Troppo (Tissue-specific RecOnstruction and Phenotype Prediction using Omics data) is a Python package containing methods for tissue specific reconstruction to use with constraint-based models. The main purpose of this package is to provide an open-source framework which is both modular and flexible to be integrated with other packages, such as cobrapy, framed or cameo whose already provide generic data structures to interpret metabolic models.
A (MI)LP solver is required to use most of the present methods. The current methods support optlang, which in turn allow the use of solvers like CPLEX or Gurobi.
- The current methods implemented are:
- FastCORE
- CORDA
- GIMME
- (t)INIT
- iMAT
- Methods to be implemented later:
- MBA
- mCADRE
- PRIME
pip install troppo
pip install git+https://github.com/BioSystemsUM/troppo.git
Developed at the Centre of Biological Engineering, University of Minho
Released under the GNU Public License (version 3.0).