Documents
Manuals
Systems Biology Workbench Java Programmer's Manual
HTML
PDF
PS
Michael Hucka, Andrew Finney, Herbert Sauro, Hamid
Bolouri
Updated 3 July 2002.
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
HTML
PDF
PS
Andrew Finney, Michael Hucka, Herbert Sauro, Hamid
Bolouri
Updated 18 February 2003.
Systems Biology Workbench C Programmer's Manual
HTML
PDF
PS
Andrew Finney, Michael Hucka, Herbert Sauro, Hamid
Bolouri
26 February 2002.
Systems Biology Workbench Delphi/Kylix Programmer's
Manual
HTML
PDF
PS
Herbert Sauro, Michael Hucka, Andrew Finney, Hamid
Bolouri
26 February 2002.
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
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
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
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
Presented by M. Hucka at the Third Workshop
on Software Platforms for Systems Biology, Caltech, June 2001.
The High Level SBW Libraries
Power Point
PDF
HTML
Presented by A. Finney at the Third Workshop on Software Platforms for Systems Biology, Caltech, June 2001.
Experimental Prototype
Power Point
PDF
HTML
Presented by H. Sauro at the Third Workshop on Software Platforms for Systems Biology, Caltech, June 2001.
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.