WO2001057775A3 - System and method for modelling genetic, biochemical, biophysical and anatomical information - Google Patents

System and method for modelling genetic, biochemical, biophysical and anatomical information Download PDF

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Publication number
WO2001057775A3
WO2001057775A3 PCT/US2001/001988 US0101988W WO0157775A3 WO 2001057775 A3 WO2001057775 A3 WO 2001057775A3 US 0101988 W US0101988 W US 0101988W WO 0157775 A3 WO0157775 A3 WO 0157775A3
Authority
WO
WIPO (PCT)
Prior art keywords
genetic
biochemical
data structure
information
biophysical
Prior art date
Application number
PCT/US2001/001988
Other languages
French (fr)
Other versions
WO2001057775A9 (en
WO2001057775A2 (en
Inventor
Ramprasad Ramakrishna
Kam-Chuen Jim
Gregory Scott Lett
Gary Anthony Pestano
Jian Li
Original Assignee
Physiome Sciences Inc
Ramprasad Ramakrishna
Kam-Chuen Jim
Gregory Scott Lett
Gary Anthony Pestano
Jian Li
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Physiome Sciences Inc, Ramprasad Ramakrishna, Kam-Chuen Jim, Gregory Scott Lett, Gary Anthony Pestano, Jian Li filed Critical Physiome Sciences Inc
Priority to AU36490/01A priority Critical patent/AU3649001A/en
Priority to EP01908645A priority patent/EP1368774A2/en
Priority to JP2001556956A priority patent/JP2004501415A/en
Priority to CA002399272A priority patent/CA2399272A1/en
Priority to IL15107001A priority patent/IL151070A0/en
Publication of WO2001057775A2 publication Critical patent/WO2001057775A2/en
Publication of WO2001057775A3 publication Critical patent/WO2001057775A3/en
Publication of WO2001057775A9 publication Critical patent/WO2001057775A9/en

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Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/20—Heterogeneous data integration
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

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  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Molecular Biology (AREA)
  • Physiology (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Complex Calculations (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

Genetic, biochemical, biophysical and anatomical information is integrated at the subcellular, cellular, tissue and organ level. At least one database containing biological information is used to generate at least one data structure having at least one attribute associated therewith. An interface interactively views, edits or links together attributes of the data structures to create at least one hierarchical description of subcellular, cellular, tissue and organ function. The hierarchical description may optionally be an elementary, binary or pathway data structure, or, alternatively, an anatomical data structure capable of being modified to form a structural model. A computational engine mathematically generates at least one data structure from the hierarchical description. Genetic information is accessed, tabulated and combined with functional information on the biochemical and physiological role of gene products. Computational models of genetic, biochemical and biophysical processes within cells and higher order systems are automatically formulated, solved and analyzed based on combination of genetic and functional information adduced. A dynamic tool is thereby provided for achieving discernible objectives, such as increased understanding of biological processes, identification of new drug targets for therapeutic intervention and predictions involving the outcome of drug screening. These objectives are accomplished by the realization of highly complex nonlinear dynamic interactions that occur between each gene or gene product.
PCT/US2001/001988 2000-02-07 2001-01-22 System and method for modelling genetic, biochemical, biophysical and anatomical information WO2001057775A2 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
AU36490/01A AU3649001A (en) 2000-02-07 2001-01-22 System and method for modeling genetic, biochemical, biophysical and anatomical information: in silico cell
EP01908645A EP1368774A2 (en) 2000-02-07 2001-01-22 System and method for modelling genetic, biochemical, biophysical and anatomical information
JP2001556956A JP2004501415A (en) 2000-02-07 2001-01-22 Genes, biochemistry, biophysics, and anatomical information systems and methods: insilico cells
CA002399272A CA2399272A1 (en) 2000-02-07 2001-01-22 System and method for modeling genetic, biochemical, biophysical and anatomical information: in silico cell
IL15107001A IL151070A0 (en) 2000-02-07 2001-01-22 System and method for modeling genetic, biochemical, biophysical and anatomical information: in silico cell

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US49957500A 2000-02-07 2000-02-07
US09/499,575 2000-02-07

Publications (3)

Publication Number Publication Date
WO2001057775A2 WO2001057775A2 (en) 2001-08-09
WO2001057775A3 true WO2001057775A3 (en) 2003-10-02
WO2001057775A9 WO2001057775A9 (en) 2003-11-27

Family

ID=23985791

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/001988 WO2001057775A2 (en) 2000-02-07 2001-01-22 System and method for modelling genetic, biochemical, biophysical and anatomical information

Country Status (6)

Country Link
EP (1) EP1368774A2 (en)
JP (1) JP2004501415A (en)
AU (1) AU3649001A (en)
CA (1) CA2399272A1 (en)
IL (1) IL151070A0 (en)
WO (1) WO2001057775A2 (en)

