LabFisUFV/lista-GEM

lista-GEM: Genome-scale metabolic reconstruction of Lipomyces starkeyi

Description

This repository contains the current genome-scale metabolic reconstruction of Lipomyces starkeyi NRRL Y-11557, named lista-GEM. The model distributed on this GitHub repository is continuously updated, with the latest releases available here. To get access to the model associated to the Almeida et al. (2023) publication, use lista-GEM 1.0.0.

Citation

• If you use lista-GEM please cite the preprint:

  Almeida et al. lista-GEM: the genome-scale metabolic reconstruction of Lipomyces starkeyi. bioRxiv (2023). DOI: 10.1101/2023.09.25.559328

Keywords

Utilisation: experimental data reconstruction; multi-omics integrative analysis;, in silico strain design; model template
Field: metabolic-network reconstruction
Type of model: reconstruction; curated
Model source: iYali and rhto-GEM
Omic source: genomics
Taxonomic name: Lipomyces starkeyi
Taxonomy ID: taxonomy:675824
Genome ID: insdc.gca:GCA_018804115.1
Metabolic system: general metabolism
Strain: NRRL Y-11557
Condition: aerobic; defined media

Installation

You can obtained the model by any of the following methods:

1. If you have a Git client installed on your computer, you can clone the main branch of the lista-GEM repository.
2. You can directly download the latest release as a ZIP file.
3. If you want to contribute to the development of lista-GEM (see below), it is best to fork the lista-GEM repository to your own Github account.

Usage

If you want to use the model for your own model simulations, you can use any software that accepts SBML L3V1 FBCv3 formatted model files. This includes any of the following:

• MATLAB-based

  • RAVEN Toolbox version 2.8.3 or later (recommended)
  • COBRA Toolbox

• Python-based

  • cobrapy

RAVEN Toolbox

model = importModel('lista-GEM.xml')
exportModel(model, 'lista-GEM.xml')

cobrapy

import cobra
model = cobra.io.read_sbml_model('lista-GEM.xml')
cobra.io.write_sbml_model(model, 'lista-GEM.xml')

COBRA Toolbox *

model = readCbModel('lista-GEM.xml')
writeCbModel(model, 'lista-GEM.xml')

* note that some annotation might be lost when exporting the model from COBRA Toolbox.

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.