PMID- 18074156
OWN - NLM
STAT- MEDLINE
DCOM- 20080709
LR  - 20080320
IS  - 1615-7591 (Print)
IS  - 1615-7591 (Linking)
VI  - 31
IP  - 3
DP  - 2008 Apr
TI  - Visual exploration of isotope labeling networks in 3D.
PG  - 227-39
AB  - 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.
FAU - Droste, P
AU  - Droste P
AD  - Simulation Group, Institute of Systems Engineering, Faculty 11/12, University of 
      Siegen, 57068 Siegen, Germany. droste@simtec.mb.uni-siegen.de
FAU - Weitzel, M
AU  - Weitzel M
FAU - Wiechert, W
AU  - Wiechert W
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20071212
PL  - Germany
TA  - Bioprocess Biosyst Eng
JT  - Bioprocess and biosystems engineering
JID - 101088505
RN  - 0 (Carbon Isotopes)
RN  - 7440-44-0 (Carbon)
SB  - IM
MH  - Algorithms
MH  - Biochemistry/methods
MH  - Biotechnology/*methods
MH  - Carbon/chemistry
MH  - Carbon Isotopes/*chemistry
MH  - Citric Acid Cycle
MH  - Computational Biology
MH  - Computer Graphics
MH  - *Isotope Labeling
MH  - Mathematical Computing
MH  - Models, Biological
MH  - Models, Theoretical
EDAT- 2007/12/13 09:00
MHDA- 2008/07/10 09:00
CRDT- 2007/12/13 09:00
PHST- 2007/09/11 00:00 [received]
PHST- 2007/11/20 00:00 [accepted]
PHST- 2007/12/13 09:00 [pubmed]
PHST- 2008/07/10 09:00 [medline]
PHST- 2007/12/13 09:00 [entrez]
AID - 10.1007/s00449-007-0177-1 [doi]
PST - ppublish
SO  - Bioprocess Biosyst Eng. 2008 Apr;31(3):227-39. doi: 10.1007/s00449-007-0177-1. 
      Epub 2007 Dec 12.