Memote Meta Study Model Collections

In order to perform the memote meta study, we resorted to various collections of genome-scale metabolic reconstructions and models. You can find the models in agora/models.

AGORA

We downloaded version 1.03 of the AGORA human gut microbes (commit 0c22ff15acaf435c11973fe847bd13b4ea6cc423). We only used the available SBML models excluding the ones with additional mucin degradation pathways.

License

Models in the AGORA collection are distributed under the CC BY-NC 2.0 license.

BiGG

We downloaded all available models from the BiGG Models database at the below version. You can find the models in bigg/models.

curl 'http://bigg.ucsd.edu/api/v2/database_version'

{
  "api_version": "v2",
  "bigg_models_version": "1.3.0",
  "last_updated": "2018-02-24 08:16:33.924054"
}

License

Models in the BiGG database are distributed under a special non-commercial license. Please refer to the full license text.

CarveME

We downloaded the EMBL GEMs collection (commit 260d0f133802adbc151de4d7b14fb34722e1d9f4) created with the CarveME tool. You can find the models in carveme/models.

License

Models in the EMBL GEMs collection are distributed under the CC BY 4.0 license.

Ebrahim et al.

We used the SBML level 3 version of the models published in the M Model collection (commit afc891b1fd6eb6662c1bfab0369649d8cb9e7e5e). You can find the models in ebrahim/models.

License

Please refer to the model table in order to see the individual locations where the models have been published and their licensing terms.

OptFlux

We downloaded the SBML models from the OptFlux models collection. You can find the models in optflux/models.

License

The collection itself can be considered public domain CC0. However, individual models should be checked for licensing at their origin of publication.

Path2Models

The Path2Models collection is available via FTP from the BioModels database. We restricted ourselves to the whole genome metabolic models. You can find the models in path/models.

License

All models in BioModels are public domain under the CC0 license.

KBase

We have received a large collection of models via private communication that was created using the KBase: The U.S. Department of Energy Systems Biology Knowledgebase. They are published here for the first time. You can find the models in kbase/models.

License

All models in the KBase collection are public domain under the CC0 license.