feat: have SLIMEr as option

[edkerk]

Description of the issue:

While there are benefits in having SLIME reactions, they can also be a nuisance. An example is when yeast-GEM is used as template model for generating other models with different acyl-chains. It would be ideal if the SLIME reactions could be transformed into a simpler representation.

Suggested solution:

Alternatives are the permissive and restrictive approaches identified in the SLIMEr paper. To provide an alternative to the flexibility of SLIMEr, it is most suitable to transform the lipid reactions to a restrictive approach:

Here, generic acyl-CoA and fatty acyl acid pseudometabolites are formed from the chain-specific metabolites. These pseudometabolites are then used whenever an acyl-CoA is used or produced in a reaction. With this approach there are no longer chain-specific reactions in lipid metabolism.

A function could search the model for SLIMEr reactions and acyl-chain involving reactions and replace this with the generic version. SLIMEr --> restrictive is relatively straightforward, while the other direction is much more complex, and would largely mimick reapplying SLIMEr's functions. So conversion in 1 direction would suffice.

Alternative ideas are also welcome!

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Done this analysis in the main branch of the repository
• Checked that a similar issue does not exist already
• If needed, asked first in the Gitter chat room about the issue