Upcoming Pathway Tools Tutorials and Workshops

We typically have two types of tutorials:

• Introduction into Pathway Tools
• Pathway Tools Tutorial on Metabolic Modeling using Flux Balance Analysis (MetaFlux)
• Tutorial Slides

Each day will be composed of a series of lectures and labs.

Introduction into Pathway Tools

Topics typically covered (final schedule subject to changes):

• Day 1 (Pathway / Genome Navigator)
  • Pathway Tools Genome Navigator
  • Omics Viewers: Cellular, Regulatory and Genome
  • Comparative Analysis
  • Structured Advanced Query
  • SmartTables
  • Enrichment/Depletion Analysis
• Day 2 (PathoLogic)
  • Pathway Prediction using PathoLogic
  • Matching Enyzme Names to Reactions
  • Protein Complexes and Operon Predictor
  • Building a PGDB using PathoLogic
  • Introduction to Flux Balance Analysis in Pathway Tools using MetaFlux
• Day 3 (PGDB Editing)
  • Pathway / Genome Editors
  • Creating Reactions and Pathways
  • Curating Genes and Enzymes
  • Open Lab

Pathway Tools Tutorial on Metabolic Modeling using Flux Balance Analysis (FBA)

Topics typically covered (final schedule subject to changes):

• Day 1: Executing metabolic models with MetaFlux
  • Steady-state metabolic models (FBA)
  • Dynamic FBA models
  • Models for organism communities
  • The MetaFlux user interface
  • Visualizing predicted fluxes on pathways and on the metabolic map
• Day 2: Constructing metabolic models with MetaFlux
  • Predicting the biomass equation
  • The reaction gap filler
  • Tools for finding blocked reactions, unbalanced reactions, dead-end metabolites
  • Open Lab