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Publications

Journal Papers (Top)

 
 
2018

The Future of Scientific Workflows

International Journal of High Performance Computing Applications (IJHPCA), 2018. E. Deelman, T. Peterka, I. Altintas, Christopher Carothers, K. Kleese van Dam, K. Moreland, M. Parashar, L. Ramakrishnan, M. Taufer, and J. Vetter.
2017

In-Situ Data Analytics and Indexing of Protein Trajectories

Journal of Computational Chemistry (JCC), 38(16): 1419-1430, 2017. T. Johnston, B. Zhang, A. Liwo, S. Crivelli, and M. Taufer.

Enabling Scalable and Accurate Clustering of Distributed Ligand Geometries on Supercomputers

Journal of Parallel Computing (ParCo), 63: 38-60, 2017. B. Zhang, T. Estrada, P. Cicotti, P. Balaji, and M. Taufer.

The Future of Scientific Workflows

International Journal of High Performance Computing Applications (IJHPCA), 32(1): 159-175, 2017. E. Deelman, T. Peterka, I. Altintas, Christopher Carothers, K. Kleese van Dam, K. Moreland, M. Parashar, L. Ramakrishnan, M. Taufer, and J. Vetter.

Creating a Portable, High-Level Graph Analytics Framework For Compute and Data-Intensive Applications

International Journal of High Performance Computing and Networking (IJHPCN), 2017. (Accepted) R. Searles, S. Herbein, T. Johnston, M. Taufer, and S. Chandrasekaran.
2016

Enhancing Reproducibility for Computational Methods - Data, code and workflows should be available and cited

Science, 354(6317), December 9, 2016.V. Stodden, M. McNutt, D. H. Bailey, E. Deelman, Y. Gil, B. Hanson, M. A. Heroux, J. P.A. Ioannidis, and M. Taufer.

Performance Characterization of Irregular I/O at the Extreme Scale

Journal of Parallel Computing, 51: 17-36, 2016.S. Herbein, S. McDaniel, N. Podhorszki, S. Klasky, and M. Taufer.
2015

It-Situ Data Analysis of Protein Folding Trajectories

CoRR abs/1510.08789: 1-40, October 30, 2015.T. Johnston, B. Zhang, A. Liwo, S. Crivelli, and M. Taufer.

Scheduling DAG-based Workflows on Single Cloud Instances: High- performance and Cost Effectiveness with a Static Scheduler

International Journal of High Performance Computing Applications, pp. 1-10, doi: 10.1177/1094342015594518, July 22, 2015.M. Taufer and A. L. Rosenberg.
2014

Pursuing Resource Utilization and Coordinated Progression in GPU-enabled Molecular Simulations

IEEE Design&Test of Computers, IEEE Design&Test of Computers, 31(1): 40-50, February 2014.S. Schlachter, S. Herbein, S. Ou, J.S. Logan, S. Patel, and M. Taufer.

MEMS Accelerometers and Distributed Sensing for Rapid Earthquake Characterization

Bulletin of the Seismological Society of America (BSSA), January 7, 2014J. F. Lawrence, E.S. Cochran, A. Chung, A. Kaiser, C.M. Christensen, R. Allen, D. Anderson, J.W. Baker, B. Fry, T. Heaton, D. Kilb, M.D. Kohler, and M. Taufer.
2013

On the Powerful Use of Simulations in the Quake-Catcher Network to Efficiently Position Low-cost Earthquake Sensors

Future Generation Computer Systems, 29(8): 2128-2142, 2013.K. Benson, S. Schlachter, T. Estrada, M. Taufer, E. Cochran, and J. Lawrence.

Enhancement of Accuracy and Efficiency for RNA Secondary Structure Prediction by Sequence Segmentation and MapReduce

BMC Structural Biology Journal, 13(Suppl 1):S3, 2013B. Zhang, D. T. Yehdego, K. L. Johnson, M.-Y. Leung, and M. Taufer.

GPU enabled Macromolecular Simulation: Challenges and Opportunities

IEEE Computing in Science and Engineering (CiSE), 15(1): 56-64, 2013.M. Taufer, N. Ganesan, and S. Patel.
2012

A Scalable and Accurate Method for Classifying Protein-Ligand Binding Geometries using a MapReduce Approach

Comp. in Bio. and Med., 42(7): 758-771, 2012.T. Estrada, B. Zhang, P. Cicotti, R. Armen, and M. Taufer.

