Network models of biochemical pathways

Abstract

This invention describes computer based systems and methods for modeling and simulation of biochemical networks of pathways, including metabolic, signal transduction and regulatory pathways within a cell or across cells. The invention comprises systems and methods for building the models and for using the models for analysis and information retrieval, for determining the effect that modulating one or more reactions in a biochemical pathway has on an operation of the biochemical pathway, and for simulating or predicting an altered physiological state of cells.

Description

PRIORITY CLAIMED [0001] This is a divisional application of pending U.S. Ser. No. 08 / 860,975, filed on Dec. 22, 1997, which is a national stage filing under 35 CFR § 371 of International Application No. PCT / US96 / 00883, filed on Jan. 17, 1996, which was published in English under PCT Article 21(2) as WO 96 / 22575, and which claims the benefit as a continuation-in-part of the combined U.S. application Ser. Nos. 08 / 373,688 and 08 / 373,992, both filed Jan. 17, 1995. U.S. Ser. No. 08 / 373,688, now abandoned, was continued as Ser. No. 08 / 889,624, filed Jul. 8, 1997, and issued as patent U.S. Pat. No. 5,930,154 on Jul. 27, 1999. U.S. Ser. No. 08 / 373,992 issued as patent U.S. Pat. No. 5,980,096, on Nov. 9, 1999. Related patent EP 0821817, entitled “Control Systems Based on Simulated Virtual Models”, was granted on Jun. 23, 1999. The specifications, drawings and appendixes of each of the above-referenced patent applications are incorporated herein by reference.COMPACT DISC APPENDIX [0002] The T...

AI Technical Summary

Benefits of technology

Enables precise modeling and control of complex biological systems, improving productivity by predicting reaction outcomes and optimizing process conditions, allowing for the intelligent control of biochemical reactions and product yield.

Problems solved by technology

Some process industries use large-scale cultivation of microorganisms or mammalian cells, which are extreme cases in terms of complexity when considering those cells as the individual manufacturing plants involved in complex chemical synthesis.

The ultimate level of complexity is using a whole animal as the live factory for continuous production for important secreted proteins.

However, the current systems only monitor very general types of phenomena, such as gas pressure, pH, and in some occasions, the concentration of some product that correlates with cell growth or production.

For example, for controlling the production of a particular secreted protein that is produced in very low amounts in relation to other proteins, the total protein amount of protein is measured, which is a very poor indicator of how much of the desired protein is produced.

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