A Workflow Management and Grid Computing Approach to Molecular Simulation-based Bio/Nano Experiments

1. Buyya, R., Branson, K., Giddy, J., Abramson, D.: The Virtual Laboratory: A Toolset for Utilising the World-Wide Grid to Design Drugs, Proceedings of 2nd IEEE International Symposium on Cluster Computing and the Grid, May 2002, Berlin, Germany.

   Google Scholar 

2. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M.: CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, Journal of Computational Chemistry, Vol. 4, 1983.

   Google Scholar 

3. Carriero, N. and Gelernter, D.: How to Write Parallel Programs, The MIT Press, 1990.

   Google Scholar 

4. Chin, G., Schuchardt, K., Myers, J., and Gracio, D.: Participatory Workflow Analysis: Unveiling Scientific Research Processes with Scientists, Proc. of the 6th Biennial Participatory Design Conference, 2000.

   Google Scholar 

5. Foster, I., Kesselman, C., Tuecke, S.: The Anatomy of the Grid: Enabling Scalable Virtual Organizations, International J. Supercomputer Applications, Vol 15., No. 3, 2001.

   Google Scholar 

6. Foster, I., Kesselman, C., Nick, J., Tuecke, S.: The Physiology of the Grid: An Open Grid Services, Architecture for Distributed Systems Integration, Jan. 2002.

   Google Scholar 

7. Freeman, E., Hupfer, S., and Arnold, K.: JavaSpaces Principles, Patterns and Practice, Addison Wesley, 1999.

   Google Scholar 

8. Frenkel, D. and Smit, B.: Understanding Molecular Simulation, Academic Press, 2002.

   Google Scholar 

9. The Official Gaussian Home Page: http://www.gaussian.com/.

10. Goble, C.: The low down on e-science and grids for biology, Comparative and Functional Genomics, Vol. 2, pp. 365–370, 2001.

    Article  Google Scholar 

11. James, H., Hawick, K., and Coddington, P.: An Environment for Workflow Applications on Wide-Area Distributed Systems, Hawaii International Conference on System Sciences, 2001.

    Google Scholar 

12. Jeong, K., Talla, S., Wyckoff, P., and Shasha, D.: An Approach to Fault Tolerant Parallel Processing on Intermittently Idle, Heterogeneous Workstations, Proc. the 27th International Symposium on Fault-Tolerant Computing, Jun. 1997.

    Google Scholar 

13. Kim, H., Jeong, K., Lee, S. and Jung, S.: Molecular Modeling of the Chiral Recognition of Propranolol Enantiomers by a β-Cyclodextrin, Bulletin of Korean Chemical Society, Vol. 24, No. 1, 2003.

    Google Scholar 

14. Kochut, K., Arnold, J., Sheth, A., Miller, J., Kraemer, E., Arpinar, B., Cardoso, J.: IntelliGEN: A Distributed Workflow System for Discovering Protein-Protein Interactions, International Journal on Distributed and Parallel Databases, Special Issue on Bioinformatics, 2002.

    Google Scholar 

15. Krishnakumar, N. and Sheth, A.: Managing Heterogeneous Multi-system Tasks to Support Enterprise-wide Operations, Distributed and Parallel Database Journal, Vol. 3, No. 2, 1995.

    Google Scholar 

16. Natrajan, A., Crowley, M., Wilkins-Diehr, N., Humphrey, M., Fox, A. and Grimshaw, A.: Studying Protein Folding on the Grid: Experiences using CHARMM on NPACI Resources under Legion, Proceeding of the HPDC Conference, San Francisco, CA, USA, Aug 7–9, 2001.

    Google Scholar 

17. Peleg, M., Yeh, I., and Altman, R.: Modeling biological processes using Workflow and Petri Net models, Bioinformatics, vol. 18, pp. 825–837, 2002.

    Article  Google Scholar 

18. Riempp, G.: Wide-Area Workflow Management, Springer-Verlag, 1998.

    Google Scholar 

19. Sun Microsystems, Jini Specifications, Available from Sun Microsystems WWW Site (http://java.sun.com/products/javaspaces), 1998.

20. Weske, M., Vossen, G., and Medeiros, C.: Scientific Workflow Management: WASA Architecture and Applications, Architecture and Applications, Fachbericht Angewandte Mathematik und Informatik 03/96-I, Universitat Munster, 1996.

    Google Scholar 

21. Wyckoff, P., McLaughry, S., Lehman, T., Ford, D.: TSpaces, IBM System Journal, 1998.

    Google Scholar 

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