fix: stoichiometric consistency

[sulheim]

Description of the issue:

According to memote report, stoichiometric concistency is one of the lowest scores of the model, and thus one obvious task for further improvement. This inconcistency is probably caused by metabolites lacking chemical formula.

The memote output:

Stoichiometric inconsistency violates universal constraints: 1. Molecular masses are always positive, and 2. On each side of a reaction the mass is conserved. A single incorrectly defined reaction can lead to stoichiometric inconsistency in the model, and consequently to unconserved metabolites. Similar to insufficient constraints, this may give rise to cycles which either produce mass from nothing or consume mass from the model. Implementation: This test first uses an implementation of the algorithm presented in section 3.1 by Gevorgyan, A., M. G Poolman, and D. A Fell. "Detection of Stoichiometric Inconsistencies in Biomolecular Models." Bioinformatics 24, no. 19 (2008): 2245. doi: 10.1093/bioinformatics/btn425 Should the model be inconsistent, then the list of unconserved metabolites is computed using the algorithm described in section 3.2 of the same publication. This model contains 1288 (62.13%) unconserved metabolites.

Expected feature/value/output:

Improved model concistency with fewer unconserved metabolites

Reproducing these results:

Run memote report snapshot to recreate memote report.

To do:

If specific curations are proposed, generate a list of checkboxes of steps that should be followed to solve this issue:

• Check the cause of these inconcistencies, i.e. find out which metabolites lacking chemical formula or unbaklanced reactions
• Add chemical formula and balance reactions as far as possible. Extract knowledge from DBs either automatically or manually

I hereby confirm that:

• This problem persists in the master branch of the repository
• A similar issue does not already exist
• I've considered asking this first in the Gitter chat room

[sulheim]

This issue connects to #79 and #80