Figure 2

Example work flow. A demonstration of practical usage of FAME. This example illustrates the addition of an objective function to a model of glycolysis, and the model's subsequent execution. (a) On the "Import existing model" screen, users can load SBML models with or without constraints. In the latter case, constraints information will be added by FAME and can be changed later. By just clicking "Go!" without supplying a model, the demo model described in this paper will be loaded. (b) Six buttons provide access to the various model editing options. Advanced users are able to enter batch commands to edit (and run) the model ("Batch commands" button), but it is also possible to edit in a graphical interface (the other five buttons). In this example, an objective is added by clicking "Reactions", selecting the desired objective reaction, and applying the changes. (c) When the model is ready to run, clicking the "Run!" button will produce the results in both tabular and graphical formats. (d) Results can be exported as tab separated values files for further analysis, or, alternatively, more detailed metabolite-centered results representations can be viewed.