A network API for accessing the SEED data.

Master List of Pages

• Introduction
• RAST Workshop Presentation Links

Installing the SEED Server Software

• Distribution of the SEED server packages

Metabolic Modeling Tutorials

• Annotations to Reactions
• Editing Your Model
• Generating Predictions on Your Model
• Model Phenotypes
• ModelView Presentation PDFs
• Reactions to Initial Model
• Viewing your Initial Model

Topics from the Tutorial Seminar

• A Simple Way to Check for Genes that Bridge Contigs
• Annotating a Genome
• Annotating a Genome Using myRAST
• Annotation with RAST
• Annotations
• Building a Metabolic Reconstruction
• Differential Expression Analysis tool
• Downloading and Checking Results
• Exporting from myRAST
• Exporting from RAST
• FIGfams
• Formulating Conjectures: Using the Browser and Atomic Regulons
• Modeling Overview
• Monitoring Your Job's Progress
• myRAST
• Overview
• P-SEED and A-SEED Servers
• RAST
• Submitting a job with web-based RAST
• Subsystems
• Support for Exploring Pangenomes
• The Components
• The SEED and the P-SEED
• Tutorial Agenda
• Uploading a genome to RAST
• Uploading Sequence Data to RAST
• What is a metabolic model?

Using the Server Software

• 1. Summary of the Individual Servers
• 2. Command Line Services
• 3. The RAST batch interface

Articles

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