• Brief Repository Description

This repository contains the consensus genome-scale metabolic model Sco-GEM for the antibiotic producer Streptomyces coelicolor A3(2), a representative species of Actinomycetales.

• Abstract:

Streptomyces coelicolor is a representative species of soil-dwelling, filamentous and gram-positive actinobacterium harbouring enriched secondary metabolite biosynthesis gene clusters. As a well-known pharmaceutical and bioactive compound producer, S. coelicolor has been exploited for antibiotic and secondary metabolite production.

• Model KeyWords:

GEM Category: Species; Utilisation: Predictive simulation; Field: Metabolic-network reconstruction; Type of Model: Reconstruction and refinement; Model Source: iKS1317; Omic Source: Genomics; Taxonomy: Streptomyces coelicolor; Metabolic System: General Metabolism; Strain: A3(2); Condition: Complex medium;

• Reference:

TBA

• Pubmed ID: TBA

• doi: https://doi.org/10.1101/796722

• Last update: 2019-10-04

• The model contains:

This repository is administered by Eduard Kerkhoven (@SysBioChalmers), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology

• A functional Matlab installation (MATLAB 7.3 or higher).
• Python 3 including standard packages and additional packages described in requirements.txt
• RAVEN Toolbox 2 for MATLAB (required for contributing to development).
• libSBML MATLAB API (version 5.16.0 is recommended).
• Gurobi Optimizer for MATLAB.
• For contributing to development: a git wrapper added to the search path.

• Clone the master branch from SysBioChalmers GitHub.
• Add the directory to your Matlab path, instructions here.

• Eduard J. Kerkhoven (@edkerk), Chalmers University of Technology, Sweden
• Snorre Sulheim (@sulheim), SINTEF Industry, Norway / Norwegian University of Science and Technology, Norway
• Tjasa Kumelj (@tjasakumelj), Norwegian University of Science and Technology, Norway
• Ali Salehzadeh-Yazdi (@alisalehzadeh-yazdi), University of Rostock, Germany