PSE Publications

  • Ramakrishnan, Watson, Kafura, Ribbens, and Shaffer, " Programming Environments for Multidisciplinary Grid Communities"
  • S. Tadepalli, C. J. Ribbens and S. Varadarajan, "GEMS: A job management system for fault tolerant grid computing," in Proc. High Performance Computing Symposium 2004, J. Meyer (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, 2004, pp 59-66.
  • P. Bora, C. J. Ribbens, S. Prabhakar, G. Swaminathan, M. Chinnusamy, A. Jeyakumar and B. Diaz-Acosta, "Issues in Runtime Algorithm Selection for Grid Environments," in Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments, I. Banicescu (ed.), IEEE Press, Los Alamitos, CA, 2003, pp 80-87. Preliminary version available here.
  • Allen, N.A., L. Calzone, K.C. Chen, A. Ciliberto, N. Ramakrishnan, C.A. Shaffer, J.C. Sible, J.J. Tyson, M.T. Vass, L.T. Watson, and J.W. Zwolak, Modeling Regulatory Networks at Virginia Tech, OMICS, A Journal of Integrative Biology 7, 3(2003), 285-299. [pdf, Journal]
  • Allen, N.A., C.A. Shaffer, M.T. Vass, N. Ramakrishnan, and L.T. Watson, Improving the Development Process for Eukaryotic Cell Cycle Models with a Modeling support environment, Simulation 79, 12(Dec 2003), 674-688. [pdf, Journal]
  • Allen, N.A., C.A. Shaffer, M.T. Vass, N. Ramakrishnan, and L.T. Watson, Improving the Development Process for Eukaryotic Cell Cycle Models with a Modeling support environment. In Proceedings of the 2003 Winter Simulation Conference, S. Chick, P.J. Sanchez, D. Ferrin, and D.J. Morrice, eds., 2003, 782-790. [pdf]
  • Borisuk, M. and J.J. Tyson, Bifurcation analysis of a model of mitotic control in frog eggs, Journal of Theoretical Biology 195, (1998), 69-85. [pdf]
  • Chen, K.C., A. Csikasz-Nagy, B. Gyorffy, J. Val, B. Novak, and J.J. Tyson, Kinetic Analysis of a molecular model of the budding yeast cell cycle, Molecular Biology of the Cell 11, (January 2000), 369-391. [pdf]
  • Chen, K.C., L. Calzone, A. Csikasz-Nagy, F.R. Cross, B. Novak, and J.J. Tyson, Integrative analysis of cell cycle control in budding yeast, Molecular Biology of the Cell 15, (August 2000), 3841-3862. [pdf (preprint)]
  • He, J., L.T. Watson, N. Ramakrishnan, C.A. Shaffer, A. Verstak, J. Jiang, K. Bae, and W.H. Tranter, Dynamic Data Structures for a Direct Search Algorithm, Computational Optimization and Applications 23, 1(October 2002), 5-25. [pdf]
  • He, J., M. Sosonkina, C.A. Shaffer, J.J. Tyson, L.T. Watson, and J.W. Zwolak, ``A hierarchical parallel scheme for a global search algorithm'', in Proceedings of the High Performance Computing Symposium 2004, J. Meyer (ed.), Society for Modeling and Simulation International, San Diego, CA, 2004, 43-50. [pdf]
  • He., J., M. Sosonkina, C.A. Shaffer, J.J. Tyson, L.T. Watson, J.W. Zwolak, "A Hierarchical Parallel Scheme for Global Parameter Estimation in Systems Biology", in Proceedings of IPDPS (International Parallel and Distributed Processing Symposium) CD-ROM, Santa Fe, New Mexico, April, 2004. [pdf]
  • Marlovits, G, C.J. Tyson, B. Novak, and J.J. Tyson, Modeling {M}-phase Control in {X}enopus Oocyte Extracts: the Surveillance Mechanism for Unreplicated {DNA}, Biophysical Chemistry 72, (1998), 169-184. [.pdf]
  • Novák, B. and J.J. Tyson, Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos. Journal of Cell Science 106 (1993), 1153-1168. [pdf]
  • Novák, B. and J.J. Tyson, Quantitative analysis of a molecular model of mitotic control in fission yeast, Journal of Theoretical Biology 173, (1995), 283-305.
