Brief. Bioinformatics - Software applications toward quantitative metabolic flux analysis and modeling.

Tópicos

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Resumo

Metabolites and their pathways are central for adaptation and survival. Metabolic modeling elucidates in silico all the possible flux pathways (flux balance analysis, FBA) and predicts the actual fluxes under a given situation, further refinement of these models is possible by including experimental isotopologue data. In this review, we initially introduce the key theoretical concepts and different analysis steps in the modeling process before comparing flux calculation and metabolite analysis programs such as C13, BioOpt, COBRA toolbox, Metatool, efmtool, FiatFlux, ReMatch, VANTED, iMAT and YANA. Their respective strengths and limitations are discussed and compared to alternative software. While data analysis of metabolites, calculation of metabolic fluxes, pathways and their condition-specific changes are all possible, we highlight the considerations that need to be taken into account before deciding on a specific software. Current challenges in the field include the computation of large-scale networks (in elementary mode analysis), regulatory interactions and detailed kinetics, and these are discussed in the light of powerful new approaches.

Resumo Limpo

metabolit pathway central adapt surviv metabol model elucid silico possibl flux pathway flux balanc analysi fba predict actual flux given situat refin model possibl includ experiment isotopologu data review initi introduc key theoret concept differ analysi step model process compar flux calcul metabolit analysi program c bioopt cobra toolbox metatool efmtool fiatflux rematch vant imat yana respect strength limit discuss compar altern softwar data analysi metabolit calcul metabol flux pathway conditionspecif chang possibl highlight consider need taken account decid specif softwar current challeng field includ comput largescal network elementari mode analysi regulatori interact detail kinet discuss light power new approach

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