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
Professor and Associate Head for Graduate Studies
| Office: | 2050B Torg |
|---|---|
| Email: | naren@vt.edu |
| Phone: | (540) 231-8451 |
| Website: | http://people.cs.vt.edu/~ramakris/ |
| Office Hours: | TR: 10:00 a.m. to 12:00 p.m. |
|---|
2008
Wang P., Randhawa R., Sha er C., Cao Y., Baumann W.,
"Converting Macromolecular Regulatory Models from Deterministic to Stochastic Formulation",
High Performance Computing and Simulation Symposium (HPCS 2008), 2008.
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2007
Mishra D., Shaffer C.A., Ramakrishnan N., Watson L.T., Bae K.K., He J., Verstak A.A., Tranter W.H.,
"S4W: a problem-solving environment for wireless system design",
Softw. Pract. Exper., vol. 37, no. 14, New York, NY, USA, John Wiley & Sons, Inc., pp. 1539–1558, 2007.
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Thomas L., Shaffer C A., Mili L., Thomas E.,
"Automated Detection of Severe Surface Defects on Barked Hardwood Logs",
Forest Product Journal, vol. 57, no. 4, pp. 50–56, April, 2007.
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2006
Vass M.T., Shaffer C.A., Ramakrishnan N., Watson L.T., Tyson J.J.,
"The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models",
IEEE/ACM Trans. Comput. Biol. Bioinformatics, vol. 3, no. 2, Los Alamitos, CA, USA, IEEE Computer Society Press, pp. 155–164, 2006.
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Allen N A., Chen K C., Shaffer C A., Tyson J J., Watson L T.,
IEE Proceedings – Systems Biology,
, vol. 153, no. 1, pp. 13–21, January, 2006.
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Sauro H.M., Harel D., Kwiatkowska M., Shaffer C.A., Uhrmacher A.M., Hucka M., Mendes P., Strömback L., Tyson J.J.,
"Challenges for modeling and simulation methods in systems biology",
WSC '06: Proceedings of the 38th conference on Winter simulation: Winter Simulation Conference, pp. 1720–1730, 2006.
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Thomas E., Thomas L., Shaffer C A., Mili L.,
"Using External High-Resolution Log Scanning to Determine Internal Defect Characteristics",
Proceedings of the 15th Central Hardwood Forestry Conference, pp. 497–505, February, 2006.
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Panning T D., Watson L T., Allen N A., Shaffer C A., Tyson J J.,
"Deterministic Global Parameter Estimation for a Budding Yeast Model",
Proceedings of the 2006 High Performance Computing Symposium (HPC'06), pp. 195–201, 2006.
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Vass M., Shaffer C A., Ramakrishnan N., Watson L T., Tyson J J.,
"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.
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2005
Allen N.A., Shaffer C.A., Watson L.T.,
"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.
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2004
He J., Verstak A., Watson L T., Stinson C A., Ramakrishnan N., Shaffer C A., Rappaport T S., Anderson C R., Bae K., Jiang J., Tranter W H.,
"Globally Optimal Transmitter Placement for Indoor Wireless Communication Systems",
IEEE Transactions on Wireless Communications, vol. 3, no. 6, pp. 1906–1911, November, 2004.
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Vass M., Allen N., Shaffer C.A., Ramakrishnan N., Watson L.T., Tyson J.J.,
"The JigCell Model Builder and Run Manager",
Bioinformatics, vol. 20, no. 18, Oxford, UK, Oxford University Press, pp. 3680–3681, 2004.
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Skidmore R.R., Verstak A., Ramakrishnan N., Rappaport T.S., Watson L.T., He J., Varadarajan S., Shaffer C.A., Chen J., Bae K., Jiang J., Tranter W.H.,
"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.
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Thomas L., Mili L., Shaffer C A., Thomas E.,
"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.
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He J., Sosonkina M., Shaffer C A., Tyson J J., Watson L T., Zwolak J W., Meyer J.,
"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.
