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IMPORTANT NOTE: I moved to the University of Delaware and therefore this page is no longer updated. Please refer to my new web page for information about my current work. (08/31/2007)



Journal Articles:

  1. K. Bhatia, M. Taufer, B. Stearn, R. Zamudio, D. Catarino: Integrate GridFTP into Firefox - Build grid protocols into Mozilla-based tools. IBM developerWorks, 10 Oct 2006.

  2. M. Taufer, M. Crowley, D. Price, A. Chien, and C.L. Brooks III: Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics. Concurrency and Computation: Practice and Experience, Volume 17, Issue 14, December 2005, Pages: 1627-1641.
    Note: Extended version of the paper presented at HiCOMB 2004.

  3. P. Cicotti, M. Taufer, and A. Chien: DGMonitor: a Performance Monitoring Tool for Sandbox-based Desktop Grid Platforms. The Journal of Supercomputing. Springer Science Business Media B.V., Formerly Kluwer Academic Publishers B.V. Volume 34, Number 2, November 2005, Pages: 113 – 133.
    Note: Extended version of the paper presented at PMEO-PDS 2004.

  4. K. Baldridge, J.P. Greenberg, W. Sudholt, K. Bhatia, S. Mock, C. Amoreira, Y. Potier, and M. Taufer: The Computational Chemistry Prototyping Environment. Proceedings of the IEEE Special Issue on Grid Computing, Volume: 93 , Issue: 3 , March 2005, Pages:510 - 521.

  5. M. Taufer, C. An, A. Kerstens , and C.L. Brooks III: Predictor@Home: A Protein Structure Prediction Supercomputer Based on Global Computing. IEEE Transactions on Parallel and Distributed Systems. In Press, 2005
    Note: Extended version of the paper presented at HiCOMB 2005.


Papers in Refereed Conferences, Symposiums, and Workshop

Research papers (peer-reviewed)


  1. T. Estrada, D. Flores, M. Taufer, P. Teller, A. Kerstens, and D. Anderson: The Effectiveness of Threshold-based Scheduling Policies in BOINC Projects. In Proceedings of the 2st IEEE International Conference on e-Science and Grid Technologies (eScience 2006). December 2006, Amsterdam, The Netherlands.


  2. T. Estrada, A. Licon, and M. Taufer: CompPknots: a Framework for Parallel Prediction and Comparison of RNA Secondary Structures with Pseudoknots. In Proceedings of 1stWorkshop on High Performance Computing in Genomic, Proteomic and Transcriptomic, in conjunction with ISPA 2006, December 2006, Sorrento, Italy.


  3. G. Aguilera, P.J. Teller, M. Taufer, and F. Wolf: A Systematic Multi-step Methodology for Performance Analysis of Communication Traces of Distributed Applications based on Hierarchical Clustering. In the Proceedings of 5th International Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems (PMEO-PDS 2006), in conjunction with IPDPS 2006, April 2006, Rhodes Island, Greece.
    Available data: abstract, paper.


  4. M. Taufer, P.J. Teller, D. P. Anderson, and C.L. Brooks III: Metrics for Effective Resource Management in Global Computing Environments. Proceedings of the 1st IEEE International Conference on e-Science and Grid Technologies (eScience 2005). December 2005. Melbourne, Australia.
    Available data: paper, talk.


  5. M. Taufer, C. An, A. Kerstens, and C.L. Brooks III: Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing. Proceedings of the Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), in conjunction with IPDPS 2005, April 2005, Denver, Colorado.
    Available data: paper, talk.


  6. M. Taufer, D. Anderson, P. Cicotti, and C.L. Brooks III: Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. Proceedings of the 14th Heterogeneous Computing Workshop (HCW 2005), in conjunction with IPDPS 2005, April 2005, Denver, Colorado.
    Available data: paper, talk.


  7. M. Taufer, M. Crowley, D. Price, A. Chien, and C.L. Brooks III: Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics. Proceedings of the Third IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004), in conjunction with IPDPS 2004, April 2004, Santa Fe, New Mexico.
    Available data: abstract, paper, talk.


  8. D. Kondo, M. Taufer, C.L. Brooks III, H. Casanova, and A. Chien: Characterizing and Evaluating Desktop Grids: An Empirical Study. Proceedings of IPDPS 2004, IEEE/ACM International Parallel and Distributed Processing Symposium, April 2004, Santa Fe, New Mexico.
    Available data: abstract, paper.