Hierarchical Fractional-step Approximations and Parallel Kinetic Monte Carlo Algorithms

J. Comput. Physics, 231(23): 7795-7814, 2012.G. Arampatzis, M.A. Katsoulakis, P. Plechac, M. Taufer, and L. Xu.
2011

Structural, Dynamic, and Electrostatic Properties of Fully Hydrated DMPC Bilayers from Molecular Dynamics Simulations Accelerated with Graphical Processing Units (GPUs)

J. Computational Chemistry, 32(14): 2958-2973, 2011.N. Ganesan, B.A. Bauer, T. Lucas, S. Patel, and M. Taufer.

Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy

Journal of Chemical Information and Modeling, J. Chemical Information and Modeling, 51(9): 2047-65, 2011.O. Rahaman, T. Estrada, D. Doren, M. Taufer, C. L. Brooks III, R.S. Armen.

Molecular Dynamics Simulations of Aqueous Ions at the Liquid-Vapor Interface Accelerated Using Graphics Processors

J. Comp. Chem., (32)3: 375–385, 2011.B.A. Bauer, J.E. Davis, M. Taufer, and S. Patel.
2010

A 3 Terminal Stem-loop Structure 
in Nodamura Virus RNA2 Forms an Essential Cis-acting Signal for RNA 
replication

Virus Research, Virus Research, 150: 12-21, 2010.J.J. Rosskopf, John H. Upton, III, M.-Y. Leung, M. Taufer, and K. L. Johnson.
2009

Performance Prediction and Analysis of BOINC Projects: An Empirical Study with EmBOINC

J. Grid Computing, 7: 537-554, 2009. T. Estrada, M. Taufer, and D. Anderson.

Computational Multi-Scale Modeling in Protein-Ligand Docking

IEEE Engineering in Medicine and Biology Magazine. 28(2): 58-69, 2009. M. Taufer, R.S. Armen, J. Chen, P.J. Teller, and C.L. Brooks III.

PseudoBase++: An Extension of PseudoBase for Easy Searching, Formatting, and Visualization of Pseudoknots

Nucleic Acids Research. Database Issue, 37, 2009. D129 doi: 10.1093/nar/gkn806 M. Taufer, A. Licon, R. Araiza, D. Mireles, A. Gultyaev, F.H.D. Van Batenburg, M-Y Leung.
2008

RNAVLab: A Virtual Laboratory for Studying RNA Secondary Structures based on Grid Computing Technology. Journal of Parallel Computing

34: 661-680, 2008.M. Taufer, M-Y. Leung, T. Solorio, A. Licon, D. Mireles, R. Araiza, K.L. Johnson.

A Distributed Evolutionary Method to Design Scheduling Policies for Volunteer Computing

ACM SIGMETRICS Performance Evaluation Review Journal. 36(3): 40-49, December 2008.T. Estrada, O. Fuentes, and M. Taufer.
2006

Integrate GridFTP into Firefox - Build grid protocols into Mozilla-based tools

IBM developerWorks, 10 Oct 2006.K. Bhatia, M. Taufer, B. Stearn, R. Zamudio, D. Catarino.

Predictor@Home: A Protein Structure Prediction Supercomputer Based on Global Computing

IEEE Transactions on Parallel and Distributed Systems. 17(8): 786-796, August 2006.M. Taufer, C. An, A. Kerstens , and C.L. Brooks III.
2005

Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics

Concurrency and Computation: Practice and Experience. (17)14: 1627-1641, December 2005. M. Taufer, M. Crowley, D. Price, A.A. Chien, and C.L. Brooks III.

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. 34(2): 113 - 133, November 2005. P. Cicotti, M. Taufer, and A.A. Chien: DGMonitor.

The Computational Chemistry Prototyping Environment

Proceedings of the IEEE Special Issue on Grid Computing. 93(3): 512-521, March 2005. K. Baldridge, J.P. Greenberg, W. Sudholt, K. Bhatia, S. Mock, C. Amoreira, Y. Potier, and M. Taufer.

