ModelMage: A Tool for Automatic Model Generation, Selection and Management

Max Flöttmann[1] (
Jörg Schaber[1] (
Stephan Hoops[2] (
Edda Klipp[1] (
Pedro Mendes[2,3] (

[1] Max-Planck-Institute for Molecular Genetics, Ihnestr 63-73, 14195 Berlin, Germany
[2] Virginia Bioinformatics Institute - 0477, Virginia Tech, Bioinformatics Facility I, Blacksburg, Va 24061, USA
[3] The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom


Mathematical modeling of biological systems usually involves implementing, simulating, and discriminating several candidate models that represent alternative hypotheses. Generating and managing these candidate models is a tedious and difficult task and can easily lead to errors. ModelMage is a tool that facilitates management of candidate models. It is designed for the easy and rapid development, generation, simulation, and discrimination of candidate models. The main idea of the program is to automatically create a defined set of model alternatives from a single master model. The user provides only one SBML-model and a set of directives from which the candidate models are created by leaving out species, modifiers or reactions. After generating models the software can automatically fit all these models to the data and provides a ranking for model selection, in case data is available. In contrast to other model generation programs, ModelMage aims at generating only a limited set of models that the user can precisely define. ModelMage uses COPASI as a simulation and optimization engine. Thus, all simulation and optimization features of COPASI are readily incorporated. ModelMage can be downloaded from and is distributed as free software.

[ Full-text PDF | Table of Contents ]

Japanese Society for Bioinformatics