  • Novák, B. and J.J. Tyson, Modeling the control of DNA replication in fission yeast. Proceedings of the National Academy of Science 94, (1997), 9147-9152. [pdf]
  • Novak, B., A. Csikasz-Nagy, B. Gyorffy, K. Nasmyth, and J.J. Tyson, Model scenarios for evolution of the eukaryotic cell cycle. Phil. Transactions Royal Society London B 353, (1998), 2063-2076. [pdf]
  • Novak, B., Z. Pataki, A. Ciliberto and J.J. Tyson, Mathematical model of the cell division cycle of fission yeast Chaos 11, 1(March, 2001), 277-286. [pdf]
  • Sha W., J. Moore, K. Chen, A.D. Lassaletta, C.-S. Yi, J.J. Tyson, and J.C. Sible, Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts, Proceedings of the National Academy of Science 100, (2003), 975-980. [pdf]
  • Sveiczer, A., J.J. Tyson, and B. Novak, Modeling the fission yeast cell cycle, Briefings in Fuctional Genomics and Proteomics 2, (2004), 298-307.
  • Tyson, J.J., K. Chen, and B. Novak, Network dynamics and cell physiology, Nature Reviews Molecular Cell Biology 2, (2001), 908-916. [pdf]
  • Tyson, J.J. and B. Novak, Regulation of the Eukaryotic Cell Cycle: Molecular Antagonism, Hysteresis, and Irreversible Transitions, Journal of Theoretical Biology (2001), 249-263. [pdf]
  • Tyson, J.J., K.C. Chen, and B. Novak, Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell, Current Opinion in Cell Biology 15, 2(2003), 221-31. [pdf]
  • Vass, M., J.M. Carroll, and C.A. Shaffer, "Supporting Creativity in Problem Solving Environments," in Proceedings of the Fourth Creativity & Cognition Conference, Loughborough, Leicestershire, UK, October 2002, 31-37. [pdf]
  • Zwolak, J.W., J.J. Tyson, and L.T. Watson, "Estimating rate constants in cell cycle models," in Proc. High Performance Computing Symposium 2001, A. Tentner (ed.), Soc. for Modeling and Simulation Internat., San Diego,CA 2001, 53-57. [ pdf]
  • Zwolak, J.W., J.J. Tyson, and L.T. Watson, "Estimating Rate Constants in Cell Cycle Models" (poster). Virginia Tech Workshop on Bioinformatics and Computational Biology, March 19, 2001. Also, Annual Student Research Symposium, Virginia Tech, March 26, 2001. [ PowerPoint]
  • Zwolak, J.W., "Parameter Estimation in Biological Cell Cycle Models Using Deterministic Optimization". Masters Thesis. Virginia Tech, October 31, 2001. [pdf]
  • Zwolak, J.W., J.J. Tyson, and L.T. Watson, "Parameter Estimation in a Cell Cycle Model for Frog Egg Extracts," in Proc. High Performance Computing Symposium 2002, A. Tentner (ed.), Soc. For Modeling and Simulation Internat., San Diego, CA, 2002, 67-74. [pdf]
  • Zwolak, J.W., J.J. Tyson, and L.T. Watson, "Finding All Steady States in Biological Models"; poster presented at the International Conference on Systems Biology in Stockholm, Sweden, December 2002. [pdf]
  • Zwolak, J.W., J.J. Tyson, and L.T. Watson, "Finding all steady state solutions of chemical kinetic models" in Proc. High Performance Computing Symposium 2003, I. Banicescu (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, 2003, 47-53. [pdf]
  • S4W: A Problem Solving Environment for Wireless System Design, Dhananjay Mishra, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, Kyung K. Bae, Jian He, Alex A. Verstak, and William H. Tranter, submitted to Computing and Visualization in Science.
  • C. J. Ribbens, L. T. Watson, and C. deSa, "Toward parallel mathematical software for elliptic partial differential equations", ACM Trans. Math. Software, 19 (1993) 457--473.
  • R. Melville, S. Moinian, P. Feldmann, and L. Watson, "Sframe: An efficient system for detailed DC simulation of bipolar analog integrated circuits using continuation methods", Analog Integrated Circuits Signal Processing, 3 (1993) 163--180.
  • C. J. Ribbens, G. G. Pitts, and L. T. Watson, "Parallel ELLPACK for shared memory multiprocessors", Comput. Systems Engrg., 4 (1993) 531--540.
  • A. Goel, C. Phanouriou, F. A. Kamke, C. J. Ribbens, C. A. Shaffer, and L. T. Watson, "WBCSim: A prototype problem solving environment for wood-based composites simulations", Engrg. Computers, 15 (1999) 198--210.
  • A. Goel, C. A. Baker, C. A. Shaffer, B. Grossman, W. H. Mason, L. T. Watson, and R. T. Haftka, "VizCraft: a problem solving environment for configuration design of a high speed civil transport", sl Comput. Sci. Engrg., 3 (2001) 56--66.
  • R. Dymond, V. Lohani, D. Kibler, D. Bosch, E. J. Rubin, R. Dietz, J. Chanat, C. Speir, C. A. Shaffer, N. Ramakrishnan, and L. T. Watson, "From landscapes to waterscapes: a PSE for landuse change analysis", Engrg. Computers, 19 (2003) 9--25.
