Journal Papers

  1. J.E. Davis, B.A. Bauer, M. Taufer, and S. Patel: Molecular Dynamics Simulations of Aqueous Ions at the Liquid-Vapor Interface Accelerated Using Graphics Processors, 2009. Submitted for Review.
  2. T. Estrada, M. Taufer, and D. Anderson: Performance Prediction and Analysis of BOINC Projects: An Empirical Study with EmBOINC. Submitted to the Journal of Grid Computing, 2009 (In Press).
  3. M. Taufer, R.S. Armen, J. Chen, P.J. Teller, and C.L. Brooks III: Computational Multi-Scale Modeling in Protein-Ligand Docking. IEEE Engineering in Medicine and Biology Magazine. Volume 28, Issue 2, Pages: 58 - 69, 2009.
  4. M. Taufer, A. Licon, R. Araiza, D. Mireles, A. Gultyaev, F.H.D. Van Batenburg, M-Y Leung: PseudoBase++: An Extension of PseudoBase for Easy Searching, Formatting, and Visualization of Pseudoknots. Nucleic Acids Research. Database Issue, Volume 37, 2009. D129 doi: 10.1093/nar/gkn806
  5. M. Taufer, M-Y. Leung, T. Solorio, A. Licon, D. Mireles, R. Araiza, K.K. Johnson: RNAVLab: A Virtual Laboratory for Studying RNA Secondary Structures based on Grid Computing Technology. Journal of Parallel Computing. Volume 34, Pages: 661-680, 2008.
  6. T. Estrada, O. Fuentes, and M. Taufer: A Distributed Evolutionary Method to Design Scheduling Policies for Volunteer Computing. ACM SIGMETRICS Performance Evaluation Review Journal. Volume 36, Issue 3, Pages: 40 – 49, December 2008.
  7. 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.
  8. M. Taufer, C. An, A. Kerstens , and C.L. Brooks III: Predictor@Home: A Protein Structure Prediction Supercomputer Based on Global Computing. Submitted to IEEE Transactions on Parallel and Distributed Systems. Volume 17, Issue 8, Pages: 786 - 796, August 2006.
  9. M. Taufer, M. Crowley, D. Price, A.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, Pages: 1627-1641, December 2005.
  10. Cicotti, M. Taufer, and A.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, Pages: 113 - 133, November 2005.
  11. 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, Pages: 512 - 521, March 2005.

Book Chapters

  1. M. Taufer and C.L. Brooks III, Predictor@Home: A Protein Structure Prediction Supercomputer Based on Volunteer Computing. (2008). In: Distributed & Grid Computing – Science Made Transparent for Everyone. Principles, Applications and Supporting Communities (Weber, M.H.W., ed). Rechenkraft.net, Marburg.

