Matthias König

Reports are very large (~3.7MB)

3

#### Problem description The current reports are very large (~3.7MB) mainly due to all the embedded javascript. This will create a lot of issues in the future. Basically every code...

Error in Non-Growth Associated Maintenance Reaction

4

#### Problem description When creating the memote report on the attached model I get an error in `Non-Growth Associated Maintenance Reaction` [tiny_example.zip](https://github.com/opencobra/memote/files/3059789/tiny_example.zip) #### Code Sample ```bash memote report snapshot --filename...

#### Problem description `compartments` are an important part of constraint-based models. Correct annotation and description of compartments is important to evaluate the quality of the model and understand the model...

Reaction annotations to biological database should not be counted on exchange and biomass reactions

3

Currently, the memote report expects reaction annotations to biological databases on the exchange reactions and biomass reaction. Exchange reactions are purely mathematical constructs to enable a FBA simulation, but don't...

If no genes are in model the gene annotation tests should be skipped

1

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...

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...

Brenda is now supporting JSON format. This could solve some issues with the substances. See https://www.brenda-enzymes.org/download.php

Parameter changes which affect compartment volumes must update species concentrations/amounts

4

Parameter changes which affect compartment volumes must update the concentrations of the species in the compartments. This is currently not done in AMICI resulting in incorrect initial concentrations/amounts and incorrect...

Pseudogenes in Recon3D

2

There are some pseudogenes in RECON3D which don't belong there and should be removed from the genes and the gene associations: https://vmh.uni.lu/#gene/645740.1 https://vmh.uni.lu/#gene/8781.1 https://vmh.uni.lu/#gene/201288.1 I will use this repository as...

Strange Gene Annotation in Recon3D/genes/0

5

I am not sure the following gene is correct. It looks like a parsing error, i.e. id "0". http://bigg.ucsd.edu/models/Recon3D/genes/0