The purpose of this web page is to document the work I did during a research internship at the KDBIO group at INESC-ID in Lisbon in the summer semester of 2007.

The general research area I was engaged in, was the mathematical modeling of biochemical systems from time series data of the involved metabolites. The bottleneck in this kind of analysis is the estimation of the parameter values of the model. My task was to combine two newly published methods for parameter estimation under the S-systems modeling framework and evaluate their performance:

• Autosmooth (Vilela M, Borges C, Vasconcelos AT, Santos H, Voit E, Almeida JS: Automated smoother for numerical decoupling of dynamic models. in press) was used for smoothing of the noisy time series data and for estimation of the slopes.
  
  
• Alternating regression (Chou I, Martens H, Voit EO: Parameter estimation in biochemical systems models with alternating regression. Theor Biol Med Model 2006, 3:25) was used for the actual parameter estimation.

A description of my results can be found in the final technical report (INESC-ID Tec. Rep. 29/2008, Jan 2008).

This file contains the Matlab code I wrote.

The poster I presented at the German Conference of Bioinformatics can be downloaded here: Abstract Poster.