 The Systems Biology Workbench (SBW)
 All components are currently in beta testing and available from our download area. Bugs remain and we are working on eliminating them as quickly as possible. We are also revising the documentation and eliminating discrepancies between the documented APIs and the implemented APIs. Check back often for updates to these documents.
Manuals |
Available Formats |
| Systems Biology Workbench Java Programmer's Manual |
HTML |
PDF |
PS |
Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri,
Frank Bergmann
Updated 21
October, 2004. |
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| Systems Biology Workbench Perl Programmer's Manual |
HTML |
PDF |
PS |
Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
Updated 3 July 2002. |
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| Systems Biology Workbench C++ Programmer's Manual |
HTML |
PDF |
PS |
Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri,
Frank Bergmann
Updated 21
October, 2004. |
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| Systems Biology Workbench C Programmer's Manual |
HTML |
PDF |
PS |
Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri,
Frank Bergmann
Updated 21
October, 2004.
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| Systems Biology Workbench Delphi/Kylix Programmer's Manual |
HTML |
PDF |
PS |
Herbert Sauro, Michael Hucka, Andrew Finney, Hamid Bolouri
Updated 12
December, 2004. |
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| Systems Biology Workbench Python Programmer's Manual |
HTML |
PDF |
PS |
Herbert Sauro, Michael Hucka, Andrew Finney, Hamid Bolouri
12 April 2002. |
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| Systems Biology Workbench Standard Modules and Menus |
HTML |
PDF |
PS |
Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
Updated 3 July 2002. |
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| Systems Biology Workbench Module Programmer's Manual |
HTML |
PDF |
PS |
Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
31 May 2002. |
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| The SBW-CORBA Gateway |
HTML |
PDF |
PS |
Michael Hucka and Andrew Finney
31 May 2002. |
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Papers |
Available Formats |
| Introduction to the Systems Biology Workbench |
HTML |
PDF |
PS |
M. Hucka, H. Sauro, A. Finney, H. Bolouri
Updated 8 August 2003. |
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| The ERATO Systems Biology Workbench: Architectural Evolution |
HTML |
PDF |
PS |
| 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. |
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| The ERATO Systems Biology Workbench: Enabling Interaction and Exchange between Software Tools for Computational Biology |
HTML |
PDF |
PS |
| 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.
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| The Systems Biology Workbench Concept Demonstrator: Design and Implementation |
HTML |
PDF |
PS |
H. Sauro, A. Finney, M. Hucka, H. Bolouri
9 May 2001. |
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| A Comparison of Two Alternative Implementations of Message-Passing in the Systems Biology Workbench |
HTML |
PDF |
PS |
M. Hucka, A. Finney, H. Sauro, H. Bolouri
12 April 2001 (revised 4 June 2001). |
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| The ERATO Systems Biology Workbench: An Integrated Environment for Multiscale and Multitheoretic Simulations in Systems Biology |
HTML |
PDF |
PS |
| 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.) |
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Posters |
Available Formats |
| The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules |
PDF (View) |
PDF (Print) |
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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. |
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| The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules |
PDF (View) |
PDF (Print) |
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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. |
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| The ERATO Systems Biology Workbench |
PDF (View) |
PDF (Print) |
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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. |
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Presentations |
Available Formats |
| The ERATO Systems Biology Workbench Project: A Simplified Framework for Application Intercommunication |
Power Point |
PDF |
HTML |
| Presentation at The O'Reilly Bioinformatics Technology Conference, Jan. 2002, by M. Hucka. |
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| The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Tools for Computational Biology |
Power Point |
PDF |
HTML |
| Presentation given by M. Hucka at the Pacific Symposium on Biocomputing 2002, Kaua'i, Hawaii, USA, Jan. 2002. |
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| Using the Systems Biology Workbench |
Power Point |
PDF |
HTML |
| Tutorial presented by M. Hucka, A. Finney and H. Sauro at ICSB2001, Caltech, Pasadena, CA, 4th November 2001. |
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| Overview of the Systems Biology Workbench |
Power Point |
PDF |
HTML |
| The High Level SBW Libraries |
Power Point |
PDF |
HTML |
| Experimental Prototype |
Power Point |
PDF |
HTML |
| The ERATO Systems Biology Workbench |
Power Point |
PDF |
HTML. |
| Presentation at In Silico Technologies in Drug Discovery, Bethesda, MD, USA, May 21-23, 2000 by Michael Hucka. |
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| The ERATO Systems Biology Workbench |
Power Point |
PDF |
HTML |
| Presentation at The First International Conference on Systems Biology (ICSB2000), Tokyo, Japan, November 2000 by Hamid Bolouri. |
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