New Script : Add integration script for MATLAB

[h-escoffier]

Add a tutorial for MATLAB on how create a medium specific medium + gap filling

[leoniethomas]

@h-escoffier -> I think I need a little more input on how exactly to do this ? So the following steps:

• load Recon ? -> so we do it for Recon3D for now ?
• set the boundaries of the rxns in the medium -> which medium -> RPMI+(FBS)
• to -1000 or to the concentration ? or to the flux ?
• gap filling script ? L1/L2/L0 regularization ? -> is the gap filling done in julia already on the github ?

[h-escoffier]

so we do it for Recon3D for now ?

I would prioritize Human-GEM but it would like to have it for both at the end

set the boundaries of the rxns in the medium -> which medium -> RPMI+(FBS)

I would use RPMI1640 + 5% FBS + 2mM Glutamine in the test but normally using another medium should not change the code to much

to -1000 or to the concentration ? or to the flux ?

For now I worked only by setting all the lb to -1000 but I would like to see how to deal more concrete values (concentration or fluxes) cf. issue#3

gap filling script ? L1/L2/L0 regularization ? -> is the gap filling done in julia already on the github ?

I'm currently working on the example in Julia, to show how to gap-fill the medium with L1 and L2 and in the case of L1 allows to provide other solutions.
Also I would like to provide the set of unwanted exchange reactions but also wip