CSL - Papers and Technical Reports

COMPUTATIONAL SCIENCE LABORATORY

2208 TMCB
Computer Science Department
Brigham Young University
Provo, UT 84602-6576
801.422.8299
801.422.7290

PAPERS AND TECHNICAL REPORTS:

2009

TR_BYU_CSL-2009-1 "On The Use of Cartographic Projections in Visualizing Phylogenetic Treespace" Kenneth Sundberg, Mark Clement, Quinn Snell 2009

2008

Sequence Alignment with Traceback on Reconfigurable Hardware, Scott Lloyd and Quinn Snell, In Proceedings of the 2008 International Conference on ReConFigurable Computing and FPGAs (ReConFig'08), Pages 259-264, Dec 2008.
Incomparability of results between phylogenetic search programs, Kenneth Sundberg, Hyrum Carroll, Quinn Snell, Mark Clement, In Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08), Pages 81-84, July 2008.
Genomic Scale Reconstruction of Gene Regulatory Networks from Microarray Data, Kenneth Sundberg, Daniel Ence, Daniel Wilcox, Quinn Snell, Mark Clement, BIOCOMP 2008.
Qnet: A Modular Architecture for Reconfigurable Computing, Scott Lloyd and Quinn Snell, In Proceedings of the 2008 International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'08), Pages 259-265, July 2008.
Parsimony accelerated Maximum Likelihood Searches, Kenneth Sundberg, Timmothy O'Connor, Hyrum Carrol, Mark Clement, Quinn Snell, International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 1, Issue 1, 2008.
An Open-Source Phylogenetic and Alignment Package, Hyrum Carroll, Adam Teichert, Jonathan Krein, Kenneth Sundberg, Quinn Snell, To be published in International Journal of Bioinformatics Research and Applications. 2007
DNA Reference Alignment Benchmarks Based on Tertiary Structure of Encoded Proteins, Hyrum Carroll, Wesley Beckstead, Timothy O'Connor, Mark Ebbert, Mark Clement, Quinn Snell and David McClellan, Bioinformatics, 23(19) 2007, p 2648-2649.
Using Parsimony to Guide Maximum Likelihood Searches, Kenneth Sundberg, Timothy O'Connor, Hyrum Carroll, Mark Clement, and Quinn Snell, IEEE Symposium on BioInformatics and BioEngineering (BIBE), Washington, D.C., October 2007, pp 774-779.
Analyzing Gene Relationships for Down Syndrome with Labeled Transition Graphs, Neha Rungta, Hyrum Carroll, Eric G. Mercer, Randall J. Roper, Mark Clement, Quinn Snell, to appear in Proceedings of Formal Methods in Computer Aided Design (FMCAD '07), November 2007, Austin, USA.
Pharmacogenomics: Analyzing SNPs in the CYP2D6 Gene Using Amino Acid Properties, Mark Ebbert, Timothy OConnor, Wesley Beckstead, Mark Clement, David McClellan, International Journal of Bioinformatics Research and Applications, 3(3) 2007.
PsodaScript: Applying Advanced Language Constructs to Open-source Phylogenetic Search , J. L. Krein, A. R. Teichert, H. D. Carroll, M. J. Clement and Q. O. Snell, Proceedings of the 4th Biotechnology and Bioinformatics Symposium, October 2007, pp 89-94.
PSODA: Better Tasting and Less Filling Than PAUP, H. Carroll, M. Ebbert, M. Clement and Q. Snell, Proceedings of the 4th Biotechnology and Bioinformatics Symposium, October 2007, pp 74-78.
Phylogenies Scores for Exhaustive Maximum Likelihood and Parsimony Scores Searches ,H. Carroll, P. Ridge, M. Clement and Q. Snell, International Journal of Bioinformatics Research and Applications (IJBRA) 3(4) 2007 pp 493-503.