Families Citing this family (24)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU3482200A (en) 1999-02-02 2000-08-25 Bernhard Palsson Methods for identifying drug targets based on genomic sequence data
JP2003524818A (en) 1999-04-16 2003-08-19 エンテロス・インコーポレーテッド Method and apparatus for performing a consolidation simulation operation using a computer-based system model
US7127379B2 (en) 2001-01-31 2006-10-24 The Regents Of The University Of California Method for the evolutionary design of biochemical reaction networks
US7353152B2 (en) 2001-05-02 2008-04-01 Entelos, Inc. Method and apparatus for computer modeling diabetes
EP1393253A4 (en) 2001-05-17 2009-12-16 Entelos Inc Apparatus and method for validating a computer model
US6862561B2 (en) 2001-05-29 2005-03-01 Entelos, Inc. Method and apparatus for computer modeling a joint
US7751981B2 (en) 2001-10-26 2010-07-06 The Regents Of The University Of California Articles of manufacture and methods for modeling Saccharomyces cerevisiae metabolism
US20030224363A1 (en) * 2002-03-19 2003-12-04 Park Sung M. Compositions and methods for modeling bacillus subtilis metabolism
US8229673B2 (en) 2002-03-29 2012-07-24 Genomatica, Inc. Human metabolic models and methods
US8949032B2 (en) 2002-03-29 2015-02-03 Genomatica, Inc. Multicellular metabolic models and methods
US20030220928A1 (en) * 2002-05-21 2003-11-27 Patrick Durand Method for organizing and querying a genomic and proteomic databases
US7856317B2 (en) 2002-06-14 2010-12-21 Genomatica, Inc. Systems and methods for constructing genomic-based phenotypic models
US7869957B2 (en) 2002-10-15 2011-01-11 The Regents Of The University Of California Methods and systems to identify operational reaction pathways
JP5064656B2 (en) 2002-10-15 2012-10-31 ザ リージェンツ オブ ザ ユニバーシティ オブ カリフォルニア Method and system for identifying conducting reaction pathways
FR2854709B1 (en) * 2003-05-07 2005-08-05 Gilbert Chauvet SYSTEM AND METHOD FOR SIMULATION OF EVOLUTION OF COMPLEX LIVING ORGANISMS
US7853406B2 (en) 2003-06-13 2010-12-14 Entelos, Inc. Predictive toxicology for biological systems
JP2007511330A (en) 2003-11-19 2007-05-10 エンテロス・インコーポレーテッド Apparatus and method for assessing utilization of metabolic substrates
US7069534B2 (en) 2003-12-17 2006-06-27 Sahouria Emile Y Mask creation with hierarchy management using cover cells
US8554486B2 (en) 2004-02-20 2013-10-08 The Mathworks, Inc. Method, computer program product, and apparatus for selective memory restoration of a simulation
US7844431B2 (en) 2004-02-20 2010-11-30 The Mathworks, Inc. Method and apparatus for integrated modeling, simulation and analysis of chemical and biochemical reactions
US10325686B2 (en) * 2012-07-05 2019-06-18 Siemens Healthcare Gmbh System and methods for integrated and predictive analysis of molecular, imaging, and clinical data for patient-specific management of diseases
EP3283989A4 (en) * 2015-02-04 2018-12-19 Rath, Matthias W. Method and system for real time visualization of individual health condition on a mobile device
US11288576B2 (en) 2018-01-05 2022-03-29 Illumina, Inc. Predicting quality of sequencing results using deep neural networks
JP6959364B2 (en) 2018-01-05 2021-11-02 イルミナ インコーポレイテッド Prediction of reagent cooler instability and flow cell heater failure in sequencing systems

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5273038A (en) * 1990-07-09 1993-12-28 Beavin William C Computer simulation of live organ
US5914891A (en) * 1995-01-20 1999-06-22 Board Of Trustees, The Leland Stanford Junior University System and method for simulating operation of biochemical systems
US5930154A (en) * 1995-01-17 1999-07-27 Intertech Ventures, Ltd. Computer-based system and methods for information storage, modeling and simulation of complex systems organized in discrete compartments in time and space
US5947899A (en) * 1996-08-23 1999-09-07 Physiome Sciences Computational system and method for modeling the heart

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5273038A (en) * 1990-07-09 1993-12-28 Beavin William C Computer simulation of live organ
US5930154A (en) * 1995-01-17 1999-07-27 Intertech Ventures, Ltd. Computer-based system and methods for information storage, modeling and simulation of complex systems organized in discrete compartments in time and space
US5914891A (en) * 1995-01-20 1999-06-22 Board Of Trustees, The Leland Stanford Junior University System and method for simulating operation of biochemical systems
US5947899A (en) * 1996-08-23 1999-09-07 Physiome Sciences Computational system and method for modeling the heart

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
DAFOE M E ET AL: "IN SILICO KNOWLEDGE DISCOVERY IN BIOMEDICAL DATABASES", PROCEEDINGS OF THE SPIE, SPIE, BELLINGHAM, VA, US, 7 November 1993 (1993-11-07), pages 239 - 243, XP000197711 *
GORYANIN I ET AL: "Mathematical simulation and analysis of cellular metabolism and regulation", BIOINFORMATICS, vol. 15, no. 9, September 1999 (1999-09-01), pages 749 - 758, XP002190906 *
SCHAFF J ET AL: "THE VIRTUAL CELL", PROCEEDINGS OF THE PACIFIC SYMPOSIUM ON BIOCOMPUTING, XX, XX, 1999, pages 228 - 239, XP002942953 *
TANDEITNIK P ET AL: "Modelling of biological neurons by artificial neural networks", ELECTRICAL AND ELECTRONICS ENGINEERS IN ISRAEL, 1996., NINETEENTH CONVENTION OF JERUSALEM, ISRAEL 5-6 NOV. 1996, NEW YORK, NY, USA,IEEE, US, 5 November 1996 (1996-11-05), pages 239 - 242, XP010211280, ISBN: 0-7803-3330-6 *

Also Published As

Publication number Publication date
IL151070A0 (en) 2003-04-10
AU3649001A (en) 2001-08-14
WO2001057775A9 (en) 2003-11-27
WO2001057775A2 (en) 2001-08-09
JP2004501415A (en) 2004-01-15
EP1368774A2 (en) 2003-12-10
CA2399272A1 (en) 2001-08-09

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