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Master thesis

Linear programming for metabolic network completion

Kerian Thuillier 1, 2
1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
2 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : Metabolic networks are a helpful tool to represent cells. They contain information about every reaction occurring inside an organism. However, metabolic networks of poorly studied species are incomplete. It is possible to complete these networks with knowledge of other well-known species. In this paper, we present a new linear programming approach for the problem of topological activation in metabolic networks based on flows and MTZ. We developed our tool Flutampl with AMPL. Flutampl completes draft networks thanks to the hybrid completion method as formulated by C. Frioux et al [4]. It returns optimal solutions for the hybrid completion directly from sbml files, data format used for modelling metabolic networks.
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https://hal.inria.fr/hal-02408003
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Submitted on : Thursday, December 12, 2019 - 5:14:48 PM
Last modification on : Sunday, July 12, 2020 - 3:13:51 AM
Long-term archiving on: : Friday, March 13, 2020 - 11:14:45 PM

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  • HAL Id : hal-02408003, version 1

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Kerian Thuillier. Linear programming for metabolic network completion. Bioinformatics [q-bio.QM]. 2019. ⟨hal-02408003⟩

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