Improvement of the extension module

[cb-Hades]

Tracker for improvements for the extension module

Current abilities of the module

1. Identify the missing genes between draft and gene list
2. map gene information from NCBI -> KEGG -> BiGG
3. add reactions to the model using a) MetaNetX or b) KEGG
   • check if reaction in model based on BiGG and KEGG annotations
     1. if so, only add new gene to gpr of reaction(s)
     2. if not, create new reaction
        1. add via MetaNetX
        2. add via KEGG

Current working areas:

• revamping of this module after finishing the gap fill class in refineGEMs

  • a lot of the stuff below will probably be somewhat solved when doing the above

• option for choosing the namespace used in the model

  • added namespace options:
    • BiGG
    • Name
    • MetaNetX
    • ...

• deal with the compartments

  • currently: just use 'c'
  • identify exchange reactions correctly
  • identify compartment from e.g. a database

• improve runtime

  • mapping to KEGG very slow
  • other ideas?