Problem Solving Environments
| The primary goal of our research is to design and develop computing systems and infrastructure that will help computational scientists get their work done more efficiently. The term problem-solving environment (PSE) refers to a problem-oriented computing environment that supports the entire range of scientific computational problem-solving activity: from problem formulation, to algorithm selection, to numerical simulation, to solution visualization. Furthermore, a PSE should support collaboration among people separated in space and time, using a diverse set of codes and machines. |
The particular strengths we bring to this topic include: object-oriented distributed computing, collaboration, parallel computation, artificial intelligence, and human-computer interaction. Our strategy has been to collaborate with practicing scientists and engineers at Virginia Tech, seeking to understand their unique problem-solving context, and building PSEs and PSE-building infrastructure that will assist them in their work.
Naren Ramakrishnan
Thomas L. Phillips Professor of Engineering
| Office: | 2050B Torg |
|---|---|
| Email: | naren@vt.edu |
| Phone: | (540) 231-8451 |
| Website: | http://people.cs.vt.edu/~ramakris/ |
| Office Hours: | TR: 9:00 to 11:00 a.m. |
|---|
2011
Lin, S., and D. G. Tatar,
"Encouraging parallel thinking through explicit coordination modeling",
SIGCSE ’11: Proceedings of the 42nd ACM technical symposium on Computer science education, New York, NY, USA, ACM, pp. 441–446, 2011.
Deshpande, S., L. T. Watson, J. Shu, and F. A. Kamke,
"Data driven surrogate-based optimization in the problem solving environment WBCSim",
Engrg. with Computers, vol. 27, pp. 211--223, 2011.
2009
Ahn, T. - H., P. Wang, L. T. Watson, Y. Cao, C. A. Shaffer, and W. T. Baumann,
"Stochastic cell cycle modeling for budding yeast",
Proceedings of 2009 Spring Simulation Multiconference: HPC, G. Wainer, M. Chinni, P. Roman, H. Rajaei, B. Zeigler, and C. Ribbens (eds.), Soc. for Modeling Simulation Internat., San Diego, CA, SCS, pp. 569-574, 03/2009.
Randhawa, R., C. A. Shaffer, and J. J. Tyson,
"Model aggregation: a building-block approach to creating large macromolecular regulatory networks",
Bioinformatics, vol. 25, no. 24, pp. 3289-3295, 2009.
2008
Wang, P., R. Randhawa, C. A. Shaffer, Y. Cao, and W. T. Baumann,
"Converting Macromolecular Regulatory Models from Deterministic to Stochastic Formulation",
Proceedings of High Performance Computing and Simulation 2008 (HPCS 2008), pp. 385–392, April, 2008.
Shu, J., L. T. Watson, N. Ramakrishnan, F. A. Kamke, and C. North,
"Unification of problem solving environment implementation layers with XML-based specifications",
Advances in Engineering Software, vol. 39, no. 3, pp. 189-201, March, 2008.
2007
Mishra, D., 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",
Software: Practice & Experience, vol. 37, no. 14, New York, NY, USA, John Wiley & Sons, Inc., pp. 1539–1558, 2007.
Thomas, L., C. A. Shaffer, L. Mili, and E. Thomas,
"Automated Detection of Severe Surface Defects on Barked Hardwood Logs",
Forest Product Journal, vol. 57, no. 4, pp. 50–56, April, 2007.
Thomas, E., L. Thomas, and C. A. Shaffer,
"Defect detection on hardwood logs using high resolution laser scan data",
Proceedings of the 15th International Symposium on Non-Distructive Testing of Wood, August, 2007.
Randhawa, R., C. A. Shaffer, and J. J. Tyson,
"Fusing and Composing Macromolecular Regulatory Network Models",
Proceedings of the 2007 High Performance Computing Symposium (HPC 2007), pp. 337–344, March, 2007.
2006
Thomas, L., L. Mili, E. Thomas, and C. A. Shaffer,
"Defect Detection on Hardwood Logs Using Laser Scanning",
Wood and Fiber Science, vol. 38, no. 4, pp. 682–695, October, 2006.
Allen, N. A., K. C. Chen, C. A. Shaffer, J. J. Tyson, and L. T. Watson,
"Computer Evaluation of Network Dynamics Models with Application to Cell Cycle Control in Budding Yeast",
IEE Proceedings – Systems Biology, vol. 153, no. 1, pp. 13–21, January, 2006.
Shaffer, C. A., R. Randhawa, and J. J. Tyson,
"The role of composition and aggregation in modeling macromolecular regulatory networks",
WSC '06: Proceedings of the 38th conference on Winter simulation: Winter Simulation Conference, pp. 1628–1636, 2006.
Thomas, E., L. Thomas, C. A. Shaffer, and L. Mili,
"Using External High-Resolution Log Scanning to Determine Internal Defect Characteristics",
Proceedings of the 15th Central Hardwood Forestry Conference, pp. 497–505, February, 2006.