Book Chapters (Top)

 
 
2016

Data Movement in Data-Intensive High Performance Computing

Conquering Big Data with High Performance Computing. Springer International Publishing AG. ISBN 9783319337401. 2016. P. Cicotti, S. Oral, G. Kestor, R. Gioiosa, S. Strande, M. Taufer, J. H. Rogers, H. Abbasi, J. Hill, and L. Carrington.
2012

Scheduling on Large Scale Volatile Desktop Grids, from Greedy and Naive to Intelligent and Adaptive Policies

Chapter in "Desktop Grid Computing", Christophe Cerin and Gilles Fedak (Eds.), Chapman and Hall/CRC, 2012.T. Estrada and M. Taufer.
2011

Protein Docking

In Encyclopedia of Parallel Computing, Padua, David (Ed.),1st Edition., 2011, 2500 p. In 4 volumes, not available separately. Hardcover. ISBN: 978-0-387-09765-7. R.S. Armen, E.R. May, and M. Taufer.
2008

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.M. Taufer and C.L. Brooks III, Predictor@Home.

Research Papers in Refereed Conferences, Symposiums, and Workshops (Top)

 
 
2018

On the Power of Combiner Optimizations in MapReduce over MPI Workflows

In Proceedings of the IEEE 24rd International Conference on Parallel and Distributed Systems (ICPADS), pp. 1-10. Singapore. December 11-13, 2018. T. Gao, Y. Guo, B. Zhang, P. Cicotti, Y. Lu, P. Balaji, and M. Taufer.

Flux: Overcoming Scheduling Challenges for Exascale Workflows

In Proceedings of the 13th Workshop on Workflows in Support of Large-Scale Science (WORKS), Supercomputing, Dallas, TX, November 2018. D. H. Ahn, N. Bass, A. Chu, J. Garlick, M. Grondona, S. Herbein, J. Koning, T. Patki, T. R. W. Scogland, B. Springmeyer, and M. Taufer.

Graphic Encoding of Proteins for Efficient High-Throughput Analysis

In Proceedings of the 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB), pp. 1-10. Washington, DC, USA. August 29 - September 1, 2018. T. Estrada, J. Benson, H. Carrillo-Cabada, A. Razavi, M. Cuendet, H. Weinstein, E. Deelman, and M. Taufer.

Leveraging Neural Networks for Resource Prediction and IO-Aware Scheduling

In Proceedings of the International Conference on Parallel Processing (ICPP), pp. 1-10. Eugene, OR, USA. August 13-16, 2018. R. Wyatt II, S. Herbein, T. Gamblin, A. Moody, D. Ahn, and M. Taufer.

KeyBin2: Distributed Clustering for Scalable and In-Situ Analysis

In Proceedings of the International Conference on Parallel Processing (ICPP), pp. 1-10. Eugene, OR, USA. August 13-16, 2018.X. Chen, M. Peterson, J. Benson, M. Taufer, and T. Estrada.

Leveraging In Situ Data Analysis to Enable Computational Steering of Brain’s NeocortexSimulations with GENESIS

In Proceedings of the International Symposium on Advances in High Performance Computing and Networking (AHPCN), pp. 1 – 8. Exeter, England, UK. June 28-30, 2018. S. McDaniel, D. L. Boothe, D. R. Shires, A. B. Yu, and M. Taufer.
2017

Bloomfish: A Highly Scalable Distributed K-mer Counting Framework

In Proceedings of the IEEE 23rd International Conference on Parallel and Distributed Systems (ICPADS). Shenzhen, China. December 15-17, 2017. T. Gao, Y. Guo, Y. Wei, B. Zhang, Y. Lu, P. Cicotti, P. Balaji, and M. Taufer.

Mimir: Memory-Efficient and Scalable MapReduce for Large Supercomputing Systems

In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS). Orlando, Florida, USA. May 29-Jun 2, 2017. T. Gao, Y. Guo, B. Zhang, P. Cicotti, Y. Lu, P. Balaji, and M. Taufer.
2016

HYPPO: A Hybrid, Piecewise Polynomial Modeling Technique for Non-Smooth Surfaces

In Proceedings of the 28th IEEEE International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD), pp. 1 – 8. Los Angeles, CA, USA. October 26-28, 2016. (One of four Best Paper Candidatate)T. Johnston, C. Zannin, and M. Taufer.

Scheduling Matters: Area-oriented Heuristics for Resource Management

In Proceedings of the 28th IEEEE International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD), pp. 1 - 8. Los Angeles, CA, USA. October 26 – 28, 2016.J. Benson, T. Estrada, A. Rosenberg, and M. Taufer.

