LMME

LMME (Large Metabolic Model Explorer) is an open-source add-on for the software VANTED. It facilitates the exploration of large metabolic models based on decompositions of the large underlying network into meaningful subsystems.

LMME offers interactive features to hierarchically explore these and provides analytic techniques that may be applied successively. In addition to the available decomposition algorithms, we offer an API that allows for the rapid implementation of custom algorithms. Its functionality is complemented by the possibility to use VANTEDs core features during any stage of exploration.

Example of large metabolic model viewed with LMME in Vanted.

Availability & License

See the Getting Started section for instructions on download and installation of LMME.

LMME source code is also available from our GitHub repository.

LMME 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 3 of the License, or (at your option) any later version.

This program 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 General Public License for more details.

API Documentation

The code itself is documented using the Javadoc standard. You also find the generated HTML files in our repository.

Contact

If you have any questions, feedback, bug reports or feature requests, please do not hesitate to contact us via E-Mail.

Citation

If you use LMME in or for a scientific publication, please cite our latest publication:

Michael Aichem, Tobias Czauderna, Yan Zhu, Jinxin Zhao, Matthias Klapperstück, Karsten Klein, Jian Li, Falk Schreiber. Visual Exploration of Large Metabolic Models. Bioinformatics, Volume 37, Issue 23, 4460–4468, 2021.

Copyright

© Chair for Life Science Informatics, University of Konstanz 2020