feat: curate lipid metabolism #28
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- otherwise xylose cannot be used as carbon source
- measured at low amounts (16:1, ~1%) or not at all (PG), so discard from lipid pseudoreactions, but keep biosynthetic reactions (but don't include in expanded lipid reactions with all chain combinations)
- one reaction added to make the pathway functional - for simplification, only model degradation of saturated fatty acids
- redefined acyl-chains for each lipid species, simplified to reduce complexity - redefined SLIMEr and transport reactions to cover only the chain-distributions that are included in the model - manual curation of missing lipid reactions
- run init_rhtoGEM to set location of some folders
- changes are part of reconstruction scripts - and end each file with empty line
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init_rhto-GEM.mscript that prepares MATLAB environment with path to repo's foldersinit_rhto-GEM.mmakeLipidRxnsnow takes list of acyl-chain configurations, instead of defining these by itself from a list of allowed acyl-chains.