All software
CICMoD - A Climate Index Collection based on Model Data
The software provides a consistent and comprehensive collection of climate indices typically used to describe Earth System dynamics and serves as a new benchmark data set. It allows users to develop new machine learning methods and to compare their results to existing methods in an objective way.
- Earth & Environment
- FAIR Data
- Image processing
- + 1
- Jupyter Notebook
- Python
- Shell
- + 1
dCache
dCache is a system for storing and retrieving huge amounts of scientific data, distributed among a large number of heterogeneous server nodes, under a single virtual filesystem tree with a variety of standard access methods including NFSv4.1 (pNFS), FTP, WebDav and xroot.
- data managment
- FAIR Data
- Java
- HTML
- JavaScript
- + 12
MoReCluster
A Python-based framework for grouping and clustering of chemicals based on shared molecular response patterns extracted from CTD. It builds on the CGPD-tetramers to identify coherent substance groups that exhibit common molecular and phenotypic effects.
- Earth & Environment
- FAIR Data
- FAIR Software
- + 2
- Python
- Shell
- Dockerfile
PeriHub
PeriHub is a platform that provides a numerical implementation of the peridynamic theory. It is an extension of the open source Peridigm software. Peridynamics is a non-local theory that overcomes discontinuity problems of the classical theory of continuum mechanics.
- Data Visualization
- High performance computing
- Modelling
- + 2
- Python
- Vue
- TypeScript
- + 7
quinex
quinex automates the large-scale extraction of quantitative information from text across many domains using lightweight and open language models
- information extraction
- Large Language Model (LLM)
- Measurement Extraction
- + 4
- Python
- TypeScript
- Shell
- + 3
Trimmomatic
Trimmomatic is a command line tool that performs a variety of functions for Illumina paired-end and single-end sequencing data, including sequence trimming and adapter removal. It is a flexible and efficient NGS preprocessing tool, which greatly improves downstream applications.
- Earth & Environment
- Illumina
- NGS
- Java
- Dockerfile
wps-command-line-tool-repository
A wrapper framework around the WPS 4.0 server by 52° North to allow easy integration of command line scripts into WPS services.
- Earth & Environment
- Remote Procedure Calls
- Web Processing Service
- Java
- Scheme
- Python
- + 3
AMPBA-workflow
AMPBA is a modular, Snakemake-based pipeline for reproducible amplicon metabarcoding, composable across markers and study designs, and lightweight enough to run independently on hardware from laptops to HPC clusters.
- Python
- Snakemake
- Shell
- + 2
base-repo
Base-repo is a generic, domain-agnostic research data repository suitable to store and manage all kinds of research data. Its content is organized as DataResources, which consist of descriptive DataCite-compliant Metadata and one or more data elements, either stored as files or linked by reference.
- Datacite
- data managment
- FAIR Data
- + 1
- Java
- Shell
- Dockerfile
Calopy
A web-based, open-source platform for the analysis of indirect calorimetry data, measuring energy metabolism in animals and humans.
- Data analysis
- Data Visualization
- Health
- + 2
- Python
- Dockerfile
- CSS
case-e
case-e is an open-source electronic case report form (eCRF) system for designing clinical studies and collecting structured research data. It supports configurable forms, validation, role-based access, audit trails, versioning, and portable exports for transparent, FAIR-oriented research workflows.
- BIDS
- Biomedical Ontologies
- Clinical Research
- + 9
- Vue
- Python
- JavaScript
- + 4
Computer Vision Experimentation Frameworks - Generalized-YOLOv5
- biomedical image analysis
- Deep Learning
- natural image analysis
- + 4
- Python
- Shell
- Dockerfile