15.1.1.2.1.9. cobra.flux_analysis.room

Provide regulatory on/off minimization (ROOM).

15.1.1.2.1.9.1. Module Contents

cobra.flux_analysis.room.room(model, solution=None, linear=False, delta=0.03, epsilon=0.001)[source]

Compute a single solution based on regulatory on/off minimization (ROOM).

Compute a new flux distribution that minimizes the number of active reactions needed to accommodate a previous reference solution. Regulatory on/off minimization (ROOM) is generally used to assess the impact of knock-outs. Thus the typical usage is to provide a wildtype flux distribution as reference and a model in knock-out state.

Parameters:
  • model (cobra.Model) – The model state to compute a ROOM-based solution for.
  • solution (cobra.Solution, optional) – A (wildtype) reference solution.
  • linear (bool, optional) – Whether to use the linear ROOM formulation or not (default False).
  • delta (float, optional) – The relative tolerance range (additive) (default 0.03).
  • epsilon (float, optional) – The absolute tolerance range (multiplicative) (default 0.001).
Returns:

A flux distribution with minimal active reaction changes compared to the reference.
Return type:

cobra.Solution

See also

add_room()
add ROOM constraints and objective
cobra.flux_analysis.room.add_room(model, solution=None, linear=False, delta=0.03, epsilon=0.001)[source]

r Add constraints and objective for ROOM.

This function adds variables and constraints for applying regulatory on/off minimization (ROOM) to the model.

Parameters:
  • model (cobra.Model) – The model to add ROOM constraints and objective to.
  • solution (cobra.Solution, optional) – A previous solution to use as a reference. If no solution is given, one will be computed using pFBA.
  • linear (bool, optional) – Whether to use the linear ROOM formulation or not (default False).
  • delta (float, optional) – The relative tolerance range which is additive in nature (default 0.03).
  • epsilon (float, optional) – The absolute range of tolerance which is multiplicative (default 0.001).

Notes

The formulation used here is the same as stated in the original paper [1]. The mathematical expression is given below:

minimize sum_{i=1}^m y^i s.t. Sv = 0

v_min <= v <= v_max v_j = 0 j ∈ A for 1 <= i <= m v_i - y_i(v_{max,i} - w_i^u) <= w_i^u (1) v_i - y_i(v_{min,i} - w_i^l) <= w_i^l (2) y_i ∈ {0,1} (3) w_i^u = w_i + delta|w_i| + epsilon w_i^l = w_i - delta|w_i| - epsilon

So, for the linear version of the ROOM , constraint (3) is relaxed to 0 <= y_i <= 1.

See also

pfba()
parsimonious FBA

References

[1]Tomer Shlomi, Omer Berkman and Eytan Ruppin, “Regulatory on/off minimization of metabolic flux changes after genetic perturbations”, PNAS 2005 102 (21) 7695-7700; doi:10.1073/pnas.0406346102