WO2002044992A3 - System for modeling biological pathways - Google Patents

System for modeling biological pathways Download PDF

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Publication number
WO2002044992A3
WO2002044992A3 PCT/US2001/026887 US0126887W WO0244992A3 WO 2002044992 A3 WO2002044992 A3 WO 2002044992A3 US 0126887 W US0126887 W US 0126887W WO 0244992 A3 WO0244992 A3 WO 0244992A3
Authority
WO
WIPO (PCT)
Prior art keywords
pathway
database
diagram
attribute
biological pathways
Prior art date
Application number
PCT/US2001/026887
Other languages
French (fr)
Other versions
WO2002044992A2 (en
Inventor
Kam-Chuen Jim
Gregory Scott Lett
Gary Anthony Pestano
Zhuang Zuo
Ramprasad Ramakrishna
Original Assignee
Physiome Sciences Inc
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 filed Critical Physiome Sciences Inc
Priority to AU2001286880A priority Critical patent/AU2001286880A1/en
Publication of WO2002044992A2 publication Critical patent/WO2002044992A2/en
Publication of WO2002044992A3 publication Critical patent/WO2002044992A3/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
    • 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
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • Molecular Biology (AREA)
  • Physiology (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)

Abstract

A computerized system for modeling biological pathways is provided. The system comprises a database having a knowledge database for storing at least one attribute of at least one entity and a pathway database for storing at least one pathway diagram; a user interface for creating, querying, manipulating and viewing data from the database; a process system having a modeling module for simulating or analyzing the behavior of an attribute on a pathway diagram and a pathway editor module for retrieving, editing and saving at least one pathway diagram. The invention may be implemented on a web-based system that provides end users with the ability to create new pathway models, edit or manipulate existing pathway models, perform sequence searches and data queries, and generate reports.
PCT/US2001/026887 2000-11-28 2001-08-29 System for modeling biological pathways WO2002044992A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2001286880A AU2001286880A1 (en) 2000-11-28 2001-08-29 System for modeling biological pathways

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US72341000A 2000-11-28 2000-11-28
US09/723,410 2000-11-28

Publications (2)

Publication Number Publication Date
WO2002044992A2 WO2002044992A2 (en) 2002-06-06
WO2002044992A3 true WO2002044992A3 (en) 2003-12-31

Family

ID=24906146

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/026887 WO2002044992A2 (en) 2000-11-28 2001-08-29 System for modeling biological pathways

Country Status (2)

Country Link
AU (1) AU2001286880A1 (en)
WO (1) WO2002044992A2 (en)

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000063793A2 (en) 1999-04-16 2000-10-26 Entelos, Inc. Method and apparatus for conducting linked simulation operations utilizing a computer-based system model
US7353152B2 (en) 2001-05-02 2008-04-01 Entelos, Inc. Method and apparatus for computer modeling diabetes
WO2002093318A2 (en) 2001-05-15 2002-11-21 Psychogenics Inc. Systems and methods for monitoring behavior informatics
JP2004533053A (en) 2001-05-17 2004-10-28 エンテロス，インコーポレイティド 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
US7853406B2 (en) 2003-06-13 2010-12-14 Entelos, Inc. Predictive toxicology for biological systems
FI117988B (en) * 2003-07-04 2007-05-15 Medicel Oy Information management system for biochemical information
FI118101B (en) * 2003-07-04 2007-06-29 Medicel Oy Information management system for biochemical information
FR2858446B1 (en) * 2003-08-01 2007-11-09 Helios Biosciences METHOD OF ANALYZING BIOLOGICAL MOLECULAR INTERACTION NETWORKS
ATE531310T1 (en) 2003-11-19 2011-11-15 Entelos Inc METHOD FOR ASSESSING METABOLIC SUBSTRATE USE AND THE EFFECTIVENESS OF A THERAPY
EP1600864B1 (en) * 2004-05-26 2007-12-19 Innetics AB Modelling tool for chemical processes
EP1865431A1 (en) 2006-06-06 2007-12-12 Waters GmbH System for managing and analyzing metabolic pathway data

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
WO2000049540A1 (en) * 1999-02-19 2000-08-24 Cellomics, Inc. Method and system for dynamic storage retrieval and analysis of experimental data with determined relationships
WO2000065523A1 (en) * 1999-04-21 2000-11-02 Physiome Sciences, Inc. System and method for modeling genetic, biochemical, biophysical and anatomical information

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
WO2000049540A1 (en) * 1999-02-19 2000-08-24 Cellomics, Inc. Method and system for dynamic storage retrieval and analysis of experimental data with determined relationships
WO2000065523A1 (en) * 1999-04-21 2000-11-02 Physiome Sciences, Inc. System and method for modeling genetic, biochemical, biophysical and anatomical information

Non-Patent Citations (7)

* Cited by examiner, † Cited by third party
Title
ARITA M: "Metabolic reconstruction using shortest paths", SIMULATION PRACTICE AND THEORY, vol. 8, no. 1-2, 2000, pages 109 - 125, XP002257055 *
GORYANIN I ET AL: "Mathematical simulation and analysis of cellular metabolism and regulation", BIOINFORMATICS, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 15, no. 9, September 1999 (1999-09-01), pages 749 - 758, XP002190906, ISSN: 1367-4803 *
HOFESTADT R ET AL: "Interactive modelling and simulation of biochemical networks", COMPUTERS IN BIOLOGY AND MEDICINE, MAY 1995, UK, vol. 25, no. 3, pages 321 - 334, XP002257054, ISSN: 0010-4825 *
MENDES PEDRO ET AL: "Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation", BIOINFORMATICS (OXFORD), vol. 14, no. 10, 1998, pages 869 - 883, XP002257057, ISSN: 1367-4803 *
PROCEEDINGS IEEE INTERNATIONAL SYMPOSIUM ON BIO-INFORMATICS AND BIOMEDICAL ENGINEERING, ARLINGTON, VA, USA, 8-10, vol. CONF, 8 November 2000 (2000-11-08), pages 214 - 218, XP002257056 *
SALAMONSEN W ET AL: "BioJAKE: a tool for the creation, visualization and manipulation of metabolic pathways", PROCEEDINGS OF THE PACIFIC SYMPOSIUM ON BIOCOMPUTING, XX, XX, 4 January 1999 (1999-01-04), pages 392 - 400, XP002143430 *
TOMITA M ET AL: "THE E-CELL PROJECT: TOWARDS INTEGRATIVE SIMULATION OF CELLULAR PROCESSES", RECOMB 2000. PROCEEDINGS OF THE 4TH. ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY. TOKYO, JAPAN, APRIL 8 - 11, 2000, PROCEEDINGS OF THE ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY, NEW YORK, NY: ACM, US, vol. CONF.4, 8 April 2000 (2000-04-08), pages 290 - 298, XP001049507, ISBN: 1-58113-186-0 *

Also Published As

Publication number Publication date
AU2001286880A1 (en) 2002-06-11
WO2002044992A2 (en) 2002-06-06

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