Research Papers in Refereed Conferences, Symposiums, and Workshops

(peer-reviewed papers)
  1. P. McClory, E. Kissel, D. M. Swany, and M. Taufer: MNEOMIC: Network Environment for Measurement and Observation for Network Interaction and Control. To appear in Proceedings of the 1st Workshop on Grid and P2P Systems and Applications (GridPeer), held together with the 18th IEEE International Conference on Computer Communications and Networks (ICCCN), 2009.
  2. S. Kamboj, T. Estrada, M. Taufer, and K. S. Decker: Applying Organizational Self-Design to a Real-world Volunteer Computing System. To appear in Proceedings of Agent Design: Advancing from Theory to Practice (ADAPT) Workshop, 2009.
  3. J. Atlas, T. Estrada, K. Decker, and M. Taufer: Balancing Scientist Needs and Volunteer Preferences in Volunteer Computing using Constraint Optimization. In Proceedings of the International Conference on Computational Science (ICCS), May 2009, Baton Rouge, Louisiana, USA.
  4. T. Estrada, K. Reed, D. Anderson, and M. Taufer: EmBOINC: An Emulator for Performance Analysis of BOINC Projects.In Proceedings of PCGrid 2009, May 2009, Rome, Italy
  5. T. Estrada, K. Reed, and M. Taufer:Modeling Job Lifespan Delays in Volunteer Computing Projects. In Proceedings of to the 9th IEEE International Symposium on Cluster Computing and Grid (CCGrid), May 2009, shanghai, China.
  6. J.E. Davis, A. Ozsoy, S. Patel, and M. Taufer: Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors. In Proceedings of the International Conference on Bioinformatics and Computational Biology (BICoB), April 2009, New Orleans, Louisiana, USA.
  7. T. Estrada, O. Fuentes, and M. Taufer: A Distributed Evolutionary Method to Design Scheduling Policies for Volunteer Computing. In Proceedings of ACM Computing Frontiers 2008, May 2008, Ischia, Italy.
  8. M. Taufer, T. Solorio, A. Licon, D. Mireles, and M.-Y. Leung: On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks. In Proceedings of the Seventh IEEE International Workshop on High Performance Computational Biology (HiCOMB 2008), April 2008, Miami, Florida, USA.
  9. G. Lopez, M. Taufer, and P.J. Teller: Evaluation of IEEE 754 Floating-Point Arithmetic Compliance Across a Wide Range of Heterogeneous Computers. In Proceedings of the 2007 Richard Tapia Celebration of Diversity in Computing Conference, October 2007, Orlando, Florida, USA.
  10. R. Araiza, M. Taufer, and M.-Y. Leung: Towards Optimal Scheduling for Global Computing Under Probabilistic, Interval, and Fuzzy Uncertainty, with Potential Applications to Bioinformatics. In Proceedings of the 26th International Conference of the North American Fuzzy Information Processing Society (NAFIPS'2007), June 2007San Diego, California, USA.
  11. M. Taufer, A. Kerstens, T. Estrada, D.A. Flores, and P.J. Teller: SimBA: a Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects. In Proceedings of the International Workshop on Principles of Advanced and Distributed Simulation 2007 (PADS'07), June 2007, San Diego, California, USA.
  12. M. Taufer, M.-Y. Leung, K. L. Johnson, A. Licon: RNAVLab: A unified environment for computational RNA structure analysis based on grid computing technology. Sixth IEEE International Workshop on High Performance Computational Biology (HiCOMB'07), in conjunction with IPDPS'07 March 2007, Long Beach, California, USA.
  13. M. Taufer, A. Kerstens, T. Estrada, D.A. Flores, R. Zamudio, P.J. Teller, R. Armen, and C.L. Brooks III: Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. In Proceedings of the First Workshop on Large-Scale, Volatile Desktop Grids (PCGrid'07), in conjunction with IPDPS'07 March 2007, Long Beach, California, USA.
  14. R. Zamudio, D. Catarino, M. Taufer, K. Bhatia, and B. Stearn: Topaz: Extending Firefox to Accommodate the GridFTP Protocol. To appear in Proceedings of the Fourth High-Performance Grid Computing Workshop (HPGC'07), in conjunction with IPDPS'07 March 2007, Long Beach, California, USA.
  15. 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.
  16. T. Estrada, A. Licon, and M. Taufer: CompPknots: a Framework for Parallel Prediction and Comparison of RNA Secondary Structures with Pseudoknots. In Proceedings of 1st Frontier on High Performance Computing and Networking Workshop (FHPCN-06), in conjunction with ISPA 2006, December 2006, Sorrento, Italy.
  17. K. Bhatia, B. Stearn, M. Taufer, R. Zamudio, and D. Catarino: Extending Grid Protocols onto the Desktop using the Mozilla Framework. In Proceedings of the 2nd International Workshop on Grid Computing Environments (GCE 2006), in conjunction with SC 2006, November 2006, Tampa, Florida.
  18. 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 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.
  19. M. Taufer, P.J. Teller, D.P. Anderson, and C.L. Brooks III: Metrics for Effective Resource Management in Global Computing Environments. In Proceedings of the 1st IEEE International Conference on e-Science and Grid Technologies (eScience 2005). December 2005, Melbourne, Australia.
  20. M. Taufer, C. An, A. Kerstens, and C.L. Brooks III: Predictor@Home: A "Protein Prediction Supercomputer" Based on Public-Resource Computing. In Proceedings Fourth IEEE International Workshop on High Performance Computational Biology 2005), in conjunction with IPDPS 2005, April 2005, Denver, Colorado.
  21. M. Taufer, D.P. Anderson, P. Cicotti, and C.L. Brooks III: Homogeneous Technique to Ensure Integrity of Molecular Simulation Results Using Public Resources. In Proceedings of the 14th Heterogeneous Computing Workshop (HCW 2005), with IPDPS 2005, April 2005, Denver, Colorado.
  22. M. Taufer, M. Crowley, D. Price, A.A. Chien, and C.L. Brooks III: Study of an Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics. In the Third IEEE International Workshop on High Performance Computational Biology 2004), in conjunction with IPDPS 2004, April 2004, Santa Fe, New Mexico.
  23. D. Kondo, M. Taufer, C.L. Brooks III, H. Casanova, and A.A. Chien: Characterizing and Evaluating Desktop Grids: An Empirical Study. In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS'04), April 2004, Santa Fe, New Mexico, USA.
  24. P. Cicotti, M. Taufer, and A.A. Chien: DGMonitor: a Performance Monitoring Tool for Sandbox-based Desktop Grid Platforms. In Proceedings of the Third International Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems (PMEO-PDS'04), in conjunction with IPDPS'04, April 2004, Santa Fe, New Mexico, USA.
  25. M. Taufer, and T. Stricker: A Performance Monitor based on Virtual Global Time for Clusters of PCs. In Proceedings of the IEEE International Conference on Cluster Computing 2003 (Cluster'03), December 2003, Hong Kong, China.
  26. 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? In Proceedings the IEEE International Symposium on Cluster Computing and the Grid (CCGRID'03), May 2003, Tokyo, Japan.
  27. 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? In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS'03), April 2003, Nice, France.
  28. M. Taufer, T. Stricker, and R. Weber: Scalability and Resource Usage of an OLAP Benchmark on Clusters of PCs. In Proceedings of the Fourteenth ACM Symposium on Parallel Algorithms and Architectures (SPAA'02), August 2002, Winnipeg, Manitoba, Canada.
  29. 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. In Proceedings of the IEEE International Symposium on Cluster Computing and the Grid (CCGRID'02), May 2002, Berlin, Germany.
  30. 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? In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS'02), April 2002, Fort Lauderdale, Florida, USA.
  31. M. Taufer, and T. Stricker: Accurate Performance Evaluation, Modeling and Prediction of a Message Passing Simulation Code based on Middleware. In Proceedings of the ACM/IEEE International Conference for High Performance Computing and Communications conference (SC'98), November 1998, Orlando, Florida, USA.
  32. 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.

