@draeger draeger released this Mar 4, 2016 · 123 commits to master since this release

Assets 5

This release includes ModelFix:

  • If raw files lack an objective function, ModelPolisher can now automatically declare the biomass reaction to the flux objective. The coefficient defaults to 1.0, but can be influenced via a new command-line argument.
  • In cases where no biomass reaction exists, i.e., no reaction whose id matches the pattern for biomass reactions, a new command-line argument can be used to specify one or multiple target reactions. This can be used in combination with the command-line argument for coefficients. ModelPolisher displays a log message in the category SEVERE if it is not possible to find a suitable target reaction. Users are then advised to manually determine appropriate reaction(s).
  • Missing required group kind attributes are added in.

Further improvements:

  • For now, we set the units of compartments to dimensionless. This might change in the future.
  • New MIRIAM resources have been added.
  • Smaller bug fixes.

To find out more about all command-line arguments, launch with -? or --help. In particular, the two new command-line arguments are:

  • --flux-coefficients={1, 2, 3} (here with sample values 1, 2, 3 separated by commas; spaces are optional)
  • --flux-objectives={R_example1:R_example2:R_example3} (here with three example reaction identifiers separated by colon).