User:Jarle Pahr/OptKnock

Notes on the OptKnock algorithm:

http://opencobra.sourceforge.net/openCOBRA/opencobra_documentation/cobra_toolbox_2/cobra/design/OptKnock.html

OptKnock is a bi-level optimization algorithm that seeks to optimize metabolite production through gene knockouts, subject to maximization of the cellular objective.

Problem formulation:

• Direct solution intractable
• Solution approach based on LP duality theory. Basis: "For every linear programming problem (primal) there exists a unique optimization problem (dual) whose optimal objective value is equal to that of the primal problem." (Burgard 2003).

http://maranas.che.psu.edu/submission/optknock_2.htm

Similar methods:

ReacKnock: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3859475/pdf/pone.0072150.pdf

Bibliography

http://www.ncbi.nlm.nih.gov/pubmed/14595777