LMME (Large Metabolic Model Explorer) is an Add-on for the open-source software VANTED. It facilitates the exploration of large metabolic models by decomposing the large network into meaningful subsystems and by providing analytic techniques that may be applied successively.
- You need a current version of the Java runtime environment (JRE) installed on your machine. You can download the latest version here (for the development of LMME, we used AdoptOpenJDK 11, which also includes a JRE).
- You also need a version of the VANTED software installed on your machine. You can download it here (for the development of LMME, we used Vanted version 2.7.1).
- If you would like to use the SBGN translation feature, you also need the SBGN-ED Add-on for Vanted. You can download it as jar file from the SBGN-ED website and install it in the same way as described for LMME below.
To install LMME, you need its jar file, which you can either download or build yourself.
You can download the current version of LMME here.
Within Eclipse, run the make.xml file as an Ant build. The jar will be created in the root directory.
There are two ways to install LMME. Within Vanted, either use a drag&drop operation (drag the jar file from your systems file manager and drop it inside the Vanted program window) or navigate to Edit > Preferences > Addon Manager > Install / Configure Add-ons > Install Add-on and select the jar file in the appearing file chooser.
As soon as LMME has been installed into your Vanted program instance, you can load a metabolic model for its analysis. As before, you can either do that by using a drag&drop operation (drag an SBML file from your systems file manager and drop it inside the Vanted program window) or navigate to File > Open and select the SBML file in the appearing file chooser. An example model of Pseudomonas Aeruginosa PAO1 can be downloaded on the LMME webpage.
After loading the model, navigate to the LMME tab on the right and press the uppermost button Set model. You will immediately see some general information about the model, appearing at the top of the tab.
You can now select a decomposition method and press the Show Overview Graph button. This computes a decomposition and shows the overview graph on the left side of the application window. For a detailed description of the individual settings, see the Learn section.
As soon as the overview graph has been constructed, you can select some of its nodes and press the Show Selected Subsystems button at the bottom of the tab to have the consolidated subsystem graph shown on the right side of the application window.
If some errors occurred during the steps described above, or if you are interested in the individual settings or additional features that have not been covered above, please have a look at the Learn section on the LMME webpage.
- Check out the VANTED repository and VANTED libraries repository (see also here for more information) as well as the LMME repository and load them into Eclipse (or the IDE of your choice).
git clone https://github.com/LSI-UniKonstanz/vanted.git
git clone https://github.com/LSI-UniKonstanz/vanted-libraries.git
git clone https://github.com/LSI-UniKonstanz/lmme.git
- Make sure the lmme project has its reference to the Vanted project (in Eclipse for example, go to Project > Properties > Java build path > Projects > Add... and add the vanted project there).
- Start coding and finally build the jar as described above.
If you have any questions, feedback, bug reports or feature requests, please do not hesitate to contact us via E-Mail.
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, Pages 4460–4468 (2021).
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.