IsoDesign: A software for optimizing the design of  13 C‐metabolic flux analysis experiments | Zendy

Millard Pierre | Zendy; Sokol Serguei | Zendy; Letisse Fabien | Zendy; Portais JeanCharles | Zendy

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IsoDesign: A software for optimizing the design of 13 C‐metabolic flux analysis experiments

Author(s) -

Millard Pierre,

Sokol Serguei,

Letisse Fabien,

Portais JeanCharles

Publication year - 2014

Publication title -

biotechnology and bioengineering

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.136

H-Index - 189

eISSN - 1097-0290

pISSN - 0006-3592

DOI - 10.1002/bit.24997

Subject(s) - metabolic flux analysis , workflow , flux (metallurgy) , software , computer science , set (abstract data type) , visualization , field (mathematics) , computational science , biological system , data mining , biochemical engineering , chemistry , engineering , mathematics , programming language , biochemistry , organic chemistry , database , metabolism , biology , pure mathematics

The growing demand for (13) C-metabolic flux analysis ((13) C-MFA) in the field of metabolic engineering and systems biology is driving the need to rationalize expensive and time-consuming (13) C-labeling experiments. Experimental design is a key step in improving both the number of fluxes that can be calculated from a set of isotopic data and the precision of flux values. We present IsoDesign, a software that enables these parameters to be maximized by optimizing the isotopic composition of the label input. It can be applied to (13) C-MFA investigations using a broad panel of analytical tools (MS, MS/MS, (1) H NMR, (13) C NMR, etc.) individually or in combination. It includes a visualization module to intuitively select the optimal label input depending on the biological question to be addressed. Applications of IsoDesign are described, with an example of the entire (13) C-MFA workflow from the experimental design to the flux map including important practical considerations. IsoDesign makes the experimental design of (13) C-MFA experiments more accessible to a wider biological community. IsoDesign is distributed under an open source license at http://metasys.insa-toulouse.fr/software/isodes/

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