Optimised value equal to zero following addition of pathway to iML1515 metabolism

[Christopher Sandbach]

Hello again.

I have added a couple of sequential reactions to the iML1515 model. For each one, I have created the reaction object, added metabolites and a (currently) arbitrary gene rule etc. But then when I try to optimise for the output of this new pathway, I am obtaining a flux of zero... 

I have just had a brainwave and I haven't checked if the reactions for mass balance so, I will investigate that now. Either way, I will post my code below.

Thank you everyone for your help!

P.S. I cannot find the best way to post a code block, so I have simply included a markdown file. Apologies if that's not standard practice

[Christopher Sandbach]

=====> BOUNDARY REACTIONS <=====