### Abstract

We present FluxDirect, a novel computational framework
for metabolic flux estimation from incomplete isotopomer
data. In FluxDirect isotopomer measurements are first
propagated in the metabolic network to obtain new
constraints to the isotopomer distributions of
metabolites in the network. The efficient propagation is
facilitated by a fragment flow analysis of a metabolic
network [1]. The method can utilize any measurement
information produced by common (tandem) MS- and
NMR-techniques [3].
After the propagation step the basic linear
stoichiometric equation system bounding the fluxes is
augmented with linear measurement constraints derived
from the propagated isotopomer information. If the rank
of the augmented linear equation system is full, the
fluxes can be easily solved. If the rank of an equation
system is less than full we can output upper and lower
bounds for the fluxes. The general stability of an
augmented equation system can be investigated by
computing the condition number of the system. Unlike in
most existing methods for flux estimation, techniques of
nonlinear optimization are not required. Thus FluxDirect
escapes the danger of convergence to local optima.
Fragment flow analysis techniques introduced for
efficient propagation of isotopomer measurement data also
facilitate the experimental planning of isotopomer tracer
experiments. As the development of measurement techniques
for internal metabolites can be tedious, it is worthwhile
to look for a small set of metabolites giving adequate
flux information. We have shown that such small sets can
be found for FluxDirect by applying computational set
cover methods [2]. The flux estimation framework is
empirically tested with a model of central carbon
metabolism of S. cerevisiae.

Original language | English |
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Title of host publication | International Specialised Symposium on Yeasts ISSY25 |

Subtitle of host publication | Systems Biology of Yeasts - from Models to Applications |

Place of Publication | Espoo |

Publisher | VTT Technical Research Centre of Finland |

Pages | 117 |

ISBN (Electronic) | 951-38-6308-5 |

ISBN (Print) | 951-38-6307-7 |

Publication status | Published - 2006 |

Event | International Specialised Symposium on Yeasts, ISSY 25 - Espoo, Finland Duration: 18 Jun 2006 → 21 Jun 2006 |

### Publication series

Series | VTT Symposium |
---|---|

Number | 242 |

ISSN | 0357-9387 |

### Conference

Conference | International Specialised Symposium on Yeasts, ISSY 25 |
---|---|

Abbreviated title | ISSY 25 |

Country | Finland |

City | Espoo |

Period | 18/06/06 → 21/06/06 |

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## Cite this

Rantanen, A., Rousu, J., Pitkänen, E., Maaheimo, H., Mielikäinen, T., & Ukkonen, E. (2006). A framework for direct metabolic flux estimation. In

*International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications*(pp. 117). [P62] VTT Technical Research Centre of Finland. VTT Symposium, No. 242 http://www.vtt.fi/inf/pdf/symposiums/2006/S242.pdf