Development of a Scalable Method for Creating Food Groups Using the NHANES Dataset and MapReduce

In Proceedings of the ACM Bioinformatics and Computational Biology Conference (BCB), pp. 1 - 10. Seattle, WA, USA. October 2 – 4, 2016.M. Wyatt, T. Johnston, M. Papas, and M. Taufer.

Machine Learning Predictions of Runtime and IO Traffic on High-end Clusters

IEEE Cluster Conference, pp. 1-4. Taipei, Taiwan. September 12-16, 2016.R. McKenna, S. Herbein, A. Moody, T. Gamblin, and M. Taufer.

Scalable I/O-Aware Job Scheduling for Burst Buffer Enabled HPC Clusters

In Proceedings of the ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC), pp. 1-10. Kyoto, Japan. May 30-Jun 4, 2016.S. Herbein, D. H. Ahn, D. Lipari, T. R.W. Scogland, M. Stearman, M. Grondona, J. Garlick, B. Springmeyer, and M. Taufer.

Resource Management for Running HPC Applications in Container Clouds

In Proceedings of the International Supercomputing Conference (ISC), pp. 1-19. Frankfurt, Germany. June 19-23, 2016.S. Herbein, A. Dusia, A. Landwehr, S. McDaniel, J. Monsalve, Y. Yang, S. R. Seelam, and M. Taufer.
2015

A Genetic Programming Approach to Design Resource Allocation Policies for Heterogeneous Workflows in the Cloud

In Proceedings of the 21th IEEE International Conference on Parallel and Distributed Systems (ICPADS), pp. 372-379. Melbourne, Australia. December 14-16, 2015. T. Estrada, M. R. Wyatt, and M. Taufer.
2014

Bandwidth Modeling in Large Distributed Systems for Big Data Applications

In Proceedings of International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT). Hong Kong, December 9-11, 2014. B. Javadi, B. Zhang, and M. Taufer.

Using Surrogate-based Modeling to Predict Optimal I/O Parameters of Applications at the Extreme Scale

In Proceedings of the 20th IEEE International Conference on Parallel and Distributed Systems (ICPADS 2014), Hsinchu, Taiwan, December 16-19, 2014. M. Matheny, S. Herbein, N. Podhorszki, S. Klasky, M. Taufer.

Applying Frequency Analysis Techniques to DAG-based Workflows to Benchmark and Predict Resource Behavior on Non-Dedicated Clusters

In Proceedings of CLUSTER 2014, Madrid, Spain, September 22-26, 2014. V.K. Pallipuram, J. DiMarco, and M. Taufer.

Benchmarking the Performance of Scientific Applications with Irregular I/O at the Extreme Scale

In Proceedings of the Seventh International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2), Minneapolis, Minnesota, 2014. S Herbein, S. Klasky, and M. Taufer.

Study the Network Impact on Earthquake Early Warning in the Quake-Catcher Network Project

In the Proceedings of the International Conference on Computational Science (ICCS), Cairns, Australia, 2014. M. Portnoi, S. Schlachter and M. Taufer.

Enabling In-situ Data Analysis for Large Protein Folding Trajectory Datasets

In the Proceedings of the 28th IEEE International Parallel and Distributed Processing Symposium (IPDPS), Phoenix (Arizona) USA, 2014. B. Zhang, T. Estarda, P. Cicotti, M. Taufer.
2013

Performance Dissection of a MD Code across CUDA and GPU Generations

In Proceedings of the 14th IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC-13), April 2013, Boston, Massachusetts, USA.M. Wezowicz, T. Estrada, S. Patel, and M. Taufer.

Secondary Structure Predictions for Long RNA Sequences based on Inversion Excursions and MapReduce

In Proceedings of 12th IEEE International Workshop on High Performance Computational Biology (HiCOMB), April 2013, Boston, Massachusetts, USA.D. Yehdego, B. Zhang, V. K. R. Kodimala, K. Johnson, M. Taufer, and M.-Y. Leung.

