# 17.1.1.2.1.11. cobra.flux_analysis.room¶

Provide regulatory on/off minimization (ROOM).

## 17.1.1.2.1.11.1. Module Contents¶

### 17.1.1.2.1.11.1.1. Functions¶

 room(model, solution=None, linear=False, delta=0.03, epsilon=0.001) Compute a single solution based on regulatory on/off minimization (ROOM). add_room(model, solution=None, linear=False, delta=0.03, epsilon=0.001) Add constraints and objective for ROOM.
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

add_room()

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

• 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.

pfba()