2006
Jumpstarting Phylogenetic Analysis, Jesse Mecham, Mark Clement, Todd Freestone, Quinn Snell, Kevin Seppi, Keith Crandall, International Journal of Bioinformatics Research and Applications, 2(1) 2006, p 19.
Pharmacogenomics: Analyzing SNPs in the CYP2D6 Gene Using Amino Acid Properties, Mark Ebbert, Timothy OConnor, Wesley Beckstead, Mark Clement, David McClellan, Biotechnology and Bioinformatics Symposium(BIOT), Provo, Utah, October 2006, pp 1.
Large Grain Size Stochastic Optimization Alignment, Perry Ridge, Hyrum Carroll, Dan Sneddon, Mark Clement, Quinn Snell, IEEE Symposium on BioInformatics and BioEngineering (BIBE), Arlington, Virginia, October 2006, pp 127
Effects of Gap Open and Gap Extension Penalties, Hyrum Carroll, Perry Ridge, Mark Clement, Quinn Snell, Biotechnology and Bioinformatics Symposium (BIOT), Provo, Utah, October 2006, pp 19.

2005
Prioritized Multiplicative Schwarz Procedures for Solutions to General Linear Systems, David Wingate, Nathaniel Powell, Quinn Snell, Kevin Seppi, Proceedings of the 2005 International Parallel and Distributed Processing Symposium, April 2005.
Phylogenetic Analysis of Large Sequence Data Sets, Hyrum Carroll, Mark Clement, Quinn Snell, Keith Crandall, Biotechnology and Bioinformatics Symposium (BIOT), Colorado Springs, CO, October 2005, pp 20-25.
Phylograph: Real-time Interactive Visualization of Phylogenetic Searches, Jesse Mecham, Mark Clement, Quinn Snell, Keith Crandall, 1st International Conference on Geometric Modeling, Visualization & Graphics (GMV), Salt Lake City, UT, .July 2005, pp 1713-1716

2004
Jumpstarting Phylogenetic Analysis, Mark Clement, Quinn Snell, Keith Crandall, Kevin Seppi, Biotechnology and Bioinformatics Symposium (BIOT), September 2004, page 17-25.
A Survivable Multi-agent Approach to Network Routing, Casey T. Deccio, Mark Clement, Quinn Snell, International Conference on Communications in Computing, June 2004, page 9-13.
Temporal Difference Learning in Network Routing, Reid Broadbent, Casey T. Deccio, Mark Clement, International Conference on Communications in Computing, June 2004, page 14-20.
A Piecewise Linear Approach to Overbooking, Feng Huang, Casey Deccio, Robert Ball, Mark Clement, Quinn Snell, High Performance Switching and Routing, April 2004, p 326-330 .
Aggressive Telecommunications Overbooking Ratios, Robert Ball, Mark Clement, Feng Huang, Quinn Snell, Casey Deccio, IEEE International Performance Computing and Communications Conference, April 2004, p 31-38.
Complex Performance Analysis Through Statistical Experimental Design: An Evaluation of Parameters Associated with Speed in Parallel Phylogenomics, David G. Whiting, Quinn Snell, Rebecca R. Nichols, Megan L. Porter, Kevin Tew, Keith A. Crandall, Michael F. Whiting, Mark Clement, Hawaii International Conference on Computer Science, January 2004, p 615-629.

2003
TR_BYU_NCL-2003-4 "TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees " Steve Woolley, Justin Johnson, Matthew J. Smith, Keith A. Crandall and David A. McClellan, Bioinformatics Vol. 19 no. 5 2003, Pages 671-672 (http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/5/671)
TR_BYU_NCL-2003-3 "Survivability of Large Networks in the Presence of Malicious Attacks" Casey T. Deccio, Spencer Cox, Matthew Smith, Jacob Wan, Mark Clement, Quinn Snell
TR_BYU_NCL-2003-2 "Securing OSPF Using Digital Signatures and Neighbor Checking" Casey T. Deccio, Mark Clement, Kent Seamons
TR_BYU_NCL-2003-1 "Temporal Difference Learning in Network Routing" Reid Broadbent, Casey T. Deccio, Mark Clement

2002
An Enterprise Based Grid Resource Management System, Quinn Snell, Kevin Tew, Joseph Ekstrom, Mark Clement. Proceedings of the Eleventh IEEE International Symposium on High Performance Distributed Computing (HPDC-11), Edinburgh, Scotland, July 2002, pages 83-90.
Effective Bandwidth Route Selection, Xiafeng Lu, Mark Clement, Quinn Snell. Proceedings of the 2001 International Symposium on Performance Evaluation of Computer and Telecommunication Systems, San Diego, CA, pp 132, July 2002.
Using Fourier Transform for REDs Active Queue Management, Lichen Dai, Peter Walker, Mark Clement, Quinn Snell. Proceedings of the 2001 International Symposium on Performance Evaluation of Computer and Telecommunication Systems, San Diego, CA, pp 188, July 2002.

