cobra.flux_analysis.room
¶
Provide regulatory on/off minimization (ROOM).
Module Contents¶
Functions¶

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

Add constraints and objective for ROOM. 
 cobra.flux_analysis.room.room(model: cobra.Model, solution: Optional[cobra.Solution] = 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 knockouts. Thus, the typical usage is to provide a wildtype flux distribution as reference and a model in knockout state.
 Parameters
model (cobra.Model) – The model state to compute a ROOMbased solution for.
solution (cobra.Solution, optional) – A (wildtype) 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
See also
add_room
add ROOM constraints and objective
 cobra.flux_analysis.room.add_room(model: cobra.Model, solution: Optional[cobra.Solution] = 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 + deltaw_i + epsilon w_i^l = w_i  deltaw_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
 1
Tomer Shlomi, Omer Berkman and Eytan Ruppin, “Regulatory on/off minimization of metabolic flux changes after genetic perturbations”, PNAS 2005 102 (21) 76957700; doi:10.1073/pnas.0406346102