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Documents

Manuals

Systems Biology Workbench Java Programmer's Manual

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Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri
Updated 3 July 2002.

Systems Biology Workbench Perl Programmer's Manual

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Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
Updated 3 July 2002.

Systems Biology Workbench C++ Programmer's Manual HTML

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Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
Updated 18 February 2003.

Systems Biology Workbench C Programmer's Manual

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Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
26 February 2002.

Systems Biology Workbench Delphi/Kylix Programmer's Manual

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Herbert Sauro, Michael Hucka, Andrew Finney, Hamid Bolouri
26 February 2002.

Systems Biology Workbench Python Programmer's Manual

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Herbert Sauro, Michael Hucka, Andrew Finney, Hamid Bolouri
12 April 2002.

Systems Biology Workbench Standard Modules and Menus

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Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
Updated 3 July 2002

Systems Biology Workbench Module Programmer's Manual

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Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
31 May 2002.

The SBW-CORBA Gateway

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Michael Hucka and Andrew Finney
31 May 2002.

Papers

Introduction to the Systems Biology Workbench

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M. Hucka, H. Sauro, A. Finney, H. Bolouri
Updated 8 August 2003.

The ERATO Systems Biology Workbench: Architectural Evolution

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M. Hucka, A. Finney, H. Sauro, H. Bolouri. In The Proceedings of the 2nd International Conference on Systems Biology, ed. T.-M. Yi, M. Hucka, M. Morohashi, and H. Kitano, 2001.

The ERATO Systems Biology Workbench: Enabling Interaction and Exchange between Software Tools for Computational Biology

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M. Hucka, A. Finney, Herbert M. Sauro, H. Bolouri, J. Doyle, and H. Kitano. In The Proceedings of the Pacific Symposium on Biocomputing 2002, Jan. 2002.

The Systems Biology Workbench Concept Demonstrator: Design and Implementation

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H. Sauro, A. Finney, M. Hucka, H. Bolouri
9 May 2001.

A Comparison of Two Alternative Implementations of Message-Passing in the Systems Biology Workbench

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M. Hucka, A. Finney, H. Sauro, H. Bolouri
12 April 2001 (revised 4 June 2001).

The ERATO Systems Biology Workbench: An Integrated Environment for Multiscale and Multitheoretic Simulations in Systems Biology

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M. Hucka, H. Sauro, A. Finney, H. Bolouri, J. Doyle, H. Kitano, Foundations of Systems Biology, ed. Hiroaki Kitano, MIT Press, Cambridge, Massachusetts, 2001. (Note: the description of the SBW architecture in this paper is out of date; please see the newer papers above for more recent descriptions.)

Posters

The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules

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A. Finney, M. Hucka, H. Sauro, H. Bolouri, A. Funahashi, B. Bornstein, B. Kovitz, J. Matthews, B. Shapiro, S. Keating, J. Doyle, H. Kitano. Presented at the 3rd International Conference on Systems Biology, Stockholm, Sweden, December 2002.

The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules

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M. Hucka, A. Finney, H. Sauro, H. Bolouri, J. Doyle, H. Kitano.Presented at the 10th International Conference on Intelligent Systems for Molecular Biology, Edmonton, Alberta, Canada, August 2002.

The ERATO Systems Biology Workbench

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A. Finney, M. Hucka, H. Sauro, H. Bolouri, J. Doyle, H. Kitano. Presented at the First International Symposium on Computational Cell Biology, Lenox, Mass., USA, Mar. 2001.

Presentations

The ERATO Systems Biology Workbench Project: A Simplified Framework for Application Intercommunication

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Presentation at The O'Reilly Bioinformatics Technology Conference, Jan. 2002, by M. Hucka.

The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Tools for Computational Biology

Power Point

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Presentation given by M. Hucka at the Pacific Symposium on Biocomputing 2002, Kaua'i, Hawaii, USA, Jan. 2002.

Using the Systems Biology Workbench

Power Point

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Tutorial presented by M. Hucka, A. Finney and H. Sauro at ICSB2001, Caltech, Pasadena, CA, 4th November 2001.

Overview of the Systems Biology Workbench

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Presented by M. Hucka at the Third Workshop on Software Platforms for Systems Biology, Caltech, June 2001.

The High Level SBW Libraries

Power Point

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Presented by A. Finney at the Third Workshop on Software Platforms for Systems Biology, Caltech, June 2001.

Experimental Prototype

Power Point

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Presented by H. Sauro at the Third Workshop on Software Platforms for Systems Biology, Caltech, June 2001.

The ERATO Systems Biology Workbench

Power Point

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Presentation at In Silico Technologies in Drug Discovery, Bethesda, MD, USA, May 21-23, 2000 by Michael Hucka.

The ERATO Systems Biology Workbench

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Presentation at The First International Conference on Systems Biology (ICSB2000), Tokyo, Japan, November 2000 by Hamid Bolouri.