dnngior 0.0.4

build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling

A novel way to gapfill metabolic models

Installation instructions

To run the dnngior gapfiller, the Gurobi solver is required (mandatory).

pip install gurobipy

To use gurobi, you need a license. If you are an acedemic, you may get a license for free.

Once you have successfully installed gurobi, you are ready to install the dnngior gapfiller.

pip install dnngior

Optionally, you may need to also get Tensorflow (or through conda) in case you would like to use the NN_Trainer.

How to use

You may find examples of gapfilling a genome scale reconstruction (GEM) with dnngior with a complete or a defined medium in this example notebook.

License

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