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chimp-classifier

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.

audio
Audio processing
bioacoustics
+ 2

Jupyter Notebook
Python
Shell

Emma

Emma is a project to create a platform for development of application for Spark and DockerSwarm clusters.

Big data

Shell
Scala
Python
+ 1

Introduction to Geospatial Raster and Vector Data with Python

This lesson material shows how practical geospatial data analysis tasks can be carried out using Python

Data Analysis
geospatial
Image processing
+ 4

iReceptor Gateway

A Distributed Data Management System and Scientific Gateway for Mining Next Generation Sequence Data from Immune Responses.

immunogenomics
Immunology
iReceptor

PHP
Shell
Blade
+ 7

Lilio

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.

AI
Preprocessing
S2S

Python
Shell

nanopub

The nanopub library provides a high-level, user-friendly python interface for searching, publishing and retracting nanopublications.

Inter-operability & linked data

Python
Shell
Batchfile

s2spy

A high-level python package integrating expert knowledge and artificial intelligence to boost sub-seasonal to seasonal (S2S) forecasting.

Python
Shell

SalientDetector-matlab

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

Image processing

MATLAB

SalientDetector-python

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

Image processing

Jupyter Notebook
Python
Makefile

SlicerRT

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.

C++
Python
CMake
+ 1

Revisited Via Appia

Create visual storylines that involve media like images and videos embedded in a 3D environment with efficient Pointcloud data directly from the web browser.

cultural heritage
Digital Twins
gis
+ 2

JavaScript
HTML
Vue
+ 3

SyGMa

SyGMa provides fast and lightweight predictions of human metabolites to support discovery scientists design better and safer drugs

Workflow technologies

Python

adhtools

Use adhtools for analyzing Arabic corpora.

Text analysis & natural language processing
Visualization
Workflow technologies

Jupyter Notebook
Python
Common Workflow Language
+ 1

dhdt

A photohypsometric Python library to estimate glacier elevation change via optical remote sensing imagery

geospatial
Glacier
image
+ 2

Python
TeX

duqtools

Duqtools is a tool for Dynamic Uncertainty Quantification for Tokamak reactor simulations modelling.

fusion-reactor
modelling
python
+ 2

Jupyter Notebook
Python
Shell

eEcology Tracker calendar

Calendar overview with daily statistics of GPS-trackers used to track bird movements.

Visualization

Python
Makefile
JavaScript
+ 5

Entangled

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.

Literate Programming
open science
python
+ 2

Python
C++
Makefile
+ 2

eOSSR

The eOSSR is the Python library to programmatically manage the ESCAPE OSSR.

jupyter-notebook
repository
research software
+ 2

Python
Dockerfile

ewatercycle

The eWaterCycle package makes it easier to use hydrological models without having intimate knowledge about how to install and run the models.

Inter-operability & linked data
Multi-scale & multi model simulations
Optimized data handling
+ 1

Python
Dockerfile

fairtally

Create comprehensive reports on compliance with the fair-software.nl recommendations.

Python
Shell
Dockerfile

fairworkflows

A python library for constructing, annotating and publishing scientific workflows described using semantic technologies.

Python
HTML
Common Workflow Language
+ 1

frbcatdb

A database to store a catalog of Fast Radio Bursts and expose them as Virtual Observation Events.

Optimized data handling

Python
Shell

frbcat-web

Provides an easy to-use web frontend to browse and filter the Fast Radio Burst Catalogue.

Optimized data handling
Visualization

JavaScript
CSS
HTML

IncompressibleNavierStokes

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.

HPC
Scientific machine learning

Julia

MOTrainer

Measurement Operator Trainer for data assimilation purposes.

Data assimilation
High performance computing
Machine learning
+ 2

Jupyter Notebook
Python
TeX
+ 1

NEWSGAC platform

Software for running the online platform of the NEWSGAC project for running explainable machine learning models on textual data

Explainable AI
Machine learning
Text analysis & natural language processing

Jupyter Notebook
Python
HTML
+ 4

ochre

A tool to clean up text generated by OCR using individual words as well as their context.

Machine learning
Text analysis & natural language processing

Common Workflow Language
Jupyter Notebook
Python
+ 2

PanVA

Variant Analysis within Pangenomes.

API
Data Analysis
pangenomics

Vue
TypeScript
Python
+ 6

PathVisio

PathVisio is a free open-source software to curate biological pathway models.

bioinformatics
PathVisio
Systems Biology
+ 2

Java
HTML
JavaScript
+ 4

PIDIMEHS library

Showcases a diachronic analysis of the Dutch Royal Library's newspaper archive.

Big data
Real time data analysis
Text analysis & natural language processing
+ 1

pyglotaran

A Python library for Global and Target Analysis of time-resolved spectroscopy data

biophysics
global analysis
glotaran
+ 3

Python
Nix

Ricgraph - Research in context graph

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.

graph
graph database
research in context graph
+ 2

Python
Makefile
Shell
+ 5

sfb-annotator

Annotate field books of natural history collections

Inter-operability & linked data

JavaScript
Java
CSS
+ 4

ShiCo

A visualization that shows how the meaning we attach to a given concept shifts over time.

Text analysis & natural language processing
Visualization

Python
JavaScript
HTML
+ 3

tortellini

GitHub action to check whether any licensing issues exist for given software.

TypeScript
JavaScript

Analizo

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.

Software Evolution
Source Code Metrics
Static Analysis

Perl
C++
C
+ 7

anonymoUUs

Python package to replace identifiable strings in multiple files and folders at once

de-identification
python
text

Python
Jupyter Notebook

Baklava

Deploys a Kubernetes cluster and big data services on the cloud.

Big data
High performance computing
Optimized data handling

Python
HCL
Dockerfile
+ 2

BenchmarkRecovery

This project simulates Landsat data and evaluates the performance of recovery indicators with respect to data and disturbance characteristics.

BIRCH

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.

bioinformatics
BLAST
genomics
+ 3

BrainBrowser

BrainBrowser is an open source JavaScript library exposing a set of web-based 3D visualization tools primarily targetting neuroimaging

3D
brainbrowser
neurology
+ 2

JavaScript
Python
CSS
+ 1

byteparsing

Parser library for reading custom binary files from Python.

Big data
Multi-scale & multi model simulations
Optimized data handling

Jupyter Notebook
Python
C++
+ 5

CBRAIN

CBRAIN is a flexible Ruby on Rails framework for accessing and processing of large data on high-performance computing infrastructures.

CBRAIN
cluster
Data Analysis
+ 6

Ruby
HTML
JavaScript
+ 3

ChemTools

ChemTools is a free and open source Python library for interpreting the results of quantum chemistry calculations.

atoms in molecules
conceptual dft
density matrices kinetic energy density
+ 2

Python

dCacheFS

Python file-system interface for dCache storages.

Data
Inter-operability & linked data
Optimized data handling
+ 1

Python
Jupyter Notebook

Emo-spectre

Interactive visualization and exploration of multi modal time-series data and video

Visualization
Workflow technologies

PLpgSQL
Vue
JavaScript
+ 5

emvoice

A Python package for computing emotion expression-related features from speech signals.

Emotion expressions
python
Speech processing

Python
Shell

Lysander

Find people on Twitter given a small initial set of interesting people.

Text analysis & natural language processing

Python