level 2 moclo support

[doublergreer]

The problem of supporting level 2 moclo designs can be summarized as follows:

1. determining appropriate backbones for TU inside MD such that the product of level 1 assembly fits into a level 2 finished plasmid
   • 4 TU design will take L1 plasmids with fusion sites AE, EF, FG, GH and backbone DVA_AH
   • 3 TU can take AE, EF, FG and backbone DVA_AG
   • 2 TU can take AE, EF and backbone DVA_AF etc

for level 2 the backbone antibiotic resistanse needed is Ampicillin. and the parts should have Kanamycin.

2. iterating through existing digestion-ligation simulation code with outputs of previous steps as the inputs to the next

inputs = module definition with >1 floating TUs

• add MoClo level attribute to mocloplasmid class
• add antibiotic resistance level to mocloplasmid class

Now assembly_lvl1, assembly_lvl2 and full_build wil have a Design as input