BIT 495/595: Metabolic Modeling

Overview:

  • Students will work asynchrously through a series of Department of Energy Knowledge Base (KBase) narratives to create, evaluate, and improve individual and community microbial metabolic models with novel isolates local to deep-sea hydrothermal vents in the Guaymas Basin.
  • Participants will be guided through narratives by an expert developer. Open labs will be available for students to work on assignments and their own models. Office hours will also be available upon request for additional help.

Active-Learning Topics:

  1. Sequence Assembly and Annotation
  2. Gapfilling and Flux Balance Analysis
  3. In silico Media Manipulation
  4. Model Assesment and Comparison
  5. Mixed Bag and Compartmentalized Models
  6. Community Member Metabolite Exchange
  7. Automated and Manual Model Validation
  8. Metabolic Map Visualization

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