Computational Systems Biology
Sauro Lab
University of Washington
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What is SBW 
Research Impact 
Published Papers 
Lab Members 
Available Positions 
CSB Links 
 
 
 
Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
4. WinSCAMP
5. Matlab Interface
6. Optimization
6. Bifurcation
 
maintained by Frank Bergmann
 
 
 

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.
Systems Biology Workbench Perl Programmer's Manual HTML PDF PS
Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
Updated 3 July 2002.
Systems Biology Workbench C++ Programmer's Manual HTML PDF PS
Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri, Frank Bergmann
Updated 21 October, 2004.
Systems Biology Workbench C Programmer's Manual HTML PDF PS
Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri, Frank Bergmann
Updated 21 October, 2004.
Systems Biology Workbench Delphi/Kylix Programmer's Manual HTML PDF PS
Herbert Sauro, Michael Hucka, Andrew Finney, Hamid Bolouri
Updated 12 December, 2004.
Systems Biology Workbench Python Programmer's Manual HTML PDF PS
Herbert Sauro, Michael Hucka, Andrew Finney, Hamid Bolouri
12 April 2002.
Systems Biology Workbench Standard Modules and Menus HTML PDF PS
Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
Updated 3 July 2002.
Systems Biology Workbench Module Programmer's Manual HTML PDF PS
Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri
31 May 2002.
The SBW-CORBA Gateway HTML PDF PS
Michael Hucka and Andrew Finney
31 May 2002.

Papers

Available Formats
Introduction to the Systems Biology Workbench HTML PDF PS
M. Hucka, H. Sauro, A. Finney, H. Bolouri
Updated 8 August 2003.
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.
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.
The Systems Biology Workbench Concept Demonstrator: Design and Implementation HTML PDF PS
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 HTML PDF PS
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 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.)

Posters

Available Formats
The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules PDF (View) PDF (Print)
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 PDF (View) PDF (Print)
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 PDF (View) PDF (Print)
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

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.
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.
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.
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.
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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