  • L. T. Watson, V. K. Lohani, D. F. Kibler, R. L. Dymond, N. Ramakrishnan, and C. A. Shaffer, "Integrated computing environments for watershed management", J. Comput. Civil Engrg., 16 (2002) 259--268.
  • N. Ramakrishnan, L. T. Watson, D. G. Kafura, C. J. Ribbens, and C. A. Shaffer, "Programming environments for multidisciplinary grid communities", Concurrency Comput.: Pract. Exper., 14 (2002) 1241--1273.
  • J. Shu, L. T. Watson, B. G. Zombori, and F. A. Kamke, "WBCSim: an environment for modeling wood-based composites manufacture", Engrg. Computers, *
  • A. Verstak, N. Ramakrishnan, L. T. Watson, J. He, C. A. Shaffer, K. K. Bae, J. Jiang, W. H. Tranter, and T. S. Rappaport, "BSML: a binding schema markup language for data interchange in problem solving environments", Sci. Programming, 11 (2003) 199--224.
  • J. He, A. Verstak, L. T. Watson, C. A. Stinson, N. Ramakrishnan, C. A. Shaffer, T. S. Rappaport, C. R. Anderson, K. Bae, J. Jiang, and W. H. Tranter, "Globally optimal transmitter placement for indoor wireless communication systems", IEEE Trans. Wireless Commun., to appear.
  • J. Shu, L. T. Watson, N. Ramakrishnan, F. A. Kamke, and B. G. Zombori, "An experiment management component for the WBCSim problem solving environment", Adv. Engrg. Software, 35 (2004) 115--123.
  • A. Verstak, N. Ramakrishnan, K. K. Bae, W. H. Tranter, L. T. Watson, J. He, C. A. Shaffer, and T. S. Rappaport, "Using hierarchical data mining to characterize performance of wireless system configurations", ACM Trans. Modeling Comput. Simulation, *
  • N. A. Allen, C. A. Shaffer, M. T. Vass, N. Ramakrishnan, and L. T. Watson, "Improving the development process for eukaryotic cell cycle models with a modeling support environment", Simulation, 79 (2003) 674--688.
  • M. Vass, N. Allen, C. A. Shaffer, N. Ramakrishnan, L. T. Watson, and J. J. Tyson, "The JigCell Model Builder and Run Manager", Bioinformatics, *
  • N. Allen, L. Calzone, K. C. Chen, A. Ciliberto, N. Ramakrishnan, C. A. Shaffer, J. C. Sible, J. J. Tyson, M. Vass, L. T. Watson, and J. Zwolak, "Modeling regulatory networks at Virginia Tech", OMICS, 7 (2003) 285--299.
  • R. Skidmore, A. Verstak, N. Ramakrishnan, T. S. Rappaport, L. T. Watson, J. He, S. Varadarajan, C. A. Shaffer, J. Chen, K. K. Bae, J. Jiang, and W. H. Tranter, "Towards integrated PSEs for wireless communications: experiences with the S4W and SitePlanner projects", ACM SIGMOBILE Mobile Comput. Commun. Rev., 8 (2004) 20--34.
  • M. Vass, C. A. Shaffer, N. Ramakrishnan, L. T. Watson, and J. J. Tyson, "The JigCell Model Builder: an error-reducing editor for creating regulatory network models", IEEE Trans. Comput. Biol. Bioinformatics, *
  • D. Mishra, C. A. Shaffer, N. Ramakrishnan, L. T. Watson, K. K. Bae, J. He, A. A. Verstak, and W. H. Tranter, " S4W: a problem solving environment for wireless system design", Comput. Visualization Sci., *
  • L. S. Auvil, C. J. Ribbens, and L. T. Watson, "Problem specific environments for parallel computing", in Proc. Scalable High Performance Computing Conf., R. Voigt (ed.), IEEE Computer Soc. Press, Los Alamitos, CA, 1992, 149--152.
  • C. A. Shaffer, L. T. Watson, and D. G. Kafura, "Component frameworks for problem solving environments in computational science", in Proc. First Symposium on Reusable Architectures and Components for Developing Distributed Information Systems, Orlando, FL, 1999, 653--656.
  • A. Goel, C. Baker, C. A. Shaffer, B. Grossman, R. T. Haftka, W. H. Mason, and L. T. Watson, "VizCraft: a multidimensional visualization tool for aircraft configuration design", in Proc. IEEE Visualization '99, San Francisco, CA, 1999, 425--428.
  • C. A. Shaffer, L. T. Watson, D. G. Kafura, and N. Ramakrishnan, "Features of problem solving environments for computational science", in Proc. High Performance Computing Symposium 2000, A. Tentner (ed.), Soc. for Computer Simulation Internat., San Diego, CA, 2000, 242--247.
