SparseQFCA.jl

Developed a registered Julia package which quantifies the redundancies in genome-scale metabolic networks and provides local sparse certificates which are both efficiently verifiable and interpretable
Author mtefagh
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1 Star
Updated Last
1 Year Ago
Started In
January 2019

Sparse Quantitative Flux Coupling Analysis

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sparseQFCA is a registered package for the sparse Quantitative Flux Coupling Analysis. Moreover, a Julia implementation of Swift Consistency Checking is also available as a preprocessing subroutine. The example data files S.csv and rev.csv are extracted from the core E. coli model.

Usage

certificates, blocked, fctable = QFCA(S, rev)

Inputs

  • S: the associated sparse stoichiometric matrix
  • rev: the boolean vector with trues corresponding to the reversible reactions

Outputs

  • certificates: the fictitious metabolites for the sparse positive certificates
  • blocked: the boolean vector with trues corresponding to the blocked reactions
  • fctable: the resulting flux coupling matrix

Quick Start

To get started, first run import Pkg; Pkg.add("sparseQFCA") to install the sparseQFCA package, and then see this Jupyter notebook for a demonstration on how to use it.

License

sparseQFCA is distributed under the GNU General Public License v3.0.