MinReact is an efficient algorithm to identify the minimal metabolic networks or minimal reactome for a genome-scale metabolic network. MinReact utilises the functional classes of parsimonious FBA to identify the minimal reactome. The algorithm identifies multiple minimal reactomes for a given metabolic network. Additionally, the algorithm also takes input of the tolerance value, growth-rate cutoff and reactions to be retained in the minimal metabolic network.
To perform synthetic lethality analysis using Fast-SL the following tools are needed:
- COBRA Toolbox
- A linear programming (LP) solver such as Gurobi, GLPK etc.
- CPLEX v12.0 or higher for the parallel version of Fast-SL. For the serial version of Fast-SL, any COBRA-supported solver can be used. CPLEX is available free for academics from IBM
If you use MinReact in your work, please cite
Gayathri Sambamoorthy and Karthik Raman (2020) "MinReact: a systematic approach for identifying minimal metabolic networks" Bioinformatics 36 doi:10.1093/bioinformatics/btaa497
The algorithm uses pFBA. The pFBA code has been modified to suit the purpose of this algorithm. The modified pFBA code is available in the package as well. Additionally, fastFVA is used in the modified pFBA code.
The algorithm is compatible with both COBRA 2.0 and COBRA 3.0. For COBRA 2.0, sparseLP and fastFVA codes are available in the additional folders.
- COBRA Toolbox
- IBM CPLEX solver; CPLEX is available free for academics from IBM
- Initiative for Biological Systems Engineering
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI)
