ 3

citation.js

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.

Bibliography
BibTeX
Data Citation
+ 2

JavaScript
TeX
Roff

eAstroViz

This tool can convert and visualize radio astronomy measurement sets, as well as most LOFAR intermediate data products. It also performs RFI mitigation.

LOFAR
radio astronomy
RFI

Java
C++
Cuda
+ 3

evidence

doc2vec-based assisted close reading with support for abstract concept-based search and context-based search

Text analysis & natural language processing

TypeScript
Go
Jupyter Notebook
+ 5

howfairis

Command line tool to analyze a git repository's compliance with the fair-software.eu recommendations.

HTML
Python
Shell
+ 1

Lightning

Lightning: Fast data processing using GPUs on distributed platforms

Big data
GPU
High performance computing

Rust
C++
Python

LUE

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.

Agent-based modeling
environmental modelling
field based modelling
+ 6

C++
Python
CMake
+ 6

nanomesh

Python workflow tool for generating meshes from 2D and 3D microscopy image data

Image processing
Visualization
Workflow technologies

Jupyter Notebook
Python
Shell
+ 1

Noodles

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.

High performance computing
Workflow technologies

Jupyter Notebook
Python
Shell
+ 2

Hercules

Retrieve recent tweets from certain users and classify them with machine learning

Machine learning
Text analysis & natural language processing

Python
Jupyter Notebook
Shell

PerfectFit

This is a virtual coach system that coaches users into being more physically active and stop smoking.

Big data
health

JavaScript
Gherkin
Shell

sv-channels

Genome-wide detection of structural variants using deep learning

Machine learning

Python
Jupyter Notebook
R
+ 1

WEARDA

WEARDA: recording wearable sensor data for human activity monitoring.

embedded software
GPS
Human activity monitoring
+ 4

Xenon gRPC server

Run applications remotely via a gRPC interface.

High performance computing

Java

AstronomicAL

An interactive dashboard for visualisation, integration and classification of data using Active Learning.

Active Learning
Classification
Data Analysis
+ 11

Python
TeX

Beyond the book

Measure the number of contributions to Wikipedia entries from individuals from different counties as a measure of cultural bias.

Text analysis & natural language processing

Jupyter Notebook
Python
JavaScript
+ 2