memote
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opencobra
memote – the genome-scale metabolic model test suite
#### 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...
When creating a model report for an SBML model with no genes the report incorrectly reports ` Presence of Gene Annotation 0%` The gene annotation section should be skipped in...
#### Problem description > With the memote API it would be quite simple to integrate memote into a pipeline that automatically addresses erroneous test results. There is a plethora of...
An important point for model quality is to be able to check a minimal model provenance, i.e., - who created the model - when was the model created Otherwise it...
#### Problem description Namespaces/ Identifiers may change over time/ become deprecated! Warn the user for this possibility => False positives! > FYI, here is an example of a KEGG ID...
Starting with pandas 0.24, it is a `ValueError` for the index and a column to have the same name as it is ambiguous. We need to fix our experimental data...
The function `find_reactions_with_identical_genes` currently does not take into account that the identifiers for two genes might be different. In a future far, far away we might even extend this to...
#### Problem description The title says it all: It would be nice if memote could recognize a reaction annotated with SBO:0000630 as the NGAM - reaction. http://www.ebi.ac.uk/sbo/main/display?sboId=SBO:0000630 System Information ==================...
#### Problem Description Many support functions seem to lack clear error descriptions. This ought to be improved before we include errors on the report.
#### Problem description Currently the function `biomass.gam_in_model` only returns a Boolean. It should return the actual GAM value to be even more useful, users then don't have to look it...