  Metabolic flux analysis using 13C labeled substrates is an important tool for
metabolic engineering. Although it has now been evolving for more than ten
years, metabolic flux analysis has still not reached the limits of its
application. First and foremost, there is only one reference software for the
analysis and identification of metabolic fluxes using stationnary carbon
labeling experiments, which is closed-source. Moreover, this software lacks
connections with the new standards of systems biology community, for example
the Systems Biology Markup Language, which allows to describe arbitrary large
metabolic networks. The first part of this paper, after recalling all the
mathematics involved in the mathematical problem of flux identification in the
case of multiple experiments (state equations, regularized cost function,
explicit computation of the gradient) concentrates on the problem of specific
automatic generation of scripts (Matlab or Scilab) implementing the numerical
resolution. To this purpose, we will describe the architecture of the software
chain implementing the transformation from the XML file describing the
metaboling network and the carbon transitions to the final collection of
scripts computing, for example, the exact gradient of the regularized
least-squares cost function and the output sensitivities. In the unstationnary
case the adjoint state method is used to speed up computations.
