GEM-hot1a3

This repo contains the Alteromonas macleodii HOT1A3 model, and code associated with its creation, curation, and testing.

The model was generated using RefSeq genome for HOT1A3 (Accession Number: NZ_CP012202.1), accessible via KBase. The narrative for generating the draft model, is available here: https://narrative.kbase.us/narrative/208263

This repo uses GtiHub actions to automatically test the model. Upon manual trigger:

1. A new MEMOTE report is generated, and saved as "index.html"
2. Run custom tests
   • Validate the SBML file
   • Test for growth on no carbon sources
   • Test known growth phenotypes, and regenerate the experimental vs predicted growth heatmap figure
   • Run the MEMOTE test to search for ATP generating cycles
3. The model is exported to JSON and excel formats

Note: MACAW is not run as part of the action due to the longer run time of the dilution test. To run MACAW use:

python run_macaw.py

To contribute to the model

1. Make a GitHub account
2. Make a fork/branch of this repo
3. Make your edits to the model on the XML file
4. Open a pull request