Performance Impact of Dynamic Parallelism on Different Clustering Algorithms and the New GPU Architecture

In Proceedings of the DSS11 SPIE Defense, Security, and Sensing Symposium - Modeling and Simulation for Defense Systems and Applications VI, April 2013, Baltimore, Maryland, USA.J. DiMarco and M. Taufer.
2012

ExSciTecH: Expanding Volunteer Computing to Explore Science, Technology, and Health

In Proceedings of the 2nd workshop on Analyzing and Improving Collaborative eScience with Social Networks (eSoN 12), October 2012, Chicago, Illinois, USA. M. Matheny, S. Schlachter, L. Crouse, E. Kimmel, T. Estrada, M. Schumann, R. Armen, G. Zoppetti, and M. Taufer.

A modularized MapReduce framework to support RNA secondary structure prediction and analysis workflows

In Proceedings of the 2012 Computational Structural Bioinformatics Workshop (CSBW), October 2012, Philadelphia, Pennsylvanian, USA.B. Zhang, D. Yehdego, K. Johnson, M.-Y. Leung, and M. Taufer.

Reengineering high-throughput molecular datasets for scalable clustering using MapReduce

In Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications (HPCC-2012), June 2012, Liverpool, England, UK.T. Estrada, B. Zhang, P. Cicotti, R. Armen, and M. Taufer.

Dealing with performance/portability and performance/accuracy trade-offs in heterogeneous computing systems: A case study with matrix multiplication modulo primes

In Proceedings of the DSS11 SPIE Defense, Security, and Sensing Symposium - Modeling and Simulation for Defense Systems and Applications VI, April 2012, Baltimore, Maryland, USA.M. Wezowicz, B. D. Saunders, and M. Taufer.
2011

On the Powerful Use of Simulations in the Quake-Catcher Network to Efficiently Position Low-cost Earthquake Sensors

In the Proceedings of the Seventh IEEE International Conference on e-Science and Grid Technologies (eScience), December 2011, Stockholm, Sweden.K. Benson, T. Estrada, M. Taufer, E. Cochran, and J. Lawrence.

Simulating Application Resilience at Exascale

In Proceedings of the 4th Workshop on Resiliency in High Performance Computing (Resilience) in Clusters, Clouds, and Grids, held in conjunction with the 17th International European Conference on Parallel and Distributed Computing (Euro-Par), August 30, 2011, Bordeaux, France. R. Riesen, K. Ferreira, M. Ruiz Varela, M. Taufer and A. Rodrigues.

Providing Application-Level QoS in Volunteer Computing

In the Proceedings of the 13th IEEE High Performance Computing and Communications (HPCC) Conference. September 2011, Banff, Canada. T. Estrada and M. Taufer.

FEN ZI: GPU Enabled Molecular Dynamics Simulation of Large Membrane Regions Based on CHARMM Force Field and PME

In Proceedings of the Tenth IEEE Workshop on Hi-Performance Computational Biology (HiCOMB), May 2011, Anchorage (Alaska) USA. N. Ganesan, B. Bauer, S. Patel and M. Taufer.

Rolling Partial Prefix-Sums to Speedup Uniform and Affine Recurrence Equations

In Proceedings of SPIE, Defense, Security and Sensing Conference. April 2011, Orlando, FL, USA.N. Ganesan , R.D. Chamberlain, J. Buhler and M. Taufer.
2010

Automatic Selection of Near-Native Protein-Ligand Conformations using a Hierarchical Clustering and Volunteer Computing

In Proceedings of the International Conference On Bioinformatics and Computational Biology (ACM-BCB), August 2010, Niagara Falls, NY, USA.T. Estrada, R. Armen, and M. Taufer.

Accelerating HMMER on GPUs by Implementing Hybrid Data and Task Parallelism

In Proceedings of the International Conference On Bioinformatics and Computational Biology (ACM-BCB), August 2010, Niagara Falls, NY, USA.N. Ganesan, R.D. Chamberlain, J. Buhler, and M. Taufer.

Parallelization of Tau-Leap Coarse-Grained Monte Carlo Simulations on GPUs

In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS), April 2010, Atlanta, Georgia, USA.L. Xu, M. Taufer, S. Collins, and D. G. Vlachos.

Improving Numerical Reproducibility and Stability in Large-Scale Numerical Simulations on GPUs

In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS), April 2010, Atlanta, Georgia, USA.M. Taufer, O. Padron, P. Saponaro, S. Patel.

