What does Metaboverse do?

Integrating multi- or single-omic metabolic data upon the metabolic network can be challenging for a variety of reasons. Metaboverse seeks to simplify this task for users by providing a simple, user-friendly interface for layering their data on a dynamic representation of the metabolic network and automatically searching the network for interesting regulatory or other patterns. Additionally, Metaboverse provides several tools to enable the contextualization of metabolic data.

Citing Metaboverse

If you use Metaboverse in your data analysis, please cite as: Berg JA, Zhou Y, Ouyang Y, Cluntun AA, Waller TC, Conway ME, Nowinski SM, Van Ry T, George I, Cox JE, Wang B, Rutter J. Metaboverse enables automated discovery and visualization of diverse metabolic regulatory patterns. Nature Cell Biology. (2023) doi: https://doi.org/10.1038/s41556-023-01117-9

Upcoming features

• To check progress on upcoming releases, please refer to our Project Roadmap.
  
• Have a feature request? Submit one here!

Getting started

Detailed walkthroughs and additional usage information can be found in the documentation.

Video walkthrough

Requirements

• An internet connection for network curation
• The most current version of the Metaboverse app for your operating system
• A Linux/macOS/Windows 64-bit operating system. Should work with an M1/2 mac with Rosetta.
• At least 4 GB RAM and 5 GB of free storage space

Installation

• Download the appropriate Metaboverse app .zip file for your operating system from this location.
• Unzip the downloaded folder
• Open the Metaboverse app
• Please refer to the documentation for more information in using the app.
• If you would like to use an example dataset, this is labeled test_data.zip and can be found within the Metaboverse app folder.

Testing out Metaboverse

With each release archive or Metaboverse, a test_data.zip file is included. Unzip this file and read the README.txt file for more information on this example dataset.

Getting Help

• If you have questions, requests, or bugs to report, please use the Metaboverse issues forum. - Please clearly describe the problem, what you have tried, as well as screenshots of any error information.
  
• Generally, for any errors occurring during network building, a file named metaboverse_session.log will be output to your specified Output folder. If you receive this file, please upload it to your GitHub Issue. This will output a lot of information, but you can try self-diagnosing by seeing if there is anything in the last ~10-15 lines of this file that might hint at the issue. Otherwise, we are happy to help diagnose the problem!
  
• It is also often helpful for us to click on the View menu tab, click Toggle Developer Tools, click the Console tab of the window that opens, and take a screenshot of the output in this panel.

Devs

To compile and distribute a new version of Metaboverse, use the script at resources/build-main.sh.

Feedback

• Have any feedback? Let us know here.
• We also have a discussion forum here.