T66-GEM: Genome-scale metabolic model of Aurantiochytrium sp. T66

Description

This repository contains the genome-scale metabolic model (GEM) of the thraustochytrid Aurantiochytrium sp. T66. Considerably improving on the model quality and scope to that of previously published thraustochytrid GEMs, this model provides a great starting point for conducting research on thraustochytrids as microbial cell factories.

Citation

If you use T66-GEM please cite the following paper:

Simensen, V., Voigt, A., Almaas, E. High-quality genome-scale metabolic model of Aurantiochytrium sp. T66. Biotechnology and Bioengineering, 118:2105–2117 (2021) doi:10.1002/bit.27726

Keywords

Utilisation: model template; in silico strain design; multi-omics integrative analysis
Field: metabolic-network reconstruction
Type of model: reconstruction; curated
Model source: iVS1191
Omic source: genomics; transcriptomics; metabolomics
Taxonomic name: Aurantiochytrium sp. T66
Taxonomy ID: taxonomy:1749249
Genome ID: insdc.gca:GCA_001462505.1
Metabolic system: general metabolism
Condition: aerobic; glucose-limited; defined media

Model Overview

Taxonomy	Template Model	Reactions	Metabolites	Genes	Memote score
Aurantiochytrium sp. T66	iVS1191	2095	1657	1191	90%

Installation

If you want to use the model, any software that accepts SBML L3V1 FBCv3 formatted model files will work. We recommend the following as they are well-maintained and used by most researchers in the constraint-based metabolic modeling community:

• MATLAB
  • COBRA Toolbox and RAVEN Toolbox
• Python
  • cobrapy

Usage

The following code shows how the model can be read and written:

• In Matlab using either COBRA or RAVEN:

  cd ./code
  % For RAVEN use cobra = false
  cobra = true;
  model = loadT66Model(cobra); % loading
  saveT66Model(model);    % saving

• In Python using cobrapy:

  from model_io import read_t66_model, write_t66_model
  model = read_t66_model() # loading
  write_t66_model(model)   # saving

Contributing

Contributions are always welcome! Please read the contributing guideline to get started.

Contributors

Code contributors are reported automatically by GitHub under Contributors, while other contributions come in as Issues.