MFA input data processing

Metabolic flux analysis prerequisites

In order to run a metabolic flux analysis (MFA), we need the information that is listed below. Except for atom mapping, all the other inputs can be prepared automatically using BFAIR.

  • Metabolic model info - INCA.parse_cobra_model

  • Atom mapping info - not automatically available yet

  • Experimental data - Obtained from SmartPeak, parser will be provided

  • Tracer info - parser will be provided

  • Flux info - Output of the exometabolomics module, link will be provided

Here we aim to describe how you should prepare your data.

Metabolic model

The information about the underlying metabolic model can be extracted from a COBRA model. This will be the basis of you MFA. The metabolic model can be provided as a .json or a .sbml file.

parse_cobra_model(model_file_name, model_id, …)

Parses reaction- and metabolite information out of a cobra model saved as a .json or .sbml file and makes it compatible with the BFAIR.INCA tools

Standard input parsers

Parsers for standard input formats are provided.

data_import_parsers

INCA reaction input parser.