PMC

System flow of the BioMet Toolbox. Central panel (gray color) represents required input files [GSMM from our repository, Metabolic Network file with interaction, Association files: Node-ORF and file with P-values (more detailed descriptions of input files can be found in the text)]. Alternative input files (dashed gray color) are allowed (Annotation for know interaction can replace Metabolic Network file with interaction and Node-ORF Association files; Transcriptome data analysis instead of file with P-values, and custom GSMM instead of models provided in the repository). Three applications with available sub-options (color-coded as corresponding application) are represented in rectangular boxes (Analysis methods) and example of the results (output files) in oval boxes: Reporter Features (orange), Reporter Subnetworks (blue) and BioOpt (green).