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.

Technical Reports

  1. Lifan Xu, Michela Taufer, Stuart Collins, and Dionisios G. Vlachos: Parallelization of Tau-Leap Coarse-Grained Monte Carlo Simulations on GPUs. Technical Report No. 2009/338, Dept. of Computer and Information Sciences, University of Delaware, Newark, DE (November 2009).
  2. Michela Taufer, Omar Padron, Philip Saponaro, Sandeep Patel: Improving Numerical Reproducibility and Stability in Large-Scale Numerical Simulations on GPUs. Technical Report No. 2009/339, Dept. of Computer and Information Sciences, University of Delaware, Newark, DE (November 2009).
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.

Posters

  1. T. Estrada, M. Taufer, and K. Reed: Performance Analysis of Volunteer Computing Traces. In Proceedings of the ACM/IEEE International Conference for High Performance Computing, Network, Storage, and Analysis conference (SC'07), November 2007, Reno, Nevada, USA.
  2. D. Flores, T. Estrada, M. Taufer, P. Teller, and A. Kerstens: SimBA: a Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects. In In Proceedings of the ACM/IEEE International Conference for High Performance Computing, Network, Storage, and Analysis conference (SC'06), November 2006, Tampa, Florida.
  3. C. An, M. Taufer, and C.L. Brooks III: Predictor@home: A Multiscale, Distributed Approach for Protein Structure Prediction. Poster presented at the 229th ACM National Meeting, March 2005, San Diego, California, USA.
  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.

Thesis

  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.
  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.