Welcome to the GEMtractor — a platform for trimming and extracting genome-scale metabolic models (GEMs)!

Farming with the GEMtractor goes like this:

1. Select an SBML model: Upload your model or choose a published model from BiGG Models or Biomodels.
2. Trim the model: Optionally delete (currency-)metabolites, reactions, genes, or enzyme complexes if you want to concentrate on a reduced version of the model.
3. Export the model: Optionally extract the enzyme-centric network before downloading the reduced model in different formats for subsequent analyses.

If you get lost during farming just click the small that will appear in the top menu bar. It will guide you through the current page.

There is an API, so you may use the GEMtractor from your software tools. The GEMtractor is free software and also available as a Docker image. Thus, running your own GEMtractor is as easy as calling a single command line — including all the benefits, such as privacy and speed! Read more about the setup at Run your own GEMtractor .

If you dare to harvest your models, click Start from the top panel.

You seem to be using a mobile device? Please be aware, that there may be quite some data shipped through the network. So be careful on metered connections!

GEMtractor was published in GEMtractor: extracting views into genome-scale metabolic models at Oxford Bioinformatics. If you found GEMtractor useful for your analyses, please consider referencing it in your publications.