A few spontaneous reactions that are not marked at spontaneous

[johan-gson]

Description of the issue:

MAR05127: {'NH4+[c] <=> H+[c] + NH3[c]'
MAR08749: {'H+[c] + HCO3-[c] <=> carbonate[c]'
MAR08750: {'H+[m] + HCO3-[m] <=> carbonate[m]'

There is an equilibrium between these.

Expected feature/value/output:

How the reaction/metabolite/gene/simulation result should look (cite literature if needed). PLEASE DELETE THIS LINE.

Current feature/value/output:

How the reaction/metabolite/gene/simulation actually looks in the main branch. PLEASE DELETE THIS LINE.

Reproducing these results:

Please attach any Matlab code used . PLEASE DELETE THIS LINE.

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Done this analysis in the main branch of the repository
• Checked that a similar issue does not exist already

Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE

[mihai-sysbio]

@johan-gson how do you expect these reactions to be marked? The only way I found this to be done in the model is by changing the name of the reaction. Is this what you expect?

[johan-gson]

There is a "spontaneous" field in reactions.tsv. I use that in GeckoLight and now also in tINIT - these reactions should not have any enzymatic cost (I otherwise fill in a standard cost for reactions without GPRs) and should always be left on after running tINIT.

[JonathanRob]

Resolved by #379