The ERATO Systems Biology Workbench: Architectural Evolution

Systems biology researchers make use of a large number of different software packages for computational modeling and analysis as well as data manipulation and visualization. To help developers easily provide the ability for their applications to communicate with other tools, we have developed a simple, open-source, application integration framework, the ERATO Systems Biology Workbench (SBW). In this paper, we discuss the architecture of SBW, focusing on our motivations for various design decisions including the choice of the message-oriented communications infrastructure.

[1]  Mitsuhisa Sato,et al.  Ninf: A Network Based Information Library for Global World-Wide Computing Infrastructure , 1997, HPCN Europe.

[2]  G. Allen,et al.  The Cactus Code: a problem solving environment for the grid , 2000, Proceedings the Ninth International Symposium on High-Performance Distributed Computing.

[3]  西 和人,et al.  MIME(Multipurpose Internet Mail Extensions)について , 1993 .

[4]  David Sweet,et al.  KDE 2.0 Development , 2000 .

[5]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .

[6]  Pedro Mendes,et al.  ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources , 2001, Bioinform..

[7]  Conrad Hughes,et al.  Java Network Programming , 1997 .

[8]  M.I.T. Press,et al.  The International Journal of Supercomputer Applications and High Performance Computing— , 1994 .

[9]  Masaru Tomita,et al.  E-CELL: software environment for whole-cell simulation , 1999, Bioinform..

[10]  Herbert M. Sauro,et al.  33 JARNAC: a system for interactive metabolic analysis , 2000 .

[11]  Andreas Kremling,et al.  Application of the process modeling tool PROMOT to the modeling of metabolic networks , 2000 .

[12]  Steve Vinoski,et al.  CORBA: integrating diverse applications within distributed heterogeneous environments , 1997, IEEE Commun. Mag..

[13]  Ian T. Foster,et al.  The Nexus Approach to Integrating Multithreading and Communication , 1996, J. Parallel Distributed Comput..

[14]  J C Schaff,et al.  Physiological modeling with virtual cell framework. , 2000, Methods in enzymology.

[15]  Guy Eddon,et al.  Inside Distributed COM , 1998 .

[16]  Henri Casanova,et al.  Netsolve: a Network-Enabled Server for Solving Computational Science Problems , 1997, Int. J. High Perform. Comput. Appl..

[17]  Dennis Gannon,et al.  A component based services architecture for building distributed applications , 2000, Proceedings the Ninth International Symposium on High-Performance Distributed Computing.

[18]  Nigel H. Goddard,et al.  Towards NeuroML: model description methods for collaborative modelling in neuroscience. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[19]  Igor Goryanin,et al.  Mathematical simulation and analysis of cellular metabolism and regulation , 1999, Bioinform..

[20]  P Mendes,et al.  Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. , 1997, Trends in biochemical sciences.

[21]  D. Box,et al.  Simple Object Access Protocol (SOAP) 1.1, W3C Note , 2000 .

[22]  Hiroaki Kitano,et al.  The ERATO Systems Biology Workbench: An Integrated Environment for Multiscale and Multitheoretic Simulations in Systems Biology , 2001 .