Network models of biological complex systems

Abstract

This invention describes computer based systems and methods for modeling and simulation of complex biological systems from the cellular, or subcellular, to the organism and population level, for using said models to predict functions of components of the biological systems and to simulate physiological and pathological states at the various levels, and for using said models in drug development for testing in a computer system substances for possible use as therapeutics by simulating their effects on the physiological and pathological states.

Description

PARENT CASES 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 U.S. Ser. No. 08 / 889,624, filed Jul. 8, 1997, and issued as 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...

AI Technical Summary

Benefits of technology

Enables the creation of detailed mechanistic models for complex biological systems, allowing for precise control of biochemical reactions and improved productivity by integrating simulation with monitoring data, providing a framework for domain experts to directly input knowledge and modify models without intermediaries, and enabling real-time monitoring and control of biochemical processes.

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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