2001
TR_BYU_NCL-2001-1 "Distributed Neural Network Routing" Joshua Menke
Livelock Avoidance for Metaschedulers, John Jardine, Quinn Snell, Mark Clement. Proceedings of the Tenth IEEE International Symposium on High Performance Distributed Computing (HPDC-10), San Francisco, CA, August 2001.
The YGuard Access Control Model: Set-Based Access Control, Ty van den Akker, Quinn O. Snell, and Mark Clement. Proceedings of SACMAT 2001, Chantilly, Virginia, May 2001.
Improving Cluster Utilization Through Set-Based Allocation Policies, David B. Jackson, Brian Haymore, Julio Facelli, Quinn O. Snell. Proceedings of the International Conference on Parallel Processing Workshops, Valencia, Spain, September 2001
Random Early Detection Parameter Tuning, Peter Walker, LiChen Dai, Mark Clement, Quinn Snell, Chris Chase. Proceedings of the 2001 International Symposium on Performance Evaluation of Computer and Telecommunication Systems, Orlando, Florida, July 2001.
The Impact of Hardware Characteristics on Firewall Performance, Bradley J. Baird, Mark Clement, Charles Knutson, Quinn Snell. Proceedings of the 2001 International Symposium on Performance Evaluation of Computer and Telecommunication Systems, Orlando, Florida, July 2001.
Load Balancing in a Parallel Chess Program, Reid Broadbent, Quinn Snell, Mark Clement, Proceedings of the 2001 International Conference on Parallel and Distributed Techniques and Applications, Las Vegas, Nevada, June 2001, page 324-330.
Fairness in TCP Networks, Xiaofeng Lu, Mark Clement, Quinn Snell, Proceedings of the 2001 International Conference on Internet Computing, Las Vegas, Nevada, June 2001, page 366-371
Effective Bandwidth for Traffic Engineering, Rob Kunz, Seth Nielson, Mark Clement, Quinn Snell, Proceedings of the IEEE Workshop on High Performance Switching and Routing (HPSR 2001), Dallas, TX, May 2001.

2000
TR_BYU_NCL-2000-3 "The Performance Impact of Advance Reservation Meta-Scheduling" Quinn Snell, Mark Clement, David Jackson and Chad Gregory; 6th Workshop of Job Scheduling Strategies for Parallel Processing In Conjunction with IPDPS 2000
TR_BYU_NCL-2000-2 "Parallel Phylogenetic Inference" Quinn Snell, Michael Whiting, Mark Clement and David McLaughlin; Published in SC2000 Proceedings
TR BYU-NCL-2000-1 "YRM: An Advanced Resource Manager" Daniel L. Reese, Scott V. Hansen, David B. Jackson, Quinn O. Snell, Mark J. Clement; Published at IASTED Conference on Parallel and Distributed Computing and Systems, Nov., 2000.

1999
TR BYU-NCL-99-100 "Parallel Algorithm and Processor Selection Based on Fuzzy Logic" Steve Chapin, Mark Clement, Quinn Snell.
TR BYU-NCL-99-?? "High Performance Computing for the Masses" Glenn Judd, Mark J. Clement, Quinn Snell. IPPS/SPDP WOrkshops 1999: 781:796.
TR BYU-NCL-99-?? "Design Issues for Efficient Implementation of MPI in Java" Glenn Judd, Mark J. Clement, Quinn Snell, Vladimir Getov. Java Grande 1999: 58-65.
TR BYU-NCL-99-?? "A Grid Resource Management Architecture" Shuling Yu, Mark J. Clement, Quinn Snell, Bryan Morse.

1998
TR BYU-NCL-98-101 " Parallel Algorithms For Image Convolution " Shuling Yu, Mark Clement, Quinn Snell and Bryan Morse.

1997
TR BYU-NCL-97-102 "DOGMA: Distributed Object Group Management Architecture" G. Judd, M. Clement, Q. Snell.
TR BYU-NCL-97-101 "Performance Surface Prediction for WAN-Based Clusters", M. J. Clement, G. Judd, J. Peterson, J. K. Flanagan, B. Morse.
TR BYU-NCL-97-100 "Simulation and ANalysis of Credit- and Rate-based Switch Interoperability in an ATM Network", Charles R. Duncan, Thesis, February 1997.

