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Upcoming Pathway Tools Tutorials and Workshops

Upcoming Pathway Tools Tutorials and Workshops


We typically have two types of tutorials:

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