The SEED Servers

A network API for accessing the SEED data.

  1. Annotating a Genome
  2. Building a Metabolic Reconstruction
  3. What is a metabolic model?
  4. Uploading a genome to RAST
  5. Uploading Sequence Data to RAST
  6. Monitoring Your Job's Progress
  7. Downloading and Checking Results
  8. A Simple Way to Check for Genes that Bridge Contigs
  9. Support for Exploring Pangenomes
  10. Formulating Conjectures: Using the Browser and Atomic Regulons
  11. Differential Expression Analysis tool
  12. Tutorial Agenda
  13. Overview
  14. The Components
  15. The SEED and the P-SEED
  16. P-SEED and A-SEED Servers
  17. RAST
  18. myRAST
  19. Annotations
  20. Subsystems
  21. FIGfams
  22. Submitting a job with web-based RAST
  23. Annotation with RAST
  24. Annotating a Genome Using myRAST
  25. Exporting from RAST
  26. Exporting from myRAST
  27. Modeling Overview

Search

  • Master Index

API Listings

  • Sapling Server
  • Annotation Server
  • RAST Server
  • Model Server
  • Server Scripts
  • Server Utilities API

SEED Utilities

  • Scan for Matches (patscan)

Recent Entries

  • What SEED Do I Use?
  • The SEED Book
  • Some simple Sapling examples
  • An Exercise to Get a List of Homologs of Virulence Factors
  • Accessing the Wireless Network at Argonne Tutorials and Workshops
  • An Etude Relating to a Metagenomics Sample
  • Upcoming Tutorials
  • A Short Note on Mapping PEGs to Subsystems
  • A Short Note on Use of Server Scripts to Access Functional Coupling Scores
  • Annotated list of Getting Started, Tutorial and Coding Examples

Tag Cloud

  • Application programming interface

Categories

  • Coding Examples (8)
  • News (5)
  • Technical Notes (1)
  • Tutorials (16)
  • Workshop (2)

Pages

  • Introduction
  • RAST Workshop Presentation Links
  • Installation
    • Distribution of the SEED server packages
  • ModelTutorials
    • Annotations to Reactions
    • Editing Your Model
    • Generating Predictions on Your Model
    • Model Phenotypes
    • ModelView Presentation PDFs
    • Reactions to Initial Model
    • Viewing your Initial Model
  • Usage
    • 1. Summary of the Individual Servers
    • 2. Command Line Services
    • 3. The RAST batch interface

Presentations

  • Analyzing Your Genomes with the SEED Servers
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