HPA Activities

Projects

Current:

Teragrid Basic Support. We support several Teragrid users to get started on various resources. Also see: Local TG webpages and Knowledge Base articles related to this.

Teragrid Advanced Support. We are working with two Geologists and one Physicist from IU to get their codes to run on Teragrid resources -- activities include installation of libraries, porting code to different architectures, data storage strategies, etc.

Hidden Markov rates in fastDNAml. HPA staff are implementing a new mutation rate generator in fastDNAml.

Nuclear Pasta. We are collaborating with a theoretical physicist in the Physics Department/IU Nuclear Theory Center to study a phase of nuclear matter (neutrons and protons) known as nuclear pasta, which may occur in neutron star crusts and in type II supernovae. We are using a classical molecular dynamics model, and our program can use the MDGRAPE-2 board, to do the O(N^2) force calculations for each MD timestep in the N-body problem. The code is parallelized with MPI, and can run on either a conventional parallel computer or a parallel MDGRAPE-2 computer.

Optimizing the MILC code The MILC code is widely used to study Lattice Quantum Chromodynamics (Lattice QCD). We are optimizing its core linear algebra routines to run on the Intel Itanium2 processor.

Seismic Analysis. Collaboration with Department of Geological Sciences for USArray/EarthScope project. Designed and Implemented a X11 Motif based GUI front end to display seismic time series data and accept seismic analyst's input to perform backend series ensemble correlation to realign the time series data, will enable effecient automation of seismic data analysis process.

Completed:

MEDLINE text mining. We are working with School of Informatics to create a system to provide a web search engine for MEDLINE documents. Several thesauri are incorporated into the system to better navigate the search process.

Penelope. Radiation Oncology. The program Penelope, which simulates the transfer of radiation through various media, is being converted and optimized for the simulation of radiation therapy with the Gamma Knife. Supercomputer versions of this code will make feasible the clinical use of much more accurate methods for targeting radiation therapy, thus eliminating one of the critical sources of failure of such therapy today (insufficiently accurate