An idealized OMZ ecosystem model for Ecological dynamics explain modular denitrification in the ocean (https://www.pnas.org/doi/abs/10.1073/pnas.2417421121)

1. model.py

The model

2. traits.py

Contains model parameters for traits of different microbial functional groups and their references

3. call_model_nopulse.py and call_model_pulse.py

Used to run models without and with organic matter pulses, respectively

4. files ended with star_Xin.py

Contain functions to calculate different R*

The metabolic model and Flux Balance Analysis

1. D2M19.xml

The curated metabolic model of Marinobacteria.

2. yOM_denitrifier_steps.ipynb

Contains scripts of Flux Balance Analysis using different media.