Getting Started

The following guide helps you to get started quickly with LMME (Large Metabolic Model Explorer).

0. Requirements

  • 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.

1. Download LMME

To install LMME, you need its jar file, which you can either download or build yourself.

Download the jar file

You can download the current version of LMME as jar file here.

Build the jar file yourself

Instead of downloading the jar file, you can also build it yourself from the source code. The code, as well as a description for building it yourself, is available from our Github repository.

Install LMME

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.

2. First steps

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 below.

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.

Example Model: iPAO1

For our publication and for the Learn section we used iPAO1, a GSMM for Pseudomonas Aeruginosa PAO1, that has been developed by Yan Zhu et al. It contains 3,022 metabolites and 4,365 reactions. You can download the model here to test LMME and get started quickly. Please use the following download link: iPAO1.zip.

See the related publication for more information:

Yan Zhu, Tobias Czauderna, Jinxin Zhao, Matthias Klapperstueck, Mohd Hafidz Mahamad Maifiah, Mei-Ling Han, Jing Lu, Björn Sommer, Tony Velkov, Trevor Lithgow, Jiangning Song, Falk Schreiber, Jian Li, Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa, GigaScience, Volume 7, Issue 4, April 2018, giy021, https://doi.org/10.1093/gigascience/giy021