Panning, T. D., L. T. Watson, N. A. Allen, C. A. Shaffer, and J. J. Tyson,
"Deterministic Global Parameter Estimation for a Budding Yeast Model",
Proceedings of the 2006 High Performance Computing Symposium (HPC'06), pp. 195–201, 2006.
Vass, M., C. A. Shaffer, N. Ramakrishnan, L. T. Watson, and J. J. Tyson,
"The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. Vol. 3, no. 2, pp. 155–164, April-June, 2006.
Polys, N., D. Bowman, C. North, R. Laubenbacher, and K. Duca,
"PathSim Visualizer: An Information-Rich Virtual Environment for Systems Biology",
Web3D Symposium, Monterey, CA, ACM Press, 2006.
Abstract
2005
Allen, N. A., C. A. Shaffer, and L. T. Watson,
"Building modeling tools that support verification, validation, and testing for the domain expert",
WSC '05: Proceedings of the 37th conference on Winter simulation: Winter Simulation Conference, pp. 419–426, 2005.
2004
He, J., A. Verstak, L. T. Watson, C. A. Stinson, N. Ramakrishnan, C. A. Shaffer, T. S. Rappaport, C. R. Anderson, K. Bae, J. Jiang, et al.,
"Globally Optimal Transmitter Placement for Indoor Wireless Communication Systems",
IEEE Transactions on Wireless Communications, vol. 3, no. 6, pp. 1906–1911, November, 2004.
Vass, M., N. Allen, C. A. Shaffer, N. Ramakrishnan, L. T. Watson, and J. J. Tyson,
"The JigCell Model Builder and Run Manager",
Bioinformatics, vol. 20, no. 18, Oxford, UK, Oxford University Press, pp. 3680–3681, 2004.
Skidmore, R. R., A. Verstak, N. Ramakrishnan, T. S. Rappaport, L. T. Watson, J. He, S. Varadarajan, C. A. Shaffer, J. Chen, K. K. Bae, et al.,
"Towards integrated PSEs for wireless communications: experiences with the S4W and SitePlanner\textregistered projects",
SIGMOBILE Mob. Comput. Commun. Rev., vol. 8, no. 2, New York, NY, USA, ACM, pp. 20–34, 2004.
Thomas, L., L. Mili, C. A. Shaffer, and E. Thomas,
"Defect Detection on Hardwood Logs Using High Resolution Three-dimensional Laser Scan Data",
IEEE International Conference on Image Processing, ICIP, pp. 243–246, October, 2004.
He, J., M. Sosonkina, C. A. Shaffer, J. J. Tyson, L. T. Watson, J. W. Zwolak, and J. Meyer,
"A Hierarchical Parallel Scheme for a Global Search Algorithm",
Proceedings of the 2004 High Performance Computing Symposium (HPC'04): Society for Modeling and Simulation International, pp. 43–50, 2004.
2003
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, vol. 79, no. 12, pp. 674–688, December, 2003.
Rubin, E. J., C. A. Shaffer, N. Ramakrishnan, L. T. Watson, R. Dymond, D. Kibler, R. Dietz, J. Chanat, V. Lohani, D. Bosch, et al.,
"From Landscapes to Waterscapes: A PSE for Landuse Change Analysis",
Engineering with Computers, vol. 19, no. 1, pp. 9–25, July, 2003.
Verstak, A., 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. Program., vol. 11, no. 3, Amsterdam, The Netherlands, The Netherlands, IOS Press, pp. 199–224, 2003.
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",
WSC '03: Proceedings of the 35th conference on Winter simulation: Winter Simulation Conference, pp. 782–790, 2003.
Allen, N., L. Calzone, K. C. Chen, A. Ciliberto, N. Ramakrishnan, C. A. Shaffer, J. C. Sible, J. J. Tyson, M. Vass, L. T. Watson, et al.,
"Modeling Regulatory Networks at Virginia Tech",
Omics Journal of Integrative Biology, vol. Vol. 7, no. 3, pp. pages 285–300, Fall, 2003.
Dymond, R., V. Lohani, D. Kibler, D. Bosch, E. J. Rubin, R. Dietz, J. Chanat, C. Speir, C. A. Shaffer, N. Ramakrishnan, et al.,
"From landscapes to waterscapes: a PSE for landuse change analysis",
Engineering with Computers, vol. 19, pp. 9–25, 2003.
2002
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",
Comput. Optim. Appl., vol. 23, no. 1, Norwell, MA, USA, Kluwer Academic Publishers, pp. 5–25, 2002.
Watson, L. T., V. K. Lohani, D. F. Kibler, R. L. Dymond, N. Ramakrishnan, and C. A. Shaffer,
"Integrated Computing Environments for Watershed Management",
ASCE Journal of Computing in Civil Engineering, vol. 16, no. 4, pp. 259–268, October, 2002.
