Model reduction

Loading a Model

Import the input community metabolic model with the cy3sbml app (see requirements). This can be done by going to File -> Import -> Network from file and then selecting the community metabolic model SBML file. Please be patient when loading models, especially larger models (>10 members). This process can take a couple of minutes, depending on your hardware.

Model Specifications

ScyNet requires some information in the community metabolic model SBML file to be in a specific format. This is required to correctly attribute metabolites to either the community members or the shared exchange compartment. SBML files need to fulfill the following:

1. There must be a shared exchange compartment containing all exchange metabolites and their respective boundary reactions, as well as transfer reactions to the respective member compartments. To detect this compartment there needs to be either
   1. A shared exchange compartment named medium.
   2. A parameter shared_compartment_id which is set to the name of the shared exchange compartment.
2. Each metabolite ID must be prefixed with the identifier of the community member they are associated with followed by an underscore: memberId_metaboliteId
3. Each compartment ID that is part of a community member must be prefixed with the identifier of the community member they are associated with, followed by an underscore: memberId_compartmentId

A metabolic model with this format can be generated from member models using the PyCoMo package.

Creating a Reduced Network

After importing the community metabolic network with cy3sbml, 3 networks should be available: All, Base, and Kinetic. Select either the All or Kinetic network and run the network simplification via Apps -> ScyNet -> Create Simplified Community Network.