How can PhenoMeNal help with your research?

When to use PhenoMeNal

You can use PhenoMeNal:

  • To analyse your metabolomics data using tools from the PhenoMeNal App Library within the Galaxy workflow environment
  • To enable scalable and reproducible research

The PhenoMeNal App Library is a catalogue of all the tools that you can expect to find in PhenoMeNal. In contrast to some of the app stores that you might be familiar with, you don’t need to do anything to use a particular tool in PhenoMeNal. The tools are automatically available. 

 PhenoMeNal and reproducible research. Each release of PhenoMeNal is associated with defined versions of the underlying tools. This means that your results are comparable as long as you use the same PhenoMeNal release each time. Additionally, the use of Galaxy workflows allows parameters and settings to be easily saved and reproducibly applied.

When not to use PhenoMeNal 

PhenoMeNal cannot be used to access cloud services for purposes other than metabolomics data analysis. For this, you need to contact the cloud providers for further information.


  • When using the free, PhenoMeNal-provided cloud, you can only upload a few gigabytes of data. You can upload more data by using PhenoMeNal in combination with a commercial cloud provider (e.g Amazon) for which you will need to buy credit, or with your institution’s OpenStack installation (a private cloud provider)
  • If an app is not in the App Library, then you won’t be able to use it as part of a Galaxy workflow in PhenoMeNal. With some joint effort, we can make new tools available and we provide extensive documentation for external developers to migrate new tools to the PhenoMeNal architecture
  • Non-standard data formats might require some additional data transformation steps before they can be uploaded in PhenoMeNal