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GEMtractor

The GEMtractor a platform for trimming and extracting genome-scale metabolic models (GEMs).

GEMtractor

Using the GEMtractor you can trim (currency-)metabolites, reactions, genes, or enzyme complexes off you GEMs, to for example focus on subnetworks as reported by prior flux balance analyses. From the trimmed model you may then extract the Reaction-centric or Enzyme-centric network, wich can be exported in different graph formats for subsequent analyses.

The GEMtractor comes with support for Docker -- installing an own instance is pretty easy, see Run your own GEMtractor. It also features an API, so you may use the GEMtractor from your software tools. There is plenty of more information at the FAQ and the Python documentation.

If you dare to harvest your models, check it out at GEMtractor.bio.informatik.uni-rostock.de!

License

The GEMtractor is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

The GEMtractor is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.