LMME-DM (Large Metabolic Model Explorer for Disease Maps) is an Add-on for the open-source software VANTED. It facilitates the visual exploration of disease maps by showing their meaningful subsystems and by providing analytic techniques that may be applied successively.
LMME-DM has been developed as part of the COVID-19 Disease Map project. If you're interested, visit our project page.
Attention: If you want to explore large metabolic models in general, check out the original version of LMME, which lives in its own repository.
- 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-DM, 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-DM below.
To install LMME-DM, you need its jar file, which you can either download or build yourself.
You can download the current version of LMME-DM 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-DM. 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-DM has been installed into your Vanted program instance, you can load a disease map 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 file in the appearing file chooser.
After loading the model, navigate to the LMME-DM tab on the right and press the uppermost button Set model. You will immediately see some general information about the disease map, appearing at the top of the tab.
You can now select the disease map 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 on the LMME webpage.
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.
Attention: As this tool version is specifically designed to work with disease maps, not all features described there may work as intended.
You can now insert data to be analysed in the context of the hierarchical disese map. To open the data mapping menu, click the button Node Highlighting at the top of the right tab. You can insert data in plain text in the form nodelabel,doublevalue (one node per line). To map the data, click on one of the buttons below, e.g. Color in Overview to have the data mapped on the node color in the right overview panel.
You can find a version of the COVID-19 disease map as well as a dataset with calculated centrality values on the LMME-DM webpage.
- Check out the VANTED repository and VANTED libraries repository (see also here for more information) as well as the LMME-DM 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-dm.git
- Make sure the lmme-dm 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-DM 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-DM 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.
As part of our teaser image, we used the following:
- COVID-19 image: from cdc on Unsplash under the Unsplash License.
- Monitor image: from clker-free-vector-images on Pixabay under the Pixabay License.
- Font: Open Sans from Steve Matteson on Google Fonts under the Open Font License