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Updated: Apr 27, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
FindPath: a Matlab solution for in silico design of synthetic metabolic pathways
Gilles Vieira1, Marc Carnicer1, Jean-Charles Portais1
1Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France and CNRS, UMR5504, F-31400 Toulouse, France Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France and CNRS, UMR5504, F-31400 Toulouse, France Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France and CNRS, UMR5504, F-31400 Toulouse, France.
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:
heux@insa-toulouse.fr
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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