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Saraiya P., Shaffer C.A., McCrickard S.D., North C.,
"Effective features of algorithm visualizations",
Proceedings of the 35th SIGCSE technical symposium on Computer Science Education, pp. 382 - 386, March , 2004.
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2003
Allen N A., Shaffer C A., Vass M T., Ramakrishnan N., Watson L T.,
"Improving the Development Process for Eukaryotic Cell Cycle Models with a Modeling support environment",
Simulation, vol. 79, no. 12, pp. 674–688, December, 2003.
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Rubin E J., Shaffer C A., Ramakrishnan N., Watson L T., Dymond R., Kibler D., Dietz R., Chanat J., Lohani V., Bosch D., Speir C.,
"From Landscapes to Waterscapes: A PSE for Landuse Change Analysis",
Engineering with Computers, vol. 19, no. 1, pp. 9–25, July, 2003.
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Verstak A., Ramakrishnan N., Watson L.T., He J., Shaffer C.A., Bae K., Jiang J., Tranter W.H., Rappaport T.S.,
"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.
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Allen N.A., Shaffer C.A., Vass M.T., Ramakrishnan N., Watson L.T.,
"Next generation modeling II - applications: 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.
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Su Y., Murali T M., Pavlovic V., Schaffer M., Kasif S.,
"RankGene: identification of diagnostic genes based on expression data.",
Bioinformatics, vol. 19, no. 12, pp. 1578–9, 2003.
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2002
He J., Watson L.T., Ramakrishnan N., Shaffer C.A., Verstak A., Jiang J., Bae K., Tranter W.H.,
"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.
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Watson L T., Lohani V K., Kibler D F., Dymond R L., Ramakrishnan N., Shaffer C A.,
"Integrated Computing Environments for Watershed Management",
ASCE Journal of Computing in Civil Engineering, vol. 16, no. 4, pp. 259–268, October, 2002.
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Ramakrishnan N., Watson L T., Kafura D G., Ribbens C.J., Shaffer C A.,
"Programming Environments for Multidisciplinary Grid Communities",
Concurrency and Computation: Practice and Experience, vol. 13–15, pp. 1241–1273, Nov–December, 2002.
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Vass M., Carroll J.M., Shaffer C.A.,
"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.
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2001
Zaffer A A., Shaffer C A., Ehrich R W., Perez M.,
NetEdit: A Collaborative Editor,
, 2001.
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Begole J., Smith R.B., Struble C.A., Shaffer C.A.,
"Resource sharing for replicated synchronous groupware",
IEEE/ACM Trans. Netw., vol. 9, no. 6, Piscataway, NJ, USA, IEEE Press, pp. 833–843, 2001.
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Goel A., Baker C.A., Shaffer C.A., Grossman B., Watson L.T., Haftka R.T., Mason W.H.,
"VizCraft: a problem-solving environment for aircraft configuration design",
Comput. Sci. Eng., vol. 3, no. 1, Washington, DC, USA, IEEE Computer Society, pp. 56–66, 2001.
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2000
Shaffer C A., Watson L T., Kafura D G., Ramakrishnan N., Tentner A.,
"Features of Problem Solving Environments for Computational Science",
Proceedings of the 2000 High Performance Computing Symposium (HPC'00): Society for Computer Simulation International, pp. 242–247, 2000.
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Shaffer C., Watson L., Lorch M., Ramakrishnan N.,
"Features of Problem Solving Environments for Computational Science",
High Performance Computing Symposium, San Diego, CA, Society for Computer Simulation International, April 2000.
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Goel A., Phanouriou C., Kamke F A., Ribbens C.J., Shaffer C A., Watson L T.,
"WBCSim: A prototype PSE for wood-based composites simulations",
Enabling Technologies for Computational Science: Frameworks, Middleware and Environments, pp. 187-196, 2000.
