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Bioprocess and Biosystems Engineering

, Volume 31, Issue 3, pp 227–239 | Cite as

Visual exploration of isotope labeling networks in 3D

  • P. Droste
  • M. Weitzel
  • W. Wiechert
Original Paper

Abstract

Isotope labeling networks (ILNs) are graphs explaining the flow of isotope labeled molecules in a metabolic network. Moreover, they are the structural backbone of metabolic flux analysis (MFA) by isotopic tracers which has been established as a standard experimental tool in fluxomics. To configure an isotope labeling experiment (ILE) for MFA, the structure of the corresponding ILN must be understood to a certain extent even by a practitioner. Graph algorithms help to analyze the network structure but produce rather abstract results. Here, the major obstruction is the high dimension of these networks and the large number of network components which, consequently, are hard to figure out manually. At the interface between theory and experiment, the three-dimensional interactive visualization tool CumoVis has been developed for exploring the network structure in a step by step manner. Navigation and orientation within ILNs are supported by exploiting the natural 3D structure of an underlying metabolite network with stacked labeled particles on top of each metabolite node. Network exploration is facilitated by rotating, zooming, forward and backward path tracing and, most important, network component reduction. All features of CumoVis are explained with an educational example and a realistic network describing carbon flow in the citric acid cycle.

Keywords

Metabolic flux analysis Isotope labeling networks Network visualization Cumomer networks Interactive network analysis 

Abbreviations

ILN

Isotope labeling network

MFA

Metabolic flux analysis

ILE

Isotope labeling experiment

CumoVis

Cumomer network visualization tool

M

Metabolite symbols

M#101

Isotopomer notation (M, metabolite symbol; 0, unlabeled; 1, labeled)

M#1X1

Cumomer notation (M, metabolite symbol; X, don’t care; 1, labeled)

M#abc

Enumeration of atom positions

v: A→B

Reaction notation

3D

Three dimensional

WL

Weight level

CC

Connected component

SCC

Strongly connected component

DAG

Directed acyclic graph

AcCoA

Acetyl-CoA

AcN

cis-Aconitate

AKG

Alpha-Ketoglutarate

Cit

Citrate

CO2

Carbon dioxide

Fum

Fumarate

GlyOx

Glyoxylate

ICit

Isocitrate

Mal

Malate

OAA

Oxaloacetate

Pyr

Pyruvate

Succ

Succinate

SucCoA

Succinyl-CoA

Notes

Acknowledgments

The project was partly funded by the German Ministry BMBF (SysMAP Project), and the German Research Foundation (DFG, project grant WI 1705/13).

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  1. 1.Simulation Group, Institute of Systems Engineering, Faculty 11/12University of SiegenSiegenGermany

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