  • A. Goel, C. Phanouriou, F. A. Kamke, C. J. Ribbens, C. A. Shaffer, and L. T. Watson, "WBCSim: A prototype PSE for wood-based composites simulations", in Enabling Technologies for Computational Science; Frameworks, Middleware and Environments, E. N. Houstis, J. R. Rice, E. Gallopoulos, and R. Bramley (eds.), Kluwer, Norwell, MA, 2000, 187--196.
  • E. J. Rubin, R. Dietz, S. Lingam, J. Chanat, C. Speir, R. Dymond, V. Lohani, D. Kibler, D. Bosch, C. A. Shaffer, N. Ramakrishnan, and L. T. Watson, "From landscapes to waterscapes: a PSE for landuse change analysis", in Proc. 16th IMACS World Congress, M. Deville and R. Owens (eds.), CD-ROM, Lausanne, Switzerland, 2000, 6 pages.
  • C. A. Shaffer, N. Ramakrishnan, L. T. Watson, R. Dymond, and V. Lohani, "The role of problem solving environments in watershed assessment", in Proc. Integrated Decision-Making for Watershed Management Symposium: Processes and Tools, Virginia Water Resources Research Center, Blacksburg, VA, VWRRC P7--2001, 2001, 677--690.
  • E. J. Rubin, R. Dietz, J. Chanat, C. Speir, R. Dymond, V. Lohani, D. Kibler, D. Bosch, C. A. Shaffer, N. Ramakrishnan, and L. T. Watson, "From landscapes to waterscapes: a PSE for landuse change analysis", in Proc. Integrated Decision-Making for Watershed Management Symposium: Processes and Tools, Virginia Water Resources Research Center, Blacksburg, VA, VWRRC P7--2001, 2001, 643--659.
  • A. Verstak, M. Vass, N. Ramakrishnan, C. Shaffer, L. T. Watson, K. K. Bae, J. Jiang, W. H. Tranter, and T. S. Rappaport, "Lightweight data management for compositional modeling in problem solving environments", in Proc. High Performance Computing Symposium 2001, A. Tentner (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, 2001, 148--153.
  • J. He, A. Verstak, L. T. Watson, T. S. Rappaport, C. R. Anderson, N. Ramakrishnan, C. A. Shaffer, W. H. Tranter, K. Bae, and J. Jiang, "Global optimization of transmitter placement in wireless communication systems", in Proc. High Performance Computing Symposium 2002, A. Tentner (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, 2002, 328--333.
  • A. Verstak, J. He, L. T. Watson, N. Ramakrishnan, C. A. Shaffer, T. S. Rappaport, C. R. Anderson, K. Bae, J. Jiang, and W. H. Tranter, "S4W: globally optimized design of wireless communication systems", in Proc. 16th Internat. Parallel and Distributed Processing Symp., CD-ROM, IEEE Computer Soc., Los Alamitos, CA, 2002, 8 pages.
  • K. K. Bae, J. Jiang, W. H. Tranter, C. R. Anderson, T. S. Rappaport, J. He, A. Verstak, L. T. Watson, N. Ramakrishnan, and C. A. Shaffer, "WCDMA STTD performance analysis with transmitter location optimization in indoor systems using ray-tracing technique", in Proc. IEEE 2002 Radio and Wireless Conference, Boston, MA, 2002, 123--127.
  • F. A. Kamke, L. T. Watson, B. Zombori, and J. Shu, "A web-based problem solving environment for wood-based composite applications", in Proc. Internat. Academy of Wood Science Annual Meeting, Bejing, China, 2002, 96--106.
  • J. Shu, L. T. Watson, N. Ramakrishnan, B. G. Zombori, and F. A. Kamke, "An experiment management component for the WBCSim problem solving environment", in Proc. High Performance Computing Symposium 2003, I. Banicescu (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, 2003, 23--29.
  • A. Sioson, J. I. Watkinson, C. Vasquez-Robinet, M. Ellis, M. Shukla, D. Kumar, N. Ramakrishnan, L. S. Heath, R. Grene, B. I. Chevone, K. Kafadar, and L. T. Watson, "Expresso and chips: creating a next generation microarray experiment management system", in Proc. Next Generation Software Workshop, 17th Internat. Parallel and Distributed Processing Symp., CD-ROM, IEEE Computer Soc., Los Alamitos, CA, 2003, 8 pages.
  • N. A. Allen, C. A. Shaffer, M. T. Vass, N. Ramakrishnan, and L. T. Watson, "Improving the development process for eukaryotic cell cycle models with a modeling support environment", in Proc. 2003 Winter Simulation Conf., S. Chick, P. J. Sanchez, D. Ferrin, and D. J. Morrice (eds.), 2003, 782--790.
Send comments and suggestions to: pse@cs.vt.edu
Last updated: 19 July, 2004