Tutorial Agenda

A Tutorial on Using the SEED Servers to

Annotate a Genome,

Formulate a Metabolic Reconstruction, and

Model Metabolic Networks

This will be a two-day tutorial, with an optional third day. 

Day 1:

8:30 -- 9 am Coffee

Overview of the Tutorial, the Annotation Strategy, and Pieces of the Puzzle

Ross Overbeek

Founding Fellow, the Fellowship for Interpretation of Genomes (FIG)

The Components
The SEED and the P-SEED
P-SEED and A-SEED Servers

Annotating with RAST

Veronika Vonstein

President of FIG and Head of Annotation Team


A Short Overview of myRAST 

Bob Olson

Leads myRAST Development Team, ANL

Installing and Running the Next Generation of RAST on Your Laptop

Terry Disz

RAST Project Manager, ANL

     Odds and Ends (Server commands, Excel Interface)
                Terry Disz, ANL 
                 Ross Overbeek, FIG

An Overview of the Metabolic Modeling Tools within the SEED

Chris Henry

Head of Metabolic Modeling Group, ANL


6:30 - 8 pm Dinner at Giordano's 

Day 2: 

In day 2 of the tutorial, we will demonstrate the web interfaces and tools available within Model SEED for the reconstruction, comparison, curation, and analysis of genome-scale metabolic models. Users who arrive with a particular genome of interest will begin the process of curating their private model for that genome.

8:30 - 9 am  Coffee

Overview of Biochemistry Data Available within the Model SEED

Chris Henry, Head of Metabolic Modeling Group, ANL

Scott Devoid, Programmer in Metabolic Model Group, ANL

Demonstration of Model Viewing and Comparison Features of Model SEED

Chris Henry, ANL

Scott Devoid, ANL


Discussion of Metagenomics

Rob Edwards

Demonstration of Interface for Reconstruction and Curation of Private Models

Chris Henry, ANL

Scott Devoid, ANL

Demonstration of Steps Required to Curate a Private Metabolic Model

Chris Henry, ANL

Scott Devoid, ANL

Use of Curation Tools in Model SEED to Improve Private Models

Chris Henry, ANL

Scott Devoid, ANL

Day 3:

We will work with any interested individuals on annotation/modeling issues relating directly to genomes of particular interest.