cobra.flux_analysis.room

cobra.flux_analysis.room#

Provide regulatory on/off minimization (ROOM).

Functions#

room(→ cobra.Solution)

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

add_room(→ None)

Add constraints and objective for ROOM.

Module Contents#

cobra.flux_analysis.room.room(model: cobra.Model, solution: cobra.Solution | None = None, linear: bool = False, delta: float = 0.03, epsilon: float = 0.001) → cobra.Solution[source]#

Compute a 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 wild-type 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 (wild-type) reference solution (default None).

  • 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: cobra.Model, solution: cobra.Solution | None = None, linear: bool = False, delta: float = 0.03, epsilon: float = 0.001) → None[source]#

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 (default None).

  • 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 le v le v_max v_j = 0 j in A for 1 le i le m v_i - y_i(v_{max,i} - w_i^u) le w_i^u (1) v_i - y_i(v_{min,i} - w_i^l) le w_i^l (2) y_i in {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 le y_i le 1.

See also

pfba

parsimonious FBA

References