GEM-atcc27126

This repo contains the Alteromonas macleodii ATCC 27126 model, and code associated with its creation, curation, and testing.

The model was generated using RefSeq genome for ATCC 27126 (Accession Number: NC_018632), accessible via KBase. The narrative for generating the draft model, is available here: https://narrative.kbase.us/narrative/208260

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 MACAW
3. 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
4. The model is exported to JSON and excel formats

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