Tutorials

Before you start

Pre-analyzed example data can be found in the tutorials folder of the GitHub repository. Before we analyze your own data, you can try to reproduce the results of these examples to get familiar with the workflow of OpenMebius2.

Installation

  1. Go to the GitHub repository and download the repository as a ZIP file by clicking the green Code button and selecting Download ZIP. If you are familiar with Git, you can also clone the repository by using the following command: 
     git clone https://github.com/metabolic-engineering/OpenMebius2.git

download_zip

  1. Unzip the downloaded ZIP file and navigate to the OpenMebius2/installer folder. This folder contains the installer for OpenMebius2. Click the installer file (depending on your operating system) to install OpenMebius2 on your computer (administrative privileges may be required).
  2. Start OpenMebius2 program by double-clicking the OpenMebius2 icon on your desktop or in your applications folder.

Opening example projects

  1. Start OpenMebius2 program.
  2. Click the Browse button in the Project field on the top left of the window.

browse_project

  1. Navigate to the tutorials/ecoli folder in the unzipped OpenMebius2 directory. Click the Select Folder button to open the example project.

open_project

  1. Click the Load button to load the example project.

load_project

  1. The example project is now loaded, and you can select Result tab to view the analysis results.

result_tab

  1. By clicking the desired row in the result table, you can view fluxes and upper/lower bounds calculated by flux variability analysis (FVA).

fva_result flux_map

  1. Choose the Details item in the drop-down menu on the top of the result table to view simulated and measured mass distribution vectors (MDVs) for each metabolite.

detailed_result

  1. You can compare fluxes of different results by selecting multiple rows in the result table while holding the Ctrl key (or Cmd key on Mac) and clicking the Comparison button above the table.

compare_fluxes

  1. You can also visualize flux maps on the right side of the window.

flux_map_visualization

Create a new project

  1. Start OpenMebius2 program.
  2. Click the Browse button in the Template Model field on the bottom left of the window.

browse_template_model

  1. Navigate to the model folder in the unzipped OpenMebius2 directory. Click the Select Folder button to select the template model.

select_template_model

  1. Click the Load button to load the template model.

load_template_model

  1. After loading the template model, click the Create project from template model button to create a new project.

new_project_button

  1. In the dialog that appears, enter the project name. Then click the OK button.

create_new_project

  1. Select the folder where you want to save the new project and click the Select Folder button.

select_new_project_folder

  1. Wait a moment while the new project is being created. The indicator icon on the model will turn green when the process is complete.

creating_new_project

  1. The new project is now created and loaded. You can start customizing the model, adding experimental data, and performing analysis.

new_project_loaded

Impoting template data

13C-metabolic flux analysis (13C-MFA)

Instationary-MFA (INST-MFA)

Evaluation of confidence intervals

Grid search method

Monte-Carlo method

Label pattern optimization

Label suggestion

results matching ""

    No results matching ""