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Saanich Inlet Gene Centric Model - MATLAB code
This MATLAB code is provided as supplementary material to the following article:
Louca et al. (2016). Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone. PNAS 113:E5925-E5933. DOI:10.1073/pnas.1602897113.

The code simulates a 1-dimensional reaction-diffusion model for several microbial metabolic pathways in the Saanich Inlet anoxic water column. Modeled variables are the metabolite concentrations and the concentrations of genes mediating reactions between the metabolites. Reaction kinetics are either 1st order or second order, with kinetic parameters either taken from the literature, or calibrated to chemical depth profiles measured in Spring 2010.

The code can be adjusted to model other similar systems near steady state. The biochemical model is defined as a list of genes, a list of metabolites and a stoichiometric matrix for all involved pathways. In addition, the user can specify optional depth profile data sets for chemical concentrations as well as metagenomics, metatranscriptomics and metaproteomics. These are then automatically compared to the model predictions, or used for model calibration. The diffusion coefficient can be provided as an external data set (e.g. calculated from standard CTD data), or internally as a mathematical function. Boundary conditions for the partial differential equations can be specified as Dirichlet (i.e. fixed value) or Neumann (i.e. fixed derivative), independently for each metabolite or gene. The set of parameters to be calibrated or perturbed for sensitivity analysis can be customized in the code.

A regular MATLAB installation should be sufficient to run this code. This code has been tested in MATLAB R2015b, on Mac OS 10.12.6. Other MATLAB versions may require some slight modifications of the code. Please consult the included README file for technical details and the license agreement.

The complete code, including all required input data for Saanich Inlet, can be downloaded here.
Saanich metabolic model
Saanich predicted chemical profiles

Saanich predicted mRNA and protein profiles

Louca lab. Department of Biology, University of Oregon, Eugene, USA
© 2019 Stilianos Louca all rights reserved