HELP HOME: "1. Welcome to Genboree Help"

Genboree Help is available for specific topics (see below). The extent of the areas covered is currently limited, but will grow over time.

The Help links within Genboree are currently of two types:

1. Pop-up help.
   • · Short context-specific information, hints, tips, and examples.
2. Links to this detailed documentation.
   • · Links that open in a new window.
   • · More in-depth information and explanations.

Please feel free to request help documentation for specific Genboree topics. Such requests help us identify and prioritize documentation writing.

• 1. Welcome to Genboree Help
  • 1.1 Genboree Help Overview
  • 1.2 Requesting Help Documentation
  • 1.3 Help Table of Contents
• 2. Defining A Genome
  • 2.1 Overview
    • 2.1.1 What are "entry points"?
    • 2.1.2 What is a "genome" in Genboree?
  • 2.2 Methods for Defining a Genome
    • 2.2.1 Use a template genome
    • 2.2.2 Define a custom genome
• 3. Uploading Entry Points
  • 3.1 How to Upload Entry Points
  • 3.2 Entry Point Formats
    • 3.2.1 Fasta file
    • 3.2.2 3-Column LFF entry point file
• 4. Uploading Annotations
  • 4.1 What Are Annotations?
  • 4.2 Uploading Annotations
  • 4.3 Annotation File Formats
    • 4.3.1 LFF format
    • 4.3.2 Other formats
• 5. The LFF Annotation Format
  • 5.1 Overview
  • 5.2 Column Descriptions
  • 5.3 LFF Annotation Examples
  • 5.4 Special Attribute=Value; Pairs
• 6. Custom Links
  • 6.1 Overview
  • 6.2 Creating Custom Links
    • 6.2.1 Constructing URL patterns
    • 6.2.2 Example URL patterns
    • 6.2.3 Simple tags
    • 6.2.4 Regular expression tags
    • 6.2.5 Special tags
  • 6.3 Assigning Links to Tracks
• 7. Tabular View and Layout Design
  • 7.1 Tabular View
    • 7.1.1 What is the tabular view?
    • 7.1.2 How to Access the Tabular View Tool
    • 7.1.3 Limitations
  • 7.2 Tabular Views and Layouts
    • 7.2.1 Using the Tabular View Tool
    • 7.2.2 Using Layouts
    • 7.2.3 Annotation Groups
    • 7.2.4 Terse / Verbose Group Modes
  • 7.3 Special Features
    • 7.3.1 Edit button
    • 7.3.2 Graphical view link
    • 7.3.3 On-demand Sorting
• 8. REST API - Overview
  • 8.1 Introduction
  • 8.2 Key Aspects
    • 8.2.1 Resource IDs (URIs)
    • 8.2.2 Uniform Methods/edit
    • 8.2.3 Resource Representations
    • 8.2.4 Authorization
  • 8.A REST API - Resource IDs
  • 8.B REST API - Methods
  • 8.C REST API - Representations
  • 8.D REST API - Authorization
• 9. Virtual Genome Painter (VGP) Interface
  • 9.1 The Virtual Genome Painter (VGP)
  • 9.2 Selecting Entry Points
    • 9.2.1 Entry Points List
    • 9.2.2 Manually Specifying Entry Points
  • 9.3 Specifying Images and Labels
    • 9.3.1 The Genome View
    • 9.3.2 The Chromosome View
    • 9.3.3 Image Labels
  • 9.4 Data Columns
    • 9.4.1 Adding Data Columns
    • 9.4.2 Update Data Columns
    • 9.4.3 Remove Data Columns
  • 9.5 Annotation Tracks
    • 9.5.1 The Reference Track
    • 9.5.2 Drawing Styles and Options
    • 9.5.3 Adding Annotation Tracks
    • 9.5.4 Updating Annotation Tracks
    • 9.5.5 Removing Annotation Tracks
  • 9.6 Submitting a VGP Job
• 10. Circos Interface
  • 10.1 Circos
  • 10.2 10.2 Entry Points
    • 10.2.1 Global Entry Point Properties
    • 10.2.2 Entry Points List
    • 10.2.3 Manually Specifying Entry Points
    • 10.2.4 Individual Entry Point Properties
    • 10.2.5 Entry Point Scales
    • 10.2.6 Entry Point Breaks
  • 10.3 Specifying Ideogram Properties
  • 10.4 Tick Marks
    • 10.4.1 Adding Tick Marks
    • 10.4.2 Updating Tick Marks
    • 10.4.3 Removing Tick Marks
  • 10.5 Annotation Tracks
    • 10.5.1 Track Types and Options
    • 10.5.2 Adding Annotation Tracks
    • 10.5.3 Updating Annotation Tracks
    • 10.5.4 Removing Annotation Tracks
    • 10.5.5 Annotation Filtering Rules
  • 10.6 Submitting a Circos Job