feat: updates related to tutorials

[edkerk]

Main improvements in this PR:

• refactor:
  • tutorials renamed to full_ecModel and light_ecModel
• feat:
  • full_ecModel:
    • more detailed discussions around kcat curation, protein usage etc.
    • plotCrabtree makes plot that demonstrates Crabtree effect in ecModels
    • plotlightVSfull makes plot comparing flux distribution in light and full ecModels
  • light_ecModel:
    • minimum code to make a light ecModel
    • distribute a modified human-GEM 1.15.0 in yml format, together with uniprotConversion.tsv and spontaneousReactions.tsv as derived from files on the Human-GEM GitHub repository, to avoid dependency on having that repo installed. See HumanGEMAdapter with explanation on how the files were obtained.
  • various functions show progress bar that indicates estimated remaining time.
  • reportEnzymeUsage can make report of top-10 used enzymes.
  • loadConventionalGEM can load yaml model files.
  • enzymeUsage reports as positive values.
  • flexibilizeProtConcs also keeps track of the ratio of protein concentration change.
  • fillProtConcs allows for selection of column from protData, if it contains multiple datasets.
  • setKcatForReactions can directly modify a kcat for all associated reactions, useful for manual curation on existing ecModels.
  • getReactionsFromEnzyme gives which reactions are catalyzed by a particular enzyme, from a provided Uniprot ID.
• fix:
  • ecFVA goes through the correct list of mapped reactions and deals with failing simulations.
  • ModelAdapterManager does not save ecModel paths to the MATLAB path, as this would be persistent.

Note: #320 should be merged to develop before this PR. done.

I hereby confirm that I have:

• Selected develop as a target branch (top left drop-down menu)

[github-actions]

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 
[�Warning: Cannot find RAVEN Toolbox in the MATLAB path, or the version is too old (before v2.8.3). Make sure you have installed RAVEN in accordance to the following instructions,
including running 'checkInstallation()': https://github.com/SysBioChalmers/RAVEN/wiki/Installation]� 
[�> In GECKOInstaller.checkRAVENversion (line 77)
In GECKOInstaller.install (line 13)]� 

Note: In the case of multiple test runs, this post will be edited.

[mihai-sysbio]

I was about to get started on the light Human-GEM but it looks like you've had some great progress. I'll happily review this when ready.

[mihai-sysbio]

• distribute a modified human-GEM 1.15.0 in yml format

I want to remember a discussion around providing ec models as part of this repository - that this should either be avoided, or restricted to a couple of exceptions; I couldn't find this written down anywhere though.

Some other notes:

• this PR will resolve part of protocol for ecEcoli, and GECKO light protocol for Human-GEM #314
• my preference is for all subfolders of tutorials/ to start with tutorial_ to strongly underline that these are examples and should not be treated as "production-ready", i.e., not used as-is in research

[edkerk]

• distribute a modified human-GEM 1.15.0 in yml format

I want to remember a discussion around providing ec models as part of this repository - that this should either be avoided, or restricted to a couple of exceptions; I couldn't find this written down anywhere though.

This is to have a functional tutorial, the discussion was whether we should distribute production-ready/curated ecModels, but for that we'll use the ecModels repo.

Some other notes:

• this PR will resolve part of protocol for ecEcoli, and GECKO light protocol for Human-GEM #314
• my preference is for all subfolders of tutorials/ to start with tutorial_ to strongly underline that these are examples and should not be treated as "production-ready", i.e., not used as-is in research

To this aim, I removed yeast-GEM and human-GEM from the tutorial names and folders. IMHO, adding tutorial_ will not have a drastic impact, more important would be to mention the non-production-ready state in the protocol.m and model adapter files. This can probably be strengthened (particularly in model adapter).

[mihai-sysbio]

This will have to a be a partial review since I got stuck at step 14 of the light model. Overall, things are looking great!

Excellent job with the progress bars, really nice way to inform the user while keeping the console clean 🤩

In addition to the specific suggestions, I also have the following very minor comments:

• it would have been simpler with separate smaller PRs, this one feels hard to review
• I had updated RAVEN in the runner to 2.8.2, and will do that again for 2.8.3
• tutorials/full_ecModel/data/ contains a mix of TSV and CSV files; it would have been nicer with consistency, if possible
• DLKcat generated a different output file that the one stored for the light tutorial, should the file be updated?

[mihai-sysbio]

My review of the light model is finished - I'll re-review once the final part of the protocol is finished.
There are some comments for the full version of the tutorial. Once those are resolved I will also have a go through that tutorial.

[ae-tafur]

I think now is ready.

[mihai-sysbio]

I am re-running both tutorials - it will take a while. My expectation is that there will be no major changes, so how about we merge the PR as-is, and transfer all remaining items to a new issue?

[mihai-sysbio]

I believe it has become urgent to merge this PR. For this outstanding addition here, I propose to create a separate issue, thus resulting in a small PR that will be easier to diff and review.

Suggested change

	% TODO: LAST FEW STEPS