OpenMebius2

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13C-metabolic flux analysis (13C-MFA) is a technique that determine an intracellular metabolic flux distribution by using tracer information. OpenMebius was developed in 2014 as a integrated platform that can perform 13C-MFA by Mr. Kajihata when he was a PhD student and it was publishd to [BioMed Research International][1] This software was able to calculate instationary metabolic flux analysis via command line. Here, we have enhanced this software to enable analysis, visualization, and data processing related to to 13C-MFA though a graphical user interface (GUI).

Installation

To get started with OpenMebius2, please download the latest release from the Releases page.

Windows Installation

1. Download the installer from the releases page.
2. Run openmebius2-vx.x.x-windows-x86-64.exe and follow the installation instructions (administrator privileges may be required).
3. After installation, launch OpenMebius2 from the Start Menu or desktop shortcut.

MacOS Installation

1. Download the DMG file from the releases page.
2. Open the openmebius2-vx.x.x-macos-x86-64.dmg file and drag the OpenMebius2 application to your Applications folder.
3. Launch OpenMebius2 from the Applications folder.

Linux Installation

1. Download the installer from the releases page.
2. Make the installer executable by running the following command in the terminal:

   chmod +x openmebius2-v2.0.0-linux-x86_64.install

3. Run the installer with the following command:

   bash ./openmebius2-v2.0.0-linux-x86_64.install

Quick Start Guide

For detailed instructions on how to use OpenMebius2, please refer to the Online documentation available in the documentation section. Here, you will find step-by-step guides on how to reproduce the figures presented in the published paper.

1. Open OpenMebius2.
2. Click Browse button and select the sample project directory article_fig1 located in the tutorial directory.

3. Click Load button to load the project.

1. In this project, the required information such as specific growth rate, extracellular fluxes, and mass distribution vectors (MDVs) are already set. If you only want to see the results, click the Result tab to view the flux distribution results.

2. To visualize the tracer suggestion with low cost experiments, right-click on the result item and select View Suggestion.

6. Selected items will be shown in the plot area.

7. If you want to perform whole analysis from the beginning, go to the Run tab and click the Auto button to make a batch row.
8. Select the created row and click the config button to open the configuration window.

How to cite

If you use OpenMebius2 in your research, please cite the following paper:

1. Kajihata, S., Furusawa, C., Matsuda, F. & Shimizu, H. OpenMebius: An Open Source Software for Isotopically Nonstationary 13 C-Based Metabolic Flux Analysis. BioMed Research International 2014, 1–10 (2014).