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ICSB 2007 Welcome to the Eighth International Conference on Systems Biology
Long Beach, California October 1-6, 2007
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Abstract Submission Tutorials WorkshopsCommitteesPosters    Posters By Topic:
A. RTK Systems Biology
B. Morphogenesis
C. Synthetic Biology
D. Mathematical Frontiers
E. Technological Froniters
F. Regulatory Systems
G. Systems Bioinformatics: Tools
H. Systems Bioinformatics: Analysis
I. Systems Biomedicine
J. Multiscale Networks
   Posters By Author
   Submission Call (archive)
LinksFAQ & InformationSponsors & HostsProceedings Journal Articles
G. Systems Bioinformatics: Tools

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G01. Biochemical Data Integration: Standardization of Parameter Units and Normalization of Chemical Compound Names in SABIO-RK
Martin Golebiewski (EML Research, Heidelberg, Germany)

G02. Development of an extensible system for the capture and storage of experimental enzyme kinetics data
Neil Swainston (Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, UK)

G03. Combinatorial Analysis of Perturbational Gene Expression Compendia
Steven Maere (Department of Plant Systems Biology, VIB, Ghent, Belgium)

G04. Genome-Scale reconstruction of the transcriptional and translational machinery in Escherichia coli: A knowledge-database and its mathematical formulation
Ines Thiele (Bioengineering Department, University of California, San Diego)

G05. EcoProDB: The protein knowledge base for Escherichia coli
Hongseok Yun (Department of Chemical and Biomolecular Engineering, KAIST)

G06. CIDMS: Cardiac Integrated Database Management System for Cardiac Systems Biology
Pradeep K. Sreenivasaiah (Department of Life Science, Gwangju Institute of Science and Technology (GIST) Gwangju, Korea)

G08. NetBuilder—A tool for the modeling and simulation of genetic regulatory networks
Katja Wegner (Biological and Neural Computation Group , Science & Technology Research Institute , University of Hertfordshire, Hatfield)

G09. The Edinburgh Pathway Editor—a graphical editor for biological pathways
Stuart L. Moodie (University of Edinburgh)

G10. Sigmoid: A Scalable System for Pathway Bioinformatics and Systems Biology
Behnam Compani-Tabrizi (1) Institute for Genomics and Bioinformatics, 2) School of Information and Computer Sciences, University of California, Irvine)

G11. CellDesigner 4.0beta: A Modeling Tool for Biochemical Networks
Akira Funahashi (Department of Biosciences and Informatics, Keio University)

G12. COPASI—A complex pathway simulator
Sven Sahle (Department for Modeling of biological Processes, University of Heidelberg, Germany)

G13. Tapping the Web for interaction data: MiTap & MiSink extensions to Firefox and Cytoscape
Lukasz Salwinski (UCLA-DOE Institute for Genomics and Proteomics, Los Angeles)

G14. "Payao": Web 2.0 community tagging system for biological networks
Hiroaki Kitano (Okinawa Institute of Science and Technology, Okinawa, Japan, The Systems Biology Institute, Tokyo, Japan)

G15. Formal description and visual modeling of complex biological systems using BioUML workbench and BioUML Network Edition
Fedor A. Kolpakov (Institute of Systems Biology, Novosibirsk, Russia; Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia)

G16. In Silico TCDD Toxicity Evaluation System
Junil Kim (Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea)

G17. Degradome project: Insights into intracellular protein degradation
Guy E. Zinman (Department of Computational Biology, Carnegie Mellon University, Pittsburgh, USA)

G18. GraphCrunch: A Tool for Large Network Analyses
Tijana Milenkovic (Department of Computer Science, University of California, Irvine)

G19. Systems Biology Graphical Notation
Yukiko Matsuoka (Systems Biology Institute, Tokyo, Japan)

G20. BiNoM: A Cytoscape plugin for using and analyzing biological networks
Laurence Calzone (Institut Curie)

G21. SBML Level 2 Version 3
Sarah M. Keating (STRI, University of Hertfordshire, Hertfordshire, UK)

G22. LibSBML 3.0: An API library for SBML
Michael Hucka (Beckman Institute BNMC, California Institute of Technology, Pasadena, CA, USA)

G23. SBML ODE Solver Library: Extensions for Inverse Analysis
James Lu (Johann Radon Institute for Computational and Applied Mathematics, Linz, Austria)

G24. Platforms for Modeling in Systems Biology: Recent Developments in MathSBML and Cellerator
Bruce E. Shapiro (Biological Network Modeling Center, Caltech, Pasadena, CA USA)

G25. High-accuracy R-leaping: Implementing and exploring a potentially exact method for accelerated stochastic simulation
David W. Orendorff (University of California, Irvine)

G26. SBMLeditor toward SBML Level 3 and modularisation
Nicolas Rodriguez (Computational Neurobiology group, EMBL-European Bioinformatics Institute)

G27. BioModels Database, a curated and annotated resource of published quantitative kinetic models
Chen Li (European Bioinformatics Institute, Hinxton, CB10 1SD, UK)

G28. Semantic annotation of kinetic models in Systems Biology
Nicolas Le Novere (EBI, EMBL)

G29. MIRIAM Resources: Robust Cross-References in Systems Biology
Camille Laibe (Computational Neurobiology, European Bioinformatics Institute, Cambridge, UK)

G30. CellML: Cellml.org, Tools and Community
Edmund J. Crampin (Bioengineering Institute, University of Auckland, New Zealand)

G31. ReConn: Explore past the edges of pathways
Willem P. A. Ligtenberg (Department of BioMedical Engineering, Eindhoven University of Technology, Eindhoven)

G32. Connecting the dots: An integrated database for studying cellular dynamics
Samik Ghosh (Deprtment of Computer Sc. & Engineering, The University of Arlington)

G33. Interaction Graph Validator a New Type of Relation Database for Protein-Protein Interaction Mapping by Mass Spectrometry-Based
Fred Elisma (Ottawa Institute of System Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa)

G34. Systematic screening of yeast kinetic parameters for metabolic models using a text mining toolbox
Irena Spasic (Manchester Centre for Integrative Systems Biology, The University of Manchester, UK)

G35. SemText: A semantically enriched information retrieval system for biology
Sophia Ananiadou (School of Computer Science, The University of Manchester, UK)

G36. Ontology driven data integration for enabling systems biology
Vladimir Mironov (VIB Department of Plant Systems Biology, Ghent University., Technologiepark 927, Ghent, Belgium )

G37. Cellular machine-based Bayesian factor analysis: Exploring drug’s mode-of-action in a cell
Sangjo Han (1 Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea)

G38. BetaWB—A language for modular representation of biological SYSTEMS
Roberto Larcher (The Microsoft Research, University of Trento Centre for Computational Systems Biology)

G39. LBS—A Language of Biological Systems
Michael D. Pedersen (LFCS, School of Informatics, University of Edinburgh)

G40. Description model of gene regulatory networks for simulation and analysis
Tetsuya Maeshiro (School of Library and Information Science)

G41. Integrating system for segmenting and tracking fluorescent objects on the image data of growing cell colonies
Tigran Bacarian (IGB, UC Ivine)

G42. EcoliHub Information Resource for Experimentation and Modeling
Barry L. Wanner (1Purdue University, Biological Sciences, West Lafayette, IN 47907 USA)


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