opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
125 stars 26 forks source link

Calculation of Metabolic Coverage should ignore pseudo-reactions #630

Open ChristianLieven opened 5 years ago

ChristianLieven commented 5 years ago

Problem description

Exchange and other pseudo-reactions are counted in the calculation of metabolic coverage which skews this value.

This needs to be fixed to allow meaningful comparisons using this value.

In addition, we should definitely cite the paper on the report. We already cite it in the source code, but not in the description of the test.