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


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.


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



Isotope labeling network


Metabolic flux analysis


Isotope labeling experiment


Cumomer network visualization tool


Metabolite symbols


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


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


Enumeration of atom positions

v: A→B

Reaction notation


Three dimensional


Weight level


Connected component


Strongly connected component


Directed acyclic graph










Carbon dioxide



















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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