Method for the evolutionary design of biochemical reaction networks
AssigneeThe Regents of the University of California
InventorsBernhard O. Palsson, Jeremy S. Edwards
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Abstract
The present invention relates to methods for achieving an optimal function of a biochemical reaction network. The methods can be performed in silico using a reconstruction of a biochemical reaction network of a cell and iterative optimization procedures. The methods can further include laboratory culturing steps to confirm and possibly expand the determinations made using the in silico methods, and to produce a cultured cell, or population of cells, with optimal functions. The current invention includes computer systems and computer products including computer-readable program code for performing the in silico steps of the invention.
Claims7
A method for achieving an optimal function of a biochemical reaction network in a cell comprising:
- (a) calculating optimal properties of a biochemical reaction network by applying a computational optimization method to a list of reactions representing said biochemical reaction network;
- (b) altering said list of reactions in the biochemical reaction network and re-computing the optimal properties;
- (c) repeating b) until a desired optimal function is reached;
- (d) constructing the genetic makeup of a cell to contain the biochemical reactions which result from (c);
- (e) placing the cell constructed under (d) in culture under a specified environment to obtain a population of cells;
- and
- (f) cultivating the cells as in step (e) for a sufficient period of time and under conditions to allow the cells to evolve to the desired optimal function determined under (c), wherein the biochemical reaction network comprises a comprehensive biochemical reaction network.
Dependencies are inferred from the claim text.