SGN Documentation
View the Project on GitHub
nickmorales/imagebreed
ImageBreed Documentation
0. Breedbase Database Description
1. Basic Website Usage
1.1. Creating a User Account
Verifying first that you do not already have an account
Creating a user account
1.2. Managing your Account
Login
Editing Account Settings
Changing Your Account Status: From “User” to “Submitter”
Submitting Feedback on an SGN Database
1.3. Menu Layout
Menu Options
Search
Manage
Analyze
1.4. Working with Lists
Creating lists
Viewing and editing lists
1.5. User Permissions
2. Searching the database
2.1 The Search Wizard
2.1.1 How the Search Wizard Works
2.1.2 How to use retrieved data
Getting more Info
Saving to a list
Downloading Data
Metadata
Phenotypes
Genotypes
Saving the wizard selections
2.1.3 Updating the Wizard
2.2 Accessions and Plot Search
2.3 Trials Search
2.4 Trait Search
2.5 Ontology Browser
2.6 Search Seedlots
3. Managing Breeding Data
3.1 Managing Breeding Programs
3.2 Managing Locations
3.3 Managing Accessions
3.4 Managing Seed Lots
3.4.1 Add New Seedlot(s)
3.4.2 Seedlot Transactions
3.4.3 Seed Inventory
3.4.4 Find Seedlots For a List of Accessions
3.4.5 Create a seedlot for an Accession or Cross
3.5.6 Add quality data to a seedlot
Deleting Seedlots
3.5 Managing Populations
3.6 Managing Crosses
Crossing Experiment
3.6.1 Add New Crossing Experiment
Cross
3.6.2 Add New Crosses
3.6.2.1 Add a cross by using the “Add New Cross” dialog
3.6.2.2 Upload New Crosses
3.6.3 Update Crosses by Uploading
Cross Wishlist
3.6.4 Create a Cross Wishlist
Step 1. Select the accessions to be crossed in your trial
Step 2. Select the female plots to be considered in the crosses
Step 3. Transfer the cross wishlist to your mobile crossing application
Crossing Experiment Detail Page
Cross Detail Page
3.7 Managing Field Trials
Trial Detail Page
Adding Trials
Prerequisites
3.7.1 Adding a trial by using “Add Trial” form
Step 1. Begin the “Design new trial” workflow
Step 2. Enter “Trial Information”
Step 3. Enter “Design Information”
Step 4. Enter “Field Map Information” (Optional)
Step 5. Custom Plot Naming (Optional)
Step 6. Review Designed Trial
Step 7. Add Field Management Factors to your design (Optional).
Step 8. Saving new trial in the database.
3.7.2 Adding a trial from an uploaded file
Step 1:
Minimum File requirements
File validation
Uploading a trial with Field Management Factors
Step 2:
Step 3:
Step 4:
Step 5:
Completion screen
3.7.3 Multi-location trials
3.7.4 Viewing Trial HeatMap
Tracking plot images on fieldMap
Viewing assayed trait heatmap
Suppressing Plot Phenotype
3.7.5 Adding additional information in the “Trial Detail” page
Uploading Physical Trial Layout
Physical Trial Layout File requirements
Downloading Field Map Spreadsheet
Editing Physical Trial Layout
3.7.6 Downloading the Trial Layout from the “Trial Detail” page
3.7.7 Adding Plant Entries To Your Trial
Automatically Generate Plant Entries
Upload Plant Entries
3.7.8 Adding Tissue Sample Entries To Your Trial
3.7.9 Uploading GPS Coordinates For Plots
3.7.10 Uploading Additional Files To Trial
3.7.11 Deleting Trial Data
3.8 Managing Genotyping Plates
3.8.1 Adding a New Genotyping Plate
3.8.2 Genotyping Plate Detail Page
3.9 Using Field Book App
A typical workflow
3.9.1 Creating Field Layout Files for the Field Book App
3.9.1.1 Creating “Field Layout Files” by using “Field Book Tools” page.
3.9.1.2 Creating “Field Layout Files” by using “Trial Detail” page.
3.9.2 Creating Trait Files for the Field Book App
3.9.2.1 Creating a Trait List
3.9.2.2 Creating a Trait File
3.9.3 Transferring Files from Your Computer to Android Tablet
Files on your computer
Files on your Android tablet
3.9.4 Setting up “Field Book App” for data collection
3.9.5 Exporting Files from Field Book App
3.9.6 Uploading Phenotype Files to an SGN database
3.10 Managing Phenotypic Data
3.10.1 Uploading Fieldbook Phenotypes
Export Field Book Database File
Upload Field Book Database File
3.10.2 Uploading Spreadsheet Phenotypes
Generating Spreadsheet File
Uploading Spreadsheet File
3.11 Managing Barcodes
3.12 Using the Label Designer
3.13 Managing Downloads
3.14 Managing ODK Data Collection
3.14.1 ONA Crossing Information
Managing ONA Crossing Information
Reviewing Plant Status
Graphical Summary For Performed Crosses
Summary Information For Performed Crosses
3.15 Managing Tissue Samples
3.15.1 Tissue samples from field trials
3.15.2 Genotyping Plate Tissue Samples (96 or 384 well plates)
3.16 Managing Observation Variables with Traits, Methods, and Scales
3.16.1 Managing Observation Variables
3.17 Managing Image Data For Phenotyping
3.17.1 Image-Phenotyping Dashboard
3.17.2 Image Input
3.17.3 Standard Process
3.18.4 Ground Control Points
3.18 Managing Genotypic Data in VCF
3.18.1 Uploading Genotyping Data in VCF
3.18.2 Searching and Downloading Genotyping Data in VCF Against Phenotyping Data
3.18.3 Searching Genotyping Protocols
3.18.4 Genotyping Protocol Detail Page and Deleting a Genotyping Protocol
3.19 Managing Spectral Data
3.19.1 Initiate upload of spectral data file
3.19.2 Evaluate and remove spectral outliers
3.19.3 Plot spectra with outliers highlighted
3.19.4 Aggregate spectra by observation units
3.19.5 References
3.21 Managing Sequence Metadata
3.21.1 What is Sequence Metadata?
3.21.2 Loading Sequence Metadata
3.21.2 Searching Sequence Metadata
Basic Search
Advanced Search
3.21.3 Marker Integration
3.21.4 Sequence Metadata API
4. Data Analysis Tools
4.1 Selection Index
4.2 Genomic Selection
4.2.1 Building a prediction model
Method 1:
Estimating breeding values in a selection population
Method 2
Method 3
4.3 Genome Browsing
4.3.1 Browsing Genotype data by Accession
4.3.2 Browsing Genotype data by Trial
4.4 Principal Component Analysis (PCA)
4.5 ANOVA
4.6 K-Means Clustering
4.7 Genetic Gain
4.8 Creating Crossing Groups
4.9 Search Wizard Genomic Relationship Matrix (GRM) Download
4.10 Search Wizard Genome Wide Association Study (GWAS)
4.11 Spectral Analysis
Dataset selection
Cross-validation
Preprocessing
Algorithms
Output: common model summary statistics
Export model for later use
Predict phenotypes from an exported model (routine use)
FAQ
4.12 General Mixed Model Tool