feat: eciYali model in caffeine

[BenjaSanchez]

Start from the BiGG compliant GEM uploaded to caffeine, available here.

• [x] Adapt pipeline in ecModels to receive that model.
• [x] Ensure model is functional (can grow on glucose minimal media)
• [x] Use this notebook to ensure a cobrapy-compliant ecModel.
• [x] Check if model works as intended in caffeine with a basic simulation.
• [x] Make model public in caffeine(staging).
• [x] Send update to IB for testing with proteomics.

[BenjaSanchez]

Update: created the new eciYali with BiGG ids here.

Dependencies:

• iYali: Latest version of the model available in caffeine (here).
• GECKO: 1.3.5 (switching to 2.0.0 would require adapting all scripts, will do it later).
• COBRA: 2.1.0 (brought in saveECmodel.m from GECKO 2.0.0 to keep compatibility with this release, with fix in this commit).
• RAVEN: 2.4.0 (Which has https://github.com/SysBioChalmers/RAVEN/pull/295 to be able to edit gene ids). Opened https://github.com/BenjaSanchez/to-dos/issues/86 to fix the compartment issue when going from COBRA to RAVEN and back.

ecModel modifications:

• Upper bounds saved as +1000 for functional model -> Opened https://github.com/SysBioChalmers/GECKO/issues/102 to address it.
• Model saved in minimal media conditions for direct simulation in caffeine.
• Genes have underscore in their id (e.g. YALI0_A08668g), for increased match rate in caffeine (but the pipeline runs without underscores, as GECKO works best that way).
• Whitespaces removed from introduced pseudo-reactions

[BenjaSanchez]

Update: downloaded the model here and made it caffeine-compliant with this notebook. The model is now available in caffeine (staging).

• Yarrowia Medium id = 84
• eciYali id = 147