  9. P. Cicotti, M. Taufer, and A. Chien: DGMonitor: a Performance Monitoring Tool for Sandbox-based Desktop Grid Platforms. Proceedings of the Third International Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems (PMEO-PDS 2004), in conjunction with IPDPS 2004, April 2004, Santa Fe, New Mexico.
    Available data: abstract, paper, talk.


  10. M. Taufer, and T. Stricker: A Performance Monitor based on Virtual Global Time for Clusters of PCs. Proceedings of the IEEE International Conference on Cluster Computing 2003, December 2003, Hong Kong, China.
    Available data: paper, talk.


  11. B. Uk, M. Taufer, T. Stricker, G. Settanni, A. Cavalli, and A. Caflisch: Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform - Is efficient protein folding possible with CHARMM on the United Devices MetaProcessor? Proceedings of CCGRID 2003, IEEE International Symposium on Cluster Computing and the Grid, May 2003, Tokyo, Japan.
    Available data: paper, talk.


  12. B. Uk, M. Taufer, T. Stricker, G. Settanni, and A. Cavalli: Implementation and Characterization of Protein Folding on a Desktop Computational Grid – Is CHARMM a suitable candidate for the United Devices MetaProcessor? Proceedings of IPDPS 2003, IEEE/ACM International Parallel and Distributed Processing Symposium, April 2003, Nice, France.
    Available data: paper, talk.


  13. M. Taufer, T. Stricker, and R. Weber: Scalability and Resource Usage of an OLAP Benchmark on Clusters of PCs. Proceedings of SPAA 2002, Fourteenth ACM Symposium on Parallel Algorithms and Architectures, August 2002, Winnipeg, Manitoba, Canada.
    Available data: abstract, paper.


  14. M. Taufer, T. Stricker, G. Roos, P. Guentert: On the Migration of the Scientific Code DYANA from SMPs to Clusters of PCs and on to the Grid. Proceedings of CCGRID 2002, IEEE International Symposium on Cluster Computing and the Grid, May 2002, Berlin, Germany.
    Available data: abstract, paper, talk.


  15. M. Taufer, E. Perathoner, A. Cavalli, A. Caflisch, and T. Stricker: Performance Characterization of a Molecular Dynamics Code on PC Clusters - Is there any easy parallelism in CHARMM? Proceedings of IPDPS 2002, IEEE/ACM International Parallel and Distributed Processing Symposium, April 2002, Fort Lauderdale, Florida.
    Available data: abstract, paper, talk.


  16. M. Taufer, and T. Stricker: Accurate Performance Evaluation, Modeling and Prediction of a Message Passing Simulation Code based on Middleware. Proceedings of SC1998, ACM/IEEE Supercomputing 98, November 1998, Orlando, Florida.
    Available data: paper.


  17. P. Arbenz, M. Billeter, P. Guentert, P. Luginbuehl, M. Taufer, and U. von Matt: Molecular Dynamics Simulations on Cray Clusters using the Sciddle-PVM Environment. Lecture Notes in Computer Science 1156 A. Bode, J. Dongarra, T. Ludwig, V. Sunderam (Eds.) Presented at the Parallel Virtual Machine - EuroPVM 96, Third European PVM Conference, October 1996, Munich, Germany.
    Available data: paper.

Educational papers

  1. M. Taufer, P.J. Teller, A. Kerstens, R. Romero: Collaborative Research Tools for Students, Staff, and Faculty. In Proceedings of the International SUN Conference on Teaching and Learning, March 2006, El Paso, Texas.
    Available data: paper,talk.
Abstracts
  1. C. An, M. Taufer, and C.L. Brooks III: Predictor@home: A Multiscale, Distributed Approach for Protein Structure Prediction. Proceedings of the 6th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP6), December 2004, Gaeta, Italy.
    Available data: abstract.



Posters:

  1. D. Flores, T. Estrada, M. Taufer, P. Teller, and A. Kerstens: SimBA: a Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects. Poster in Proceedings of SC2006,  ACM/IEEE Supercomputing 06, November 2006, Tampa, Florida.

  2. M. Taufer, P.J. Teller, M. Ceberio, D.P. Anderson, R. Armen, C.L. Brooks III: DAPLDS: a Dynamically Adaptive Protein-Ligand Docking System based on Multi-Scale Modeling. Poster presented at the SC'05 Booth of the HEC along the Rio Grande Alliance, November 2005, Seattle, Washington.
    Available data: poster (pdf format, US letter).