1996
TR BYU-NCL-96-103 "The Chordal Spoke ATM Interconnection Network", W. Wei and M. J. Clement and J. K. Flanagan.
TR BYU-NCL-96-102 "A Dependency-based Strategy for Handling ATM Cell Loss", Dean L. Scoville, Thesis, July 1996.
TR BYU-NCL-96-101 "Performance Prediction and Network Media Selection for PVM Clusters", Michael R. Steed, Thesis, January 1996.
TR BYU-NCL-96-100 "Performance Prediction of PVM Programs", Michael R. Steed and Mark J. Clement. Also appeared in Proceedings of the 10th International Parallel Processing Symposium, April 1996.

1995
TR BYU-NCL-95-110 "Locality of Distributed Architectures and Algorithms" Kevin Butler.
TR BYU-NCL-95-109 "Simulation and Analysis of the Performance of EPRCA in a Wide Area ATM Network Consisting of Both ER and EFCI Switch Mechanisms ", Robert Walthall and Mark Clement
TR BYU-NCL-95-108 "Using Rate Based Flow Control to Manage Available Bit Rate Traffic in Asynchronous Transfer Mode Networks ", Robert Walthall
TR BYU-NCL-95-107 "ATM Switch Based Interconnection Networks", Wei Wei, Thesis, December 1995.
TR BYU-NCL-95-106 "Network Performance Modelling for PVM Clusters", Michael R. Steed, Mark J. Clement and Phyllis E. Crandall.
TR BYU-NCL-95-105 "The Chordal Spoke ATM Interconnection Network", Wei Wei, Mark J. Clement and J. Kelly Flanagan.
TR BYU-NCL-95-104 "Automated Performance Prediction for Scalable Parallel Computing", Mark J. Clement and Michael J. Quinn.
TR BYU-NCL-95-103 "The Round Table ATM Interconnection Network", W. Wei, M. J. Clement and J. K. Flanagan. Also appeared in International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'95)
TR BYU-NCL-95-102 "Using Analytical Performance Prediction for Architectural Scaling", Mark J. Clement and Michael J. Quinn. Also appeared in Computer Systems Science and Engineering, 1995
TR BYU-NCL-95-101 "Symbolic Performance Prediction of Scalable Parallel Programs", Mark J. Clement and Michael J. Quinn. Also appeared in Proceedings of the 9th International Parallel Processing Symposium, April 1995.
TR BYU-NCL-95-100 "Multivariate Statistical Techniques for Parallel Performance Prediction", Mark J. Clement and Michael J. Quinn. Also appeared in Proceedings of the 28th Hawaii International Conference on System Sciences, HICSS-28 January 3-6, 1995.

1994
TR BYU-NCL-94-103 "Architectural Scaling and Analytical Performance Prediction", Mark J. Clement and Michael J. Quinn. Also appeared in Proceedings of the ISCA International Conference on Parallel and Distributed Computing Systems PDCS-7, October 6-8, 1994.
TR BYU-NCL-94-102 "Analytical Performance Prediction of Data-Parallel Programs", Mark J. Clement. Dissertation, August, 1994
TR BYU-NCL-94-101 "Overlapping Computations, Communications and I/O in Parallel Sorting", Mark J. Clement and Michael J. Quinn. Also appeared in Journal of Parallel and Distributed Computing December, 1994.
TR BYU-NCL-94-100 "Dynamic Performance Prediction for Scalable Parallel Computing", Mark J. Clement and Michael J. Quinn, July 1994.
TR OSU-94-80-6 "Symbolic Performance Prediction of Scalable Parallel Programs", Mark J. Clement and Michael J. Quinn, April 1994.

1993
TR BYU-NCL-93-100 "Analytical Performance Prediction on Multicomputers", Mark J. Clement and Michael J. Quinn. Also appeared in Proceedings of Supercomputing '93 November, 1993.

1992
TR BYU?-NCL-92-?? "Hyperweave: A Fault-Tolerant Expandable Interconnection Network" Gowri Ramanathan, Mark J. Clement, Phyllis Crandall. SPDP 1992: 479-482.

Updated Fri Feb 23 16:00:12 MST 2001
Comments: clement@cs.byu.edu

Please send suggestions and questions to Quinn Snell (snell@cs.byu.edu)