Utility that compares two models and makes a recall matrix (for genes and reactions)

[hgscott]

The Palsson group has called for a framework to better document content removal. They use matrices called the recall-reaction matrix (rR matrix) and recall-gene (rG matrix) which save the information of reactions and genes removed from a model.

The rR matrix is structured similarly to the stoichiometric matrix, with rows representing each metabolite’s mass
balance and columns representing each reaction’s stoichiometry.

The rG matrix has rows representing the genes, and columns representing the reactions, and is filled with binary entries (with ‘‘1’’ representing exclusion, and ‘‘0’’ signifying no action).

Each entry of the rR and rG matrices should be accompanied by a confidence score, a reference, and ideally a note, justifying the reason for exclusion.

Read more: Seif, Yara, and Bernhard Ørn Palsson. 2021. “Path to Improving the Life Cycle and Quality of Genome-Scale Models of Metabolism.” Cell Systems 12 (9): 842–59.
Recall matrices specifically discussed