swiftcc

Introduction

swiftcc is a tool for finding the largest flux consistent subnetwork of the original metabolic network. swiftccTest provides a benchmark to compare its performance against fastcc. When referencing SWIFTCC, please cite the following:

• Tefagh, M., & Boyd, S. P. (2020). SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks. BMC Bioinformatics, 21(1), 1-14. https://doi.org/10.1186/s12859-020-3440-y

Usage

consistent = swiftcc(S, rev [, solver])

Inputs:

• S: the associated sparse stoichiometric matrix
• rev: the 0-1 vector with 1’s corresponding to the reversible reactions

Optional inputs

• solver: the LP solver to be used; the currently available options are gurobi, linprog, and cplex with the default value of linprog. It fallbacks to the COBRA LP solver interface if another supported solver is called.

Outputs:

• consistent: the 0-1 indicator vector of the reactions constituting the maximum flux consistent metabolic subnetwork

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swiftcore

Introduction

swiftcore is a tool for the context-specific reconstruction of genome-scale metabolic networks. swiftcoreTest and weightedTest provide a benchmark to compare its performance against fastcore. When referencing SWIFTCORE, please cite the following:

• Tefagh, M., & Boyd, S. P. (2020). SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks. BMC bioinformatics, 21(1), 1-14. https://doi.org/10.1186/s12859-020-3440-y

Usage

[reconstruction, reconInd, LP] = swiftcore(model, coreInd, weights, tol, reduction [, solver])

Inputs

1. model: the metabolic network with fields:
   • .S - the associated sparse stoichiometric matrix
   • .lb - lower bounds on reaction rates
   • .ub - upper bounds on reaction rates
   • .rxns - the cell array of reaction abbreviations
   • .mets - the cell array of metabolite abbreviations
2. coreInd: the set of indices corresponding to the core reactions
3. weights: the weight vector for the penalties associated with each reaction
4. tol: zero-tolerance, i.e., the smallest flux value considered nonzero
5. reduction: boolean enabling the metabolic network reduction preprocess

Optional inputs

1. solver: the LP solver to be used; the currently available options are gurobi, linprog, and cplex with the default value of linprog. It fallbacks to the COBRA LP solver interface if another supported solver is called.

Outputs

1. reconstruction: the flux consistent metabolic network reconstructed from the core reactions
2. reconInd: the 0-1 indicator vector of the reactions constituting the reconstruction
3. LP: the number of solved LPs

Requirements

To run the test files in the test folder, one needs to download the FASTCORE package and the Recon3D model and add them to the Matlab path.

License

The swift family is distributed under the GNU General Public License v3.0.