binfalse/gemtractor repository overview

⁠GEMtractor

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

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/>.