PSAMM Tutorials

• Installation and Materials
  • Downloading the PSAMM Tutorial Data
  • PSAMM Installation
  • PSAMM Model Collection
• Importing, Exporting, and working with Models with PSAMM
  • Import Functions in PSAMM
  • Importing Existing Models (psamm-import)
  • YAML Format and Model Organization
  • Version Control with the YAML Format
  • Using PSAMM to export the model to other Software
• Model Curation
  • Materials
  • Common Errors in Metabolic Reconstructions
  • PSAMM Warnings
  • Reaction Consistency in PSAMM
  • Gap Identification in PSAMM
  • Search Functions in PSAMM
  • Duplicate Reaction Checks
• Constraint Based Analysis with PSAMM
  • Tutorial Materials
  • Constraint-based Flux Analysis with PSAMM
  • FBA in PSAMM
• Reactant/Product Pair Prediction and Visualization Using FindPrimaryPairs
  • Materials
  • Reactant/Product Pair Prediction using PSAMM
  • Visualizing Models using PSAMM-Vis
• Automated Comparison of Models Using ModelMapping
  • Materials
  • Sub-commands in modelmapping function
  • Automatically map metabolic models
  • Manually curate the mapping result using using interactive interface
  • Translate ids in the query model based on curated mapping result
• Supplementing your model with other data
  • Materials
  • Subsetting a Metabolic Models Using Expression Data with Gimme
  • Generating a Draft Model From a Template Using Psammotate
  • Thermodynamics-Based Metabolic Flux Analysis
• Generating Metabolic Models Based On Functional Annotations
  • Materials
  • Basic use of the generate-database command
  • Basic use of the generate-transporters command