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integrate RIPTiDe into DEXOM

RIPTiDe references:

https://pmc.ncbi.nlm.nih.gov/articles/PMC7188308/
https://github.com/mjenior/riptide/tree/master
https://pypi.org/project/riptide/

TODO:

In all enumeration functions:

  • add a parameter allowing to choose between imat & riptide
  • add an if-else to switch between the two

In rxn-enum & icut:

  • replace calls to imat with calls to riptide.contextualize
  • extract fluxes & binaries from solution object

In maxdist and diversity-enum:

  • replace create_maxdis_constraint with create_riptide_constraint
  • need 2 constraints: minimize pruning coefficients, maximize sampling coefficients (see github code lines 1024 & 1046, publication subsections "Linear coefficient assignment" and "Flux sampling")
Edited by Maximilian Stingl