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strain-design

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Computes metabolic-engineering strain designs on genome-scale models with StrainDesign (OptKnock, RobustKnock, minimal cut sets, OptCouple) and cameo (heuristic knockout and FSEOF over/under-expression targets), finding gene/reaction interventions that couple product formation to growth. Use when designing knockouts to overproduce a target chemical, choosing between OptKnock and RobustKnock, growth-coupling a product so evolution maintains it, computing minimal cut sets, finding amplification targets with FSEOF, or understanding why MILP strain design needs a strong solver and why a design is only a hypothesis.

When to use

• designing knockouts to overproduce a target chemical
• choosing between OptKnock and RobustKnock
• growth-coupling a product so evolution maintains it
• computing minimal cut sets
• finding amplification targets with FSEOF
• understanding why MILP strain design needs a strong solver
• understanding why a design is only a hypothesis

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