A Dynamic Programming Algorithm for Finding the Optimal Segmentation of an RNA Secondary Structure Prediction

In Proceedings of the International Conference on Bioinformatics and Computational Biology (BICoB), March 2010, Honolulu, Hawaii, USA.A. Licon, M. Taufer, M.-Y. Leung, and K.L. Johnson.
2009

MNEOMIC: Network Environment for Measurement and Observation for Network Interaction and Control

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.P. McClory, E. Kissel, D. M. Swany, and M. Taufer.

Applying Organizational Self-Design to a Real-world Volunteer Computing System

In Proceedings of Agent Design: Advancing from Theory to Practice (ADAPT) Workshop, 2009. S. Kamboj, T. Estrada, M. Taufer, and K. S. Decker.

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.J. Atlas, T. Estrada, K. Decker, and M. Taufer.

EmBOINC: An Emulator for Performance Analysis of BOINC Projects

In Proceedings of PCGrid 2009, May 2009, Rome, ItalyT. Estrada, K. Reed, D. Anderson, 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.T. Estrada, K. Reed, 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, USAJ.E. Davis, A. Ozsoy, S. Patel, and M. Taufer.
2008

A Distributed Evolutionary Method to Design Scheduling Policies for Volunteer Computing

In Proceedings of ACM Computing Frontiers 2008, May 2008, Ischia, Italy.T. Estrada, O. Fuentes, and M. Taufer.

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.M. Taufer, T. Solorio, A. Licon, D. Mireles, and M.-Y. Leung.
2007

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.G. Lopez, M. Taufer, and P.J. Teller.

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.R. Araiza, M. Taufer, and M.-Y. Leung.

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.M. Taufer, A. Kerstens, T. Estrada, D.A. Flores, and P.J. Teller.

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.M. Taufer, M.-Y. Leung, K. L. Johnson, A. Licon.

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.M. Taufer, A. Kerstens, T. Estrada, D.A. Flores, R. Zamudio, P.J. Teller, R. Armen, and C.L. Brooks III.

Topaz: Extending Firefox to Accommodate the GridFTP Protocol

In Proceedings of the Fourth High-Performance Grid Computing Workshop (HPGC'07), in conjunction with IPDPS'07 March 2007, Long Beach, California, USA.R. Zamudio, D. Catarino, M. Taufer, K. Bhatia, and B. Stearn.
2006

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.T. Estrada, D. Flores, M. Taufer, P. Teller, A. Kerstens, and D. Anderson.

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.T. Estrada, A. Licon, and M. Taufer.

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.K. Bhatia, B. Stearn, M. Taufer, R. Zamudio, and D. Catarino.

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.G. Aguilera, P.J. Teller, M. Taufer, and F. Wolf.
2005

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.M. Taufer, P.J. Teller, D.P. Anderson, 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.M. Taufer, C. An, A. Kerstens, 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.M. Taufer, D.P. Anderson, P. Cicotti, and C.L. Brooks III.
2004

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.M. Taufer, M. Crowley, D. Price, A.A. Chien, and C.L. Brooks III.

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.D. Kondo, M. Taufer, C.L. Brooks III, H. Casanova, 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.P. Cicotti, M. Taufer, and A.A. Chien.
2003

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.M. Taufer, and T. Stricker.

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.B. Uk, M. Taufer, T. Stricker, G. Settanni, A. Cavalli, and A. Caflisch.

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.B. Uk, M. Taufer, T. Stricker, G. Settanni, and A. Cavalli.
2002

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. M. Taufer, T. Stricker, and R. Weber.

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.M. Taufer, T. Stricker, G. Roos, P. Guentert.

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. M. Taufer, E. Perathoner, A. Cavalli, A. Caflisch, and T. Stricker.
1998

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. M. Taufer, and T. Stricker.
1996

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.P. Arbenz, M. Billeter, P. Guentert, P. Luginbuehl, M. Taufer, and U. von Matt.

Educational Papers (Top)

2006

Collaborative Research Tools for Students, Staff, and Faculty

In Proceedings of the International SUN Conference on Teaching and Learning, March 2006, El Paso, Texas.M. Taufer, P.J. Teller, A. Kerstens, R. Romero.

Posters (Top)

 
 
2012

Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions

Poster in Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Orlando, FL, October 7-10, 2012. D.T. Yehdego, V. K. R. Kodimala, S. Viswakula, B. Zhang, R. Vegesna, K. L. Johnson, M. Taufer and M.-Y. Leung.