  3. C. An, M. Taufer, and C.L. Brooks III: Predictor@home: A Multiscale, Distributed Approach for Protein Structure Prediction. The 229th ACM National Meeting, March 2005, San Diego, California.

  4. C. An, M. Taufer, and C.L. Brooks III: Predictor@home: A Multiscale, Distributed Approach for Protein Structure Prediction. Poster presented at the 6th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP6), December 2004, Gaeta, Italy.
    Available data: poster (pdf format, US letter).

  5. M. Taufer, M. Crowley, D. Price, A. A. Chien, C. L. Brooks III: Study of a Highly Accurate and Fast Protein-Ligand Docking Method based on Molecular Dynamics for Desktop Grids. Poster presented during NSF visit at The Scripps Research Institute (TSRI), The Center for Theoretical Biological Physics (CTBP), and UCSD Jacobs School of Engineering (CSE/UCSD), January 2004, La Jolla California.
    Available data: poster (pdf format, US letter).

  6. M. Taufer, M. Crowley, J. Karanicolas, P. Cicotti, A. A. Chien, C. L. Brooks III: Moving towards Desktop Grid Solutions for Large-scale Modeling Simulations in Computational Chemistry. Poster presented during NSF visit at University of California at San Diego and The Scripps Research Institute (TSRI), May 2003, La Jolla California.
    Available data: poster (pdf format, US letter).



Theses:

  1. M. Taufer: Inverting Middleware: Performance Analysis of Layered Application Codes in High Performance Distributed Computing. Dissertation ETH No. 14845, Institute for Computer Systems, Swiss Federal Institute of Technology Zurich (ETHZ), December 2002, Zurich, Switzerland. Published by Hartung Gorre Verlag Konstanz, Germany, ISBN 3-89649-821-5 ISSN 1611-0943.
    Available data: Theses web-page.


  2. M. Taufer: Development of the Parallelization of the Software Package OPAL for the Simulation of Dynamic Molecules on Supercomputers. Master Thesis, Department of Computer Science, University of Padova, December 1996, Padova, Italy.


Technical Reports:

  1. R. Zamudio, D. Catarino, M. Taufer, B. Stearn, and K. Bhatia: Topaz: a Firefox Protocol Extension for GridFTP based on Data Flow Diagrams. Technical Report UTEP-CS-06-18, University of Texas, El Paso, April 2006.

  2. D. Kondo, M. Taufer, J. Karanicolas, C. L. Brooks III, H. Casanova, and A. Chien: Characterizing and Evaluating Desktop Grids: An Empirical Study. Technical Report CS2003-069. University of California, San Diego, November 2003, La Jolla, California.

  3. P. Cicotti, M. Taufer, and A. Chien: DGMonitor: a Performance Monitoring Tool for Sandbox-based Desktop Grid Platforms. Technical Report CS2003-070, University of California, San Diego, November 2003, La Jolla, California.

  4. B. Uk, M. Taufer, T. Stricker, G. Settanni, A. Cavalli, and A. Caflisch: Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform - Is efficient protein folding possible with CHARMM on the United Devices MetaProcessor? Technical Report 386, Department of Computer Science, Swiss Federal Institute of Technology Zurich (ETHZ), November 2002, Zurich, Switzerland.

  5. B. Uk, M. Taufer, T. Stricker, G. Settanni, and A. Cavalli: Implementation and Characterization of Protein Folding on a Desktop Computational Grid – Is CHARMM a suitable candidate for the United Devices MetaProcessor? Technical Report 385, Department of Computer Science, Swiss Federal Institute of Technology Zurich (ETHZ), October 2002, Zurich, Switzerland.

  6. M. Taufer, T. Stricker, and R. Weber: Inverting Middleware Framework: Framework for Performance Analysis of Distributed OLAP Benchmarks on Clusters of PCs by Filtering and Abstracting Low Level Resource Usage. Technical Report 367, Department of Computer Science, Swiss Federal Institute of Technology Zurich (ETHZ), March 2002, Zurich, Switzerland.

  7. P. Arbenz, T. Stricker, M. Taufer, and U. von Matt: Performance Characterization and Modeling of the Molecular Simulation Code OPAL. Technical Report 310, Department of Computer Science, Swiss Federal Institute of Technology Zurich (ETHZ), November 1998, Zurich, Switzerland.






Last Change: Mar 2005
Author: Taufer Michela