sequentialScanner

Description

• A customisable sequential gene scanner for optimising combinations of both gene deletions and upregulations using flux balance analysis
• Allows adapting the number of affected genes, the loop selection percentile, the upregulation factor & the growth rate threshold
• Created by: @LucoDevro, Lucas De Vrieze, Department of Chemical Engineering, KU Leuven, Heverlee (Belgium)
• Developed as part of a MSc thesis under supervision of prof. dr. ir. Kristel Bernaerts and prof. dr. ir. Steffen Waldherr
• Last updated: 14th April 2021

Theoretical basis

Sequential scanning algorithm based on pFBA, including MOMA extension to deal with genetically perturbed networks

• Scanning algorithm: Alper et al., Met. Eng., doi: https://doi.org/10.1016/j.ymben.2004.12.003
• MOMA integration: Wang et al., Biochem Eng J, doi: https://doi.org/10.1016/j.bej.2017.03.017

Contents

• The master function (sequentialScanner.m)
• The worker function (sequentialScannerWorker.m)
• Auxiliary function altering the model flux bounds for a gene upregulation (upregulateModelGenes.m)
• Auxiliary functions interconverting consensus gene names and systematic gene names (GetGeneNameFromSysGeneName.m & GetSysGeneNameFromGeneName)
• MOMA.m from the COBRA Toolbox, with added bypass for wild-type solutions
• An example overhead script calling the main function with appropiate parameters (sequentialScannerOverhead.m): optimise ammonium efflux
• The COBRA model necessary for this example script (model100.mat): Bacillus subtilis in protein hydrolysate medium (genome-scale metabolic model iYO844 with custom-made GECKO extension)

Installation & software dependencies

Required software

• MATLAB 2019b or higher
• COBRA toolbox 3.0 for MATLAB
• IBM Cplex optimiser for MATLAB (or Gurobi Optimiser, or any other software capable of solving quadratic optimisation problems)

Other remarks

• This code currently uses a separate geneNames field. If your metabolic model happens to contain a complete genes field, just replace the appropiate field accessions.