Benchmarking Gender Differences in Voluntary Computer Projects

Poster in Proceedings of the 2012 Grace Hopper Celebration of Women in Computing (GHC12), October 2012, Baltimore, Maryland, USA. T. Estrada, K. Pusecker, M. Torres, J. Cohoon, and M. Taufer.
2011

Study of Protein-ligand Binding Geometries using a Scalable and Accurate Octree-based Algorithm in MapReduce

Poster in Proceedings of the ACM/IEEE International Conference for High Performance Computing and Communications conference (SC), November 2011, Seattle, Washington, USA.T. Estrada, B. Zhang, R.S. Armen, and M. Taufer.
2010

Simulations of Large Membrane Regions using GPU-enabled Computations - Preliminary Results

2010 Symposium on Application Accelerators in High Performance Computing (SAAHPC10). July 13-15, 2010. University of Tennessee Conference Center, Knoxville, Tennessee, USA. Narayan Ganesan, Sandeep Patel, and Michela Taufer.
2009

Parallelization of Tau-Leaping Coarse-Grained Monte Carlo Method for Efficient and Accurate Simulations on GPUs

Poster in Proceedings of the ACM/IEEE International Conference for High Performance Computing and Communications conference (SC’09), November 2009, Portland, Washington, USA. Lifan Xu, S. Collins, M. Taufer, and D.G. Vlachos.

Improving Reproducibility and Stability of Numerically Intensive Applications on Graphics Processing Units

Poster at the NVIDIA Research Summit,Sep 30- Oct 2, 2009, San Jose, CA.M. Taufer, P. Saponaro, and O. Padron.

Docking@Home: Searching for New Drugs using Volunteer’s Computers

In Proceedings of The Grace Hopper Celebration of Women in Computing 2009, September 30 – October 3, 2009, Tucson, AZ.T. Estrada, M. Taufer.

Role of RNA secondary structure in replication of Nodamura virus RNA2

Poster at the American Society for Virology, Twenty-seventh Annual Meeting, 2009, Cornell University, Ithaca, NY.K.S. Hogle, J.H. Upton, A. Licon, M.-Y. Leung, and K.L. Johnson.
2007

Performance Analysis of Volunteer Computing Traces

In Proceedings of the ACM/IEEE International Conference for High Performance Computing, Network, torage, and Analysis conference (SC07), November 2007, Reno, Nevada, USA. T. Estrada, M. Taufer, and K. Reed.
2006

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 (SC06), November 2006, Tampa, Florida.D. Flores, T. Estrada, M. Taufer, P. Teller, and A. Kerstens.
2005

Predictor@home: A Multiscale, Distributed Approach for Protein Structure Prediction

Poster presented at the 229th ACM National Meeting, March 2005, San Diego, California, USA.C. An, M. Taufer, and C.L. Brooks III.
2004

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.C. An, M. Taufer, and C.L. Brooks III.

Technical Reports (Top)

2009

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).Lifan Xu, Michela Taufer, Stuart Collins, and Dionisios G. Vlachos.

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).Michela Taufer, Omar Padron, Philip Saponaro, Sandeep Patel.
2006

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.R. Zamudio, D. Catarino, M. Taufer, B. Stearn, and K. Bhatia.
2003

Characterizing and Evaluating Desktop Grids: An Empirical Study

Technical Report CS2003-069. University of California, San Diego, November 2003, La Jolla, California. D. Kondo, M. Taufer, J. Karanicolas, C. L. Brooks III, H. Casanova, and A. Chien.

a Performance Monitoring Tool for Sandbox-based Desktop Grid Platforms

Technical Report CS2003-070, University of California, San Diego, November 2003, La Jolla, California.P. Cicotti, M. Taufer, and A. Chien: DGMonitor.
2002

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. B. Uk, M. Taufer, T. Stricker, G. Settanni, A. Cavalli, and A. Caflisch.

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.B. Uk, M. Taufer, T. Stricker, G. Settanni, and A. Cavalli.

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.M. Taufer, T. Stricker, and R. Weber.
1998

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.P. Arbenz, T. Stricker, M. Taufer, and U. von Matt.

Thesis (Top)

2002

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.M. Taufer.
1996

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.M. Taufer.