bio-systems-biology-strain-design

name	bio-systems-biology-strain-design
description	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.
tool_type	python
primary_tool	straindesign

Version Compatibility

Reference examples tested with: StrainDesign 1.15+, COBRApy 0.29+, Python 3.10+ (cameo optional)

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Note: OptKnock/RobustKnock/MCS are MILP problems and are far harder than plain FBA; StrainDesign supports GLPK/SCIP (open source) and CPLEX/Gurobi (academic, much faster and more robust for genome-scale). Set a time_limit. Reaction-based designs must be translated back to gene knockouts via GPRs.

Strain Design