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Tutorials

Step-by-step tutorials that follow a real genome-scale model from file to figure. They are written together with the GEMs MAP author and tested end to end in the application; every screenshot comes from that test run.

  • Quick start: from model to map

    E. coli iJO1366 from BiGG: import, explore, simulate with and without oxygen, compare the two solutions, make subsystem figures, and turn the comparison into a pathway map with templates, plots, collapsed arrows and routes. About 45 minutes.

    Start the quick start

  • Templates: create and review your own

    In preparation Designing a template in the Template Builder, defining identities, validating it, and applying it to different models.

Before you start

  • Install and start GEMs MAP with its backend: Installation.
  • The tutorials download models from BiGG Models; the first run of the metabolite analysis also needs the internet.
  • Values such as growth rates are reproducible; individual fluxes can differ slightly between runs because of alternative optimal solutions. The tutorials say what to expect and why.