FindPath: a Matlab solution for in silico design of synthetic metabolic pathways

Gilles Vieira; Marc Carnicer; Jean Charles Portais; Stéphanie Heux

doi:10.1093/bioinformatics/btu422

FindPath: a Matlab solution for in silico design of synthetic metabolic pathways

Gilles Vieira
, Marc Carnicer
, Jean Charles Portais
, Stéphanie Heux

Producció científica: Article en revista indexada › Article › Avaluat per experts

15 Cites (Scopus)

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SUMMARY: Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files.

AVAILABILITY AND IMPLEMENTATION: http://metasys.insa-toulouse.fr/software/findpath/.

CONTACT: [email protected]

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Idioma original	Anglès
Pàgines (de-a)	2986-2988
Nombre de pàgines	3
Revista	Bioinformatics (Oxford, England)
Volum	30
Número	20
DOIs	https://doi.org/10.1093/bioinformatics/btu422
Estat de la publicació	Publicada - 15 d’oct. 2014
Publicat externament	Sí

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abstract = "SUMMARY: Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files.AVAILABILITY AND IMPLEMENTATION: http://metasys.insa-toulouse.fr/software/findpath/.CONTACT: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.",

author = "Gilles Vieira and Marc Carnicer and Portais, \{Jean Charles\} and St{\'e}phanie Heux",

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AU - Vieira, Gilles

AU - Carnicer, Marc

AU - Portais, Jean Charles

AU - Heux, Stéphanie

PY - 2014/10/15

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N2 - SUMMARY: Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files.AVAILABILITY AND IMPLEMENTATION: http://metasys.insa-toulouse.fr/software/findpath/.CONTACT: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.

AB - SUMMARY: Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files.AVAILABILITY AND IMPLEMENTATION: http://metasys.insa-toulouse.fr/software/findpath/.CONTACT: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.

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FindPath: a Matlab solution for in silico design of synthetic metabolic pathways

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