Data processing: structural design – modeling – simulation – and em – Modeling by mathematical expression
Reexamination Certificate
2006-01-03
2006-01-03
Phan, Thai (Department: 2128)
Data processing: structural design, modeling, simulation, and em
Modeling by mathematical expression
C703S011000, C345S419000, C715S700000
Reexamination Certificate
active
06983227
ABSTRACT:
A computer based virtual models of complex systems, together with integrated systems and methods provide a development and execution framework for visual modeling and dynamic simulation of said models. The virtual models can be used for analysis, monitoring, or control of the operation of the complex systems modeled, as well as for information retrieval. More particularly, the virtual models in the present implementation relate to biological complex systems. In the current implementation the virtual models comprise building blocks representing physical, chemical, or biological processes, the pools of entities that participate in those processes, a hierarchy of compartments representing time-intervals or the spatial and/or functional structure of the complex system in which said entities are located and said processes take place, and the description of the composition of those entities. The building blocks encapsulate in different layers the information, data, and mathematical models that characterize and define each virtual model, and a plurality of methods is associated with their components. The models are built by linking instances of the building blocks in a predefined way, which, when integrated by the methods provided in this invention, result in multidimensional networks of pathways. A number of functions and graphical interfaces can be selected for said instances of building blocks, to extract in various forms the information contained in said models. Those functions include: a) on-the-fly creation of displays of interactive multidimensional networks of pathways, according to user selections; b) dynamic quantitative simulations of selected networks; and c) complex predefined queries based on the relative position of pools of entities in the pathways, the role that the pools play in different processes, the location in selected compartments, and/or the structural components of the entities of those pools. The system integrates inferential control with quantitative and scaled simulation methods, and provides a variety of alternatives to deal with complex dynamic systems and with incomplete and constantly evolving information and data.
REFERENCES:
patent: 5319740 (1994-06-01), Yamada et al.
patent: 5379366 (1995-01-01), Noyes
patent: 5412756 (1995-05-01), Bauman et al.
patent: 5443791 (1995-08-01), Cathcart et al.
patent: 5657255 (1997-08-01), Fink et al.
patent: 5680590 (1997-10-01), Parti
patent: 5732192 (1998-03-01), Malin et al.
patent: 5757678 (1998-05-01), Leeke
patent: 5801942 (1998-09-01), Nixon et al.
patent: 5808918 (1998-09-01), Fink et al.
patent: 5835758 (1998-11-01), Nochur et al.
patent: 5845270 (1998-12-01), Schatz et al.
patent: 5914891 (1999-06-01), McAdams et al.
patent: 5930154 (1999-07-01), Thalhammer-Reyero
patent: 5980096 (1999-11-01), Thalhammer-Reyero
patent: 6038540 (2000-03-01), Krist et al.
patent: 6051029 (2000-04-01), Paterson et al.
patent: 6069629 (2000-05-01), Paterson et al.
patent: 6078739 (2000-06-01), Paterson et al.
patent: 0 367 544 (1990-05-01), None
patent: 0 367 544 (1990-09-01), None
patent: WO 91/06050 (1991-05-01), None
Ackers, G.K. er al. (1997) Quantitative model for gene regulation by phage repressor.Proc. Natl. Acad. Sci. USA, 79, 1129-1133.
Deville Y. et al. (2003) “An Overview of Data Models for the Analysis of Biochemical Pathways”,Brief Bioinform. 2003 Sep;4(3):246-59.
Fadel F.G. (1994) “A Resource Ontology for Enterprise Modelling” in 3rdIndustrial Engineering Research Conference Proceedings, 455-.
Foster R.O. et al (1973) “Short Term Glucose Homeostatis in Man: A Systems Dynamic Model”J. of Dynamical Systems, Management abd Control, in Transactions of the ASME, 308-314.
Fox, M. et al. (1993), “A Common Sense Model of the Enterprise”,Proceedings of the 2nd Industrial Engineering Research Conference, pp. 425-429, Norcross GA: Institute for Industrial Engineers.
Galper A.R. et al. (1993) “Knowledge-Based Simulation of DNA Metabolism: Prediction of Action and Envisionment of Pathways”,Chapter 10 in Artificial Intelligence and Molecular Biology, Ed. Hunter L., AAAI Press, 365-395.
Goldbeter, A. (1991) A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase.Proc. Natl. Acad. Sci. USA, 88, 9107-9111.
Grass G.M. et al (1993) “A Model to Predict Aqueous Humor and Plasma Pharmacokinetics of Oculary Applied Drugs”,35 Investigative Ophtalmology & Visual Science, 2251-2259.
Gruninger, M., Fox, M.S. (1994), “An Activity Ontology for Enterprise Modelling”,Submitted to: Workshop on Enabling Technologies-Infrastructures for Collaborative Enterprises, West Virginia University.
Ironi L et al., (1994) “A Framework for Building and Simulating Qualitative Models of Compartmental Systems”Computer Methods and Programs in Biomedicine, 233-254.
Iyengar S.S. (1992) Ed. “Structuring Biological Systems-A Computer Modeling Approach”,Chapter7, 210-226.
Jensen K. et al. (1985) “Self-Sustained Oscillations and Chaotic Behaviour in Kidney Pressure Regulation” in1. Prigogine and M. Sanglier, eds., Laws of Nature and Human Conduct. Brussels: Taskforce of Research Information and Study on Science, 91-109.
Karp P.D. (1993) “A Quantitative Biochemistry and Its Application to the Regulation of the Tryptophan Operon”,Chapter 8 in Artificial Intelligence and Molecular Biology, Ed. Hunter L., AAAI Press, 289-324.
Kim, H., Fox, M.S., (1994), “Formal Models of Quality and ISO 9000 Compliance: An Information Systems Approach”,American Quality Congress (AQC) Conference, American Society for Quality Control, Las Vegas NV.
Loomis W.F., Thomas S.R. (1976) “Kinetic Analysis of Biochemical Differentiation in Dictyostelium”,The Journal. of Biological Chemistry, 251 (20) 6252-638.
Mavrovouniotis M.L. (1993) “Identification of Qualitatively Feasible Metabolic Pathways”,Chapter 9 in Artificial Intelligence and Molecular Biology, Ed. Hunter L., AAAI Press, 325-364.
Mendes P. (1993) “GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems”.Comput Appl Biosci9(5):563-71.
Novak B., Tyson J.J. (1995). “Quantitative Analysis of a Molecular Model of Mitotic Control in Fission Yeast”J. Theor. Biol.173:283-305.
Reed J.L., Palsson B. O. (2003) “Minireview -Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli”J. Bacteriol. 185(9): 2692-2699.
Riggs D.S. (1970) “Control Theory and Physiological Feedback Mechanisms”,The Williams and Wilkins Co. Eds. 500-503.
Sauro H.M. (1993) “Scamp: a general-purpose simulator and metabolic control analysis program”Comput Appl Biosci.Aug; 9(4): 441-50.
Sturis J et al (1991) “Computer Model for Mechanisms Underlaying Utlradian Oscillations of Insulin and Glucose”Am. J. Physiol. 801-809.
Intertech Ventures, Ltd.
Phan Thai
LandOfFree
Virtual models of complex systems does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Virtual models of complex systems, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Virtual models of complex systems will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3557891