modelMaGe is a software application that
- automatically generates SBML or
Copasi candidate models
by removing specified model components from a given master model,
- automatically documents candidate models,
- automatically fits candidate models to data using CopasiSE,
- provides a ranking of candidate models fits based on the AIC.
Features
- Version v1.0beta:
- Read and write SBML or Copasi files.
- Removal of elements in candidate models including reactions, species, modifiers and logical combinations thereof:
- Removal of reactions with check for validity and connectedness of the resulting model.
- Removal of species and automatic rewiring, resulting in a new fully defined and simulatable model.
- Removal of modifiers in reactions, either by just removing the interaction or by removing the modifying species, resulting in a new fully defined and simulatable model.
- Creation of candidate models with alternative kinetics.
- Automatic parameter estimation for candidate models using Copasi.
- Easy discrimination of fitted candidate models using AIC.
Licensing
- modelMaGe is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation; either version 2, or
(at your option) any later version. modelMaGe is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.
See the GNU public license for more details.
Publications
- Schaber J., Flöttmann M., Hoops S., Mendes P., Klipp E. (2009)
ModelMaGe: management, generation, documentation and discrimination of candiate SBML models. submitted.
- Flöttmann M., Schaber J., Hoops S., Klipp E., Mendes P. (2008)
ModelMage: A Tool for Automatic Model Generation, Selection and Management. Genome Informatics 20.
<PubMed>
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Funding
-
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- QUASI Contract number 503230
- CELLCOMPUT Contract number 043310
|
Related Projects
