Fig. 2.

Automated search for parameter values. In order to automatically find all measured kinetic rates from online databases, a subroutine was constructed as part of our pipeline (see Additional file 1). Upon registering the databases to be searched and how their identifiers can be converted between each other (Step 1), all the reactions within the parsed genome-scale model are listed (Step 2). Then, the algorithm finds all possible paths relating a modelled reaction with a database entry (Step 3). These data-paths are then exhaustively searched for all measured kinetic rates of a reaction (Step 4)