CI Publications

Cyberinfrastructure Publications

(See Publications for an Extended List of Publications)

Journal Papers


1. J. Rappleye, M. Innus, C.M. Weeks, and R. Miller, SnB v2.2: An Example of Crystallographic Multiprocessing, Journal of Applied Crystallography 35, 2002, pp. 374-376. Paper.pdf
2. M.L. Green and R. Miller, Grid computing in Buffalo, New York, Annals of the European Academy of Sciences, 2003, pp. 191-218. Paper.pdf
3. M.L. Green and R. Miller, A client-server prototype for application grid-enabling template design, Parallel Processing Letters, Vol. 14, No. 2 (2004), pp. 241-253. Paper.pdf Paper.ps
4. M.L. Green and R. Miller, Molecular structure determination on a computational & data grid, Parallel Computing Journal 30 (2004), pp. 1001-1017. Paper.pdf
5. M.L. Green and R. Miller, Evolutionary molecular structure determination using grid-enabled data mining, Parallel Computing Journal 30 (2004), pp. 1057-1071. Paper.pdf
6. C.L. Ruby, M.L. Green, and R. Miller, The Operations Dashboard: A Collaborative Environment for Monitoring Virtual Organization-Specific Compute Element Operational Status, Parallel Processing Letters, Vol. 16, No. 4 (2006), pp. 485-500. Paper.pdf
7. R. Miller, N. Shah, M. Green, W. Furey, and C. Weeks, Shake-and-Bake on the grid, Journal of Applied Crystallography 40, 2007, pp. 938-944. Paper.pdf

   Workshop Papers
   

8. M.L. Green and R. Miller, Molecular structure determination on a computational & data grid, BioGrid'04: Second International Workshop on Biomedical Computations on the Grid, 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2004), 2004. Paper.pdf
9. M.L. Green and R. Miller, Evolutionary molecular structure determination using grid-enabled data mining, BioGrid'04: Second International Workshop on Biomedical Computations on the Grid, 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2004), 2004. Paper.pdf

   Book Chapters
   

10. R. Miller and M.L. Green, Molecular Structure Determination on a Computational and Data Grid, Parallel Computing in Bioinformatics and Computational Biology, A. Zomaya, ed., John Wiley & Sons, Ltd., New Jersey, 2006, pp. 583-621. Paper.pdf
11. C.L. Ruby and R. Miller, Effectively Managing Data on a Grid, Handbook of Parallel Computing: Models, Algorithms, and Applications, S. Rajasekaran and J. Reif, eds., CRC Press, 2007, in press.
12. J.J. Bednasz, K. Chiu, S.M. Gallo, M. Govindaraju, M. Lewis, R. Miller, C.L. Ruby, and C.M. Weeks, Cyberinfrastructure in New York State, Grid Computing: Infrastructure, Service, and Application, L. Wang and W. Jie, eds., CRC Press, 2009, in press.

    Conference Papers
    

13. I. Foster, J. Gieraltowski, S. Gose, N. Maltsev, A. Rodriguez, D. Dulakhe, A. Vaniachine, J. Shank, S. Youssef, D. Adams, R. Baket, W. Deng, J. Smith, D. Yu, I. Legrand, S. Singh, C. Steenberg, A. Afaq, E. Berman, J. Annis, L.A.T. Bauerdick, M. Ernst, I. Fisk, L. Giacchetti, G. Graham, A. Heavy, J. Kaiser, N. Kuropatkin, R. Pordes, V. Sekhri, J. Weigand, Y. Wu, K. Baker, L. Sorrillo, J. Huth, M. Allen, L. Grundhoefer, J. Hicks, F. Luehring, S. Peck, R. Quick, S. Simms, G. Fekete, J. vandenBerg, K. Cho, K. Kwon, D. Son, H. Park, S. Canon, K. Jackson, D.E. Konerding, J. Lee, D. Olson, I. Sakrejda, B. Tierney, M. Green, R. Miller, J. Letts, T. Martin, D. Bury, C. Dumitrescu, D. Engh, R. Gardner, M. Mambelli, Y. Smirnov, J. Voeckler, M. Wilde, Y. Zhao, X. Zhao, P. Avery, R. Cavanaugh, B. Kim, C. Prescott, J. Rodriguez, A. Zahn, S. McKee, C. Jordan, J. Prewett, T. Thomas, H. Severini, B. Clifford, E. Deelman, L. Flon, C. Kesselman, G. Mehta, N. Olomu, K. Vahi, K. De, P. Couvares, A. De Smet, C. Kireyev, E. Paulson, A. Roy, S. Koranda, B. Moe, B. Brown, and P. Sheldon, The Grid2003 production grid: principles and practice, IEEE International Symposium on High-Performance Distributed Computing, HPDC-2004, June 4-6, 2004, Honolulu, Hawaii, pp. 236-245.
14. M.L. Green, S.M. Gallo, and R. Miller, vrid-enabled virtual organization based dynamic firewall, Grid Workshop, SC2004, Pittsburgh, PA, November, 2004.
15. C.L. Ruby, M.L. Green, and R. Miller, The operations dashboard: an interactive, collaborative environment for monitoring virtual organization-specific compute element operational status, 2006 International Conference on Computational Science and Education, Rochester, NY, August, 2006.
16. A. Ghadersohi, M.L. Green, D. Pape, and R. Miller, A reliable and robust software architecture for distributed collaborative Visualization, 2006 International Conference on Computational Science and Education, Rochester, NY, August, 2006.
17. J. Bednasz, S. Gallo, R. Miller, C. Ruby, and C. Weeks, Grid Computing in New York State, USA, Second International Workshop on Semantic and Grid Computing (SGC07), The Fifth International Symposium on Parallel and Distributed Processing and Applications (ISPA-2007): Frontiers of High Performance Computing and Networking - ISPA 2007 Workshops: ISPA 2007 International Workshops SSDSN, UPWN, WISH, SGC, ParDMCom, HiPCoMB, and IST-AWSN, Niagara Falls, Canada, August 2007, Proceedings, P. Thulasiraman, X. He, T.L. Xu, M.K. Denko, R.K. Thulasiram, and L.T. Yang, eds, Lecture Notes in Computer Science 4743, LNCS Springer, Germany, 2007, pp. 273-284.
18. R. Miller, Cyberinfrastructure and Grid Computing in New York State, 2007 AIChE Annual Meeting, November 4-9, 2007, Salt Lake City (invited).

    Conference Abstracts
    

19. R. Miller, M. L. Green, and C. M. Weeks, BnP on the Grid, Annual Meeting of the American Crystallographic Association, 06.03.01, Chicago, IL, July, 2004.
20. W. Furey, L. Pasupulati, S.A. Potter, H. Xu, R. Miller, and C.W. Weeks, Recent Developments in the BnP Package for Automated Protein Structure Determination, Annual Meeting of the American Crystallographic Association, 01.03.07, W0324, Orlando, FL, May-June, 2005.
21. A. Ghadersohi, D. Pape, C. Weeks, M. Green, and R. Miller, Shake-and-Bake Visualizer, Annual Meeting of the American Crystallographic Association, P088, W0094, Orlando, FL, May-June, 2005.
22. C. M. Weeks, S. A. Potter, N. Shah, H. Xu, M. L. Green, R. Miller, L. Pasupulati, and W. Furey, Adapting BnP for Different Computing Environments, Annual Meeting of the American Crystallographic Association, 2006.