Ramakrishnan, N., L. T. Watson, D. G. Kafura, C. J. Ribbens, and C. A. Shaffer,
"Programming Environments for Multidisciplinary Grid Communities",
Concurrency and Computation: Practice and Experience, vol. 13–15, pp. 1241–1273, Nov–December, 2002.
Vass, M., J. M. Carroll, and C. A. Shaffer,
"Supporting creativity in problem solving environments",
C&C '02: Proceedings of the 4th conference on Creativity & cognition, New York, NY, USA, ACM, pp. 31–37, 2002.
2001
Goel, A., 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",
Computer Science and Engineering, vol. 3, no. 1, pp. 56–66, 2001.
2000
Shaffer, C. A., L. T. Watson, D. G. Kafura, N. Ramakrishnan, and A. Tentner,
"Features of Problem Solving Environments for Computational Science",
Proceedings of the 2000 High Performance Computing Symposium (HPC'00), San Diego, CA, Society for Computer Simulation International, pp. 242–247, April 2000.
Goel, A., C. Phanouriou, F. A. Kamke, C. J. Ribbens, C. A. Shaffer, and L. T. Watson,
"WBCSim: A prototype PSE for wood-based composites simulations",
Enabling Technologies for Computational Science: Frameworks, Middleware and Environments, pp. 187-196, 2000.
1999
Begole, J. M. A., M. B. Rosson, and C. A. Shaffer,
"Flexible collaboration transparency: supporting worker independence in replicated application-sharing systems",
ACM Trans. Comput.-Hum. Interact., vol. 6, no. 2, New York, NY, USA, ACM, pp. 95–132, 1999.
Goel, A., 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",
Engineering with Computers, vol. 15, no. 2, pp. 198–210, 1999.
Goel, A., C. Baker, C. A. Shaffer, B. Grossman, R. Haftka, W. Mason, and L. T. Watson,
"VizCraft: A Multidimensional Visualization Tool for Aircraft Configuration Design",
VISUALIZATION '99: Proceedings of the 10th IEEE Visualization 1999 Conference (VIS '99), Washington, DC, USA, IEEE Computer Society, 1999.
Shaffer, C. A., L. T. Watson, and D. G. Kafura,
"Component Frameworks for Problem Solving Environments in Computational Science",
Proceedings of the 1st Symposium on Reusable Architectures and Components for Developing Distributed Information Systems (RACDIS'99), pp. 653–656, August, 1999.
Shah, A., and M. Lorch,
"Symphony: A Java-based Composition and Manipulation Framework for Distributed Legacy Resources",
International Symposium on Software Engineering for Parallel and Distributed Systems, Los Angeles, CA, May 1999.
1998
Begole, J. M. A., M. B. Rosson, and C. A. Shaffer,
"Supporting worker independence in collaboration transparency",
UIST '98: Proceedings of the 11th annual ACM symposium on User interface software and technology, New York, NY, USA, ACM, pp. 133–142, 1998.
Shaffer, C. A., D. L. Knill, and L. T. Watson,
"Visualization for multiparameter aircraft designs",
VIS '98: Proceedings of the conference on Visualization '98, Los Alamitos, CA, USA, IEEE Computer Society Press, pp. 491–494, 1998.
Goel, A., 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,
, Blacksburg, VA, USA, Virginia Polytechnic Institute && State University, 1998.
1990
Oskard, D. N., T. - H. Hong, and C. A. Shaffer,
"Real-Time Algorithms and Data Structures for Underwater Mapping",
IEEE Transactions on Systems, Man, and Cybernetics, vol. 20, no. 6, pp. 1469–1475, November/Decembe, 1990.
1988
Oskard, D. N., T. - H. Hong, and C. A. Shaffer,
"Real-Time Algorithms and Data Structures for Underwater Mapping",
SPIE Symposium on Sensor Fusion: Spatial Reasoning and Scene Interpretation, November, 1988.
Refinement and Analysis of Log Surface Defect Detection Methods using High-Resolution Laser Scanner
Granting Institution: USDA Forest Service
Amount: $50,000
Stochastic Models Of Cell Cycle Regulation In Eukaryotes
Granting Institution: National Institute of General Medical Sciences
Amount: $3,424,192
TCNP Driving Biological Problem: Year 4 Renwal: Using Composition to Integerate a Cell Cycle Model with Morphological Checkpoints
Granting Institution: University of Connecticut
Amount: $20,925
TCNP Driving Biological Problems: Using Composition to Integrate a Cell Cycle Model with Morphological Checkpoints
Granting Institution: University of Connecticut
Amount: $17,738
The Eukaryotic Cell Cycle as a Test Case for Modeling Cellular Regulation in a Collaborative PSE
Granting Institution: DARPA
Amount: $2,442,399