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Breedbase Developers' Documentation

Installation

• Basic Docker setup
• Basic Catalyst Configuration

Database setup

• Configuration keys in sgn.conf

Database description

• User management
• SSO Login
• Login for BrAPI
• Lists
• Datasets
• Database Schema

Ontologies

Searches

• Wizard
• Accession Search
• Trial Search
• Image Search
• People Search
• Genotyping Searches
• Trait Search

Germplasm

• Stocks
• Crosses and pedigrees
• Seedlots

Trials

• Breeding programs
• Locations
• Phenotype data
• NIRS data
• Labeldesigner
• FieldManagementFactors

Images

• Image Introduction
• Automated Image Analysis

Tools

• Creating new tools on Breedbase
• Slurm Setup
• Analyses
• Blast
• MixedModels
• SolGS
• GWAS
• Processing Drone Imagery

Genotyping data

• Genotyping plates
• Genotyping protocols

Bulk loading of data

• Ontologies
• Accessions
• Locations
• Trials

JavaScript

• JavaScript Setup

Reference Sequence Annotation

Brapi Implementation

Updating the User Manual

Writing Tests

Running Tests

Troubleshooting

Using QBMS with Breedbase