No reaction reaction pruned from Recon3D model using mCADRE

[boyu jiang]

Hi, 

when I run mCADRE to get tissue-specific model from the Recon3D model, there is no reaction removed from the original model. I have prepared all required input files including the ExpressionData, confidenceScore and protectedRxn({'biomass_reaction', 'ATPS4mi'}). Also, the upper and lower boundaries of the "Ex_" reactions are setted as -100 and 100, respectively.  There is no error reported, but no reaction pruned from the original Recon3D model.

Any feedback would be sincerely appreciated.

[PAVAN KUMAR S bt19d200]

Hi boyu, 
Try to include options.tol in your input. Because by default, mCADRE uses 1e-8 as tolerance level for active reactions. Your feasible tolerance level should be lesser than or equal to this value if you did not provide any input for 'tol'. Use the command "getCobraSolverParams('LP', 'feasTol');" to get the feasible tolerance level in your machine.

Thanks and regards
Pavan Kumar S
Research scholar | BioSystems Engineering and Control Lab, IIT Madras.

[boyu jiang]

Hi  Pavan, 

Thanks a lot for your kind reply! I have checked tol with getCobraSolverParams('LP', 'feasTol') and the feasible tolerance level is 1e-6. Then I have tried the tol with both 0 and 1e-8, but still, there was no reaction pruned. Then I used tol = 1e-6, and the mCADRE runs very slowly. 

By the way, do you know if I need to set the lb and ub of the Recon3D "EX_" reactions with -100 and 100 before I run mCADRE? 

Thank you again!

Best

Boyu