All software
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
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
DataFlow
A comprehensive framework for automated data processing and manual postprocessing, including quality control and flagging. Modular and extensible design allows to create customizable pipelines and monitor their performance throughout the data lifecycle.
- data managment
- Data Visualization
- Pipeline
- + 2
- TSX
- Python
- TypeScript
- + 2
EcoToxFred
EcoToxFred (ETF) is a digital domain expert that enables simple, natural-language access to complex, integrated ecotoxicological data. It combines knowledge graphs, large language models, and agent-based workflows to support intuitive exploration and analysis of environmental risk information.
- Conversational AI
- Environmental Toxicology
- knowledge graph
- + 2
- Python
- Cypher
- Dockerfile