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1999
Begole J., Rosson M., Shaffer C.A.,
"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.
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Goel A., Phanouriou C., Kamke F A., Ribbens C.J., Shaffer C A., Watson L T.,
"WBCSim: A Prototype Problem Solving Environment for Wood-Based Composites Simulations",
Engineering with Computers, vol. 15, no. 2, pp. 198–210, 1999.
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Begole J., Isenhour P L., Shaffer C A.,
"Can You Share JavaBeans?",
Dr. Dobb's Journal, no. 300, pp. 121–122, June, 1999.
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Goel A., Baker C., Shaffer C A., Grossman B., Haftka R., Mason W., Watson L.,
"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.
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Shaffer C A., Watson L T., Kafura D G.,
"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.
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Shah A., Lorch M.,
"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.
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1998
Begole J., Rosson M., Shaffer C.A.,
"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.
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1996
Shaffer C A., Heath L S., Nielsen J M., Yang J.,
"SWAN: A Student-Controllable Data Structure Visualization System",
Proceedings of ED-MEDIA 96, pp. 632–637, June, 1996.
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1995
Fox E A., Barnette N D., Shaffer C A., Heath L., Wake W., Nowell L T., Lee J A N., Hix D., Hartson H R.,
"Progress in Interactive Learning with a Digital Library in Computer Science",
Proceedings ED-MEDIA 95, World Conf. on Educational Multimedia and Hypermedia, June, 1995.
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1994
Bright J S., Shaffer C A., Nagarkatti P S., Nagarkatti M.,
"Computer Simulation of the Immune System",
Proceedings of the Fourteenth Annual Seminar of Cancer Researchers in Virginia, pp. {17}., March, 1994.
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1993
Shaffer C.A., Brown P.R.,
"A Paging Scheme for Pointer-Based Quadtrees",
SSD '93: Proceedings of the Third International Symposium on Advances in Spatial Databases, London, UK, Springer-Verlag, pp. 89–104, 1993.
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Shankar J., Ribbens C.J., Haftka R T., Watson L T.,
"Computational study of a nonhierarchical decomposition algorithm",
Comput. Optim. Appl., vol. 2, pp. 273–293, 1993.
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1992
Shaffer C A., Herb G M.,
"A Real-Time Robot Arm Collision Avoidance System",
IEEE Transactions on Robotics, vol. 8, no. 2, pp. 149–160, 1992.
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Shaffer C A.,
Data representations for Geographic Information Systems,
, vol. 27, Medford, NJ, American Society for Information Science, pp. 135–172, 1992.
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Shaffer C.A., Feustel C.D.,
Exact computation of 2–D intersections,
, San Diego, CA, USA, Academic Press Professional, Inc., pp. 188–192, 1992.
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Ryan T.L., Shaffer C.A.,
Device Independent Perspective Volume Rendering Using Octrees,
, Blacksburg, VA, USA, Virginia Polytechnic Institute && State University, 1992.
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1991
Shaffer C.A.,
"Real-time robot arm collision detection for telerobotics",
Comput. Electr. Eng., vol. 17, no. 3, Tarrytown, NY, USA, Pergamon Press, Inc., pp. 205–215, 1991.
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Shaffer C.A., Stout Q.F.,
"Linear time distance transforms for quadtrees",
CVGIP: Image Underst., vol. 54, no. 2, Orlando, FL, USA, Academic Press, Inc., pp. 215–223, 1991.
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Lattanzi M.R., Shaffer C.A.,
"An optimal boundary to quadtree conversion algorithm",
CVGIP: Image Underst., vol. 53, no. 3, Orlando, FL, USA, Academic Press, Inc., pp. 303–312, 1991.
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1990
Oskard D N., Hong T -H., Shaffer C A.,
"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.
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Refinement and Analysis of Log Surface Defect Detection Methods using High-Resolution Laser Scanner
Granting Institution: USDA Forest Service
Amount: $50,000