Welcome to isotopomer-soup! isotopomer-soup is a model designed to solve for N2O production rates from 15N label experiments. Below is an overview of the directory structure and descriptions of each script.

• isotopomer-soup
  • Citation
  • Files and Directories
    • Root Directory
    • figures/
    • sherlock_output/
    • scripts/
      • functions submodule
      • initialization submodule
      • model submodule
      • montecarlo submodule
      • optimization submodule
      • postprocessing submodule
      • preprocessing submodule
      • runscripts submodule
  • Getting Started
  • License

A paper describing this model is freely available:

C. L. Kelly, N. M. Travis, P. A. Baya, C. Frey, X. Sun, B. B. Ward, & K. L. Casciotti (2024). Isotopomer Labeling in Hybrid Nitrous Oxide Production. Biogeosciences preprint. doi:10.5194/egusphere-2023-2642.

• LICENSE: Contains the license information for the package.
• model.py: example script to run one instance of the model.
• montecarlo.py: run full monte carlo simulation with n optimizations for given station and feature.
• montecarlo.sh: SLURM batch script to submit montecarlo.py as a job to the Sherlock computer cluster.
• PS1Interface.py (and similar files): example Python script to run monte carlo simulation for PS1 Interface.
• PS1Interface.sh (and similar files): example SLURM batch script to submit PS1Interface.py to Sherlock computer cluster.
• README.md: The file you are currently reading. Provides an overview of the package and its structure.
• requirements.txt: Lists the dependencies required to run the package.
• runerrors.py: run mini-Monte Carlo simulation with only three model optimizations.
• runerrors.sh: SLURM batch script to submit runerrors.py to Sherlock computer cluster.

Directory to save out model output figures.

Directory to save .out files and .err files from Sherlock jobs.

This is the main package directory containing all the core code and submodules.

• init.py: Makes the directory a Python package. Can be used to import core modules or set up package-level variables.
• Data/: directory containing input and output data

• binomial.py: Probabilities of formation of different isotopic species of N2O based on binomial probability tree.
• binomial_stoichiometry.py: Probabilities of formation of different isotopic species of N2O based on binomial probability tree, taking the stoichiometry of NO+NH2OH into account
• convert_af.py: Convert atom fraction into 15R/14R ratio and d15N.
• convert_delta.py: Convert concentration and d15N into concentrations of 15N and 14N as well as atom fraction.

• bgc.py: Initialize substrate concentrations and rates of transformation.
• initialize_n2o.py: Initialize concentrations of N2O isotopomers based on experimental t0.species of N2O based on binomial probability tree, taking the stoichiometry of NO+NH2OH into account
• intialize.py: Initialize inputs for model.
• isotope_effects.py: Define isotope effects to be used in the model.
• metadata.py: Giant dictionary containing relevant metadata for all N2O experiments.
• modelparams.py: Initialize model parameters.
• tracers.py: Initialize model parameters and arrays of state variables.

• modelv1.py: Version of the model containing no intermediates; N2O is produced from NH4+, NO2-, NO3-, and two hybrid pathways, which produce N2O from a combination of NH4+ and NO2-.
• modelv2.py: Version of the model containing intermediates NH2OH and NO; N2O is produced from NH4+, NO2-, NO3-, and two hybrid pathways, which produce N2O from a combination of NH2OH and NO.
• modelv3.py: Version of the model containing intermediates NH2OH and NO; N2O is produced from NH4+, NO, NO3-, and two hybrid pathways, which produce N2O from a combination of NH2OH and NO.
• modelv4.py: Version of the model containing intermediates NH2OH and NO; N2O is produced from NH4+, NO2-, NO3-, and two hybrid pathways, which produce N2O from a combination of NH2OH and NO2-.
• modelv5.py: Version of the model used in publication. Version of the model containing no intermediates; N2O is produced from NH4+, NO2-, NO3-, and one hybrid pathway, which produces N2O from a combination of NH4+ and NO2-. In addition to rate constants, solve for "f" parameter, which is the proportion of the alpha nitrogen that is derived from nitrite.

• genmontecarlo.py: Create nxm Numpy array of model parameters randomly sampled from a range of values from 75% to 125% of the parameter value, where n is the number of rows and m is the number of parameters.
• runmontecarlo.py: Run Monte Carlo simulation, running the model n times and varying key model parameters randomly by up to 25% for each iteration.

• costfxn.py: Calculate cost from model output and N2O incubation data at each of 2-3 timepoints.
• initialguess_modelv1.py: Run the forward model, version 3, with 0 N2O production and estimate rate constants to feed to the optimization.
• initialguess.py: Run the forward model, version 3, with 0 N2O production and estimate rate constants to feed to the optimization.
• modelv5objective.py: Set up objective function that calculates cost of a model solution across all three tracer experiments.

• plotmodeloutput.py: Plot model output with averaged incubation data at each timepoint and save figure as a PDF.
• plotmodeloutput2.py: Plot model output, showing triplicate incubation data at each timepoint and save figure as a PDF.
• postprocess.py: Calculate rates in nM/day from solved rate constants (x) and modeled substrate concentrations.

• read_data.py: Read in incubation data to train N2O production model.

• datapath.py: Define paths to data files.
• errors.py: mini-Monte Carlo simulation with only three optimizations
• run.py: run one instance of a modelv1 optimization
• runmodelv5: run one instance of a modelv5 optimization

To run the model, follow these steps:

1. Clone the repository:

git clone https://github.com/ckelly314/isotopomer-soup.git
cd isotopomer-soup

2. Install the dependencies:

pip install -r requirements.txt

3. Run the model:

from isotopomer-soup import scripts
scripts.runmodelv5("PS3", "SCM")

This project is licensed under the MIT License - see the LICENSE file for details.

Thank you for using isotopomer-soup! If you have any questions or issues, feel free to open an issue or contact me.