v2.2.2

Main improvements in this release:

• feature:

  • new function setMetExchange allows users to set the exchange flux bounds for a given list of metabolites. This should be helpful for specifying e.g., media conditions, or other nutrient uptake/export fluxes (PR #222)
  • setParam can set upper and lower bounds with a defined variance in percentage: setting this value to 5 results in the lower bound being set at 97.5% of the provided value, and the upper bound at 102.5%. This is inverted for negative bounds. (PR #225)
  • addTransport now allows adding multiple rxns and provides the list of added rxn IDs as optional output (PR #226)
  • enable illegal character removal of grRules in exportModel (PR #226)
  • allow multiple compartments either in rows or columns in addMets (PR #226)

• fix:

  • getRxnsFromKEGG: increased the number for preallocated reactions from 11k to 15k as KEGG now includes reactions (PR #229)
  • getKEGGModelForOrganism: fixed several small typos (PR #229)
  • slightly decrease tolerance when using gurobi solver, particularly when solving MILP, because fillGaps does not function well with less strict tolerance (PR #226)
  • refine error message in addRxnsGenesMets (PR #226)
  • fix getModelFromHomology bugs: keeping rxns without homologous genes while using multiple template models, and partial matches of gene ids when updating grRules: YAL001W is not YAL001W-A (PR #226)
  • fix fillGaps bug to keep all genes from template models, not only the ones annotated to gap-filling reactions (PR #226)

• chore:

  • detach HMR2 (Human Metabolic Reactions 2), which is upgraded to Human-GEM and distributed through its own repo. No functions mentioned HMR2, removal of binary is sufficient (PR #227)