Computational environments for modeling biochemical networks

Computational modeling is an integral and crucial part of systems biology. It relies on accessible and user-friendly software to set up models, model management and model analysis. Here, two systems are presented that have been implemented for these needs. The first one, COPASI, has been around since 2004 and is a standalone software suite that encompasses many of the commonly used algorithms and approaches in computational modeling. Amongst others, it allows parameter estimation of model on the basis of experimental data sets with diverse methods. The second software is SYCAMORE which is a web based application designed to allow database driven modeling. Thus, it interacts directly with databases for enzymatic kinetics and with tools to estimate parameters based on protein structural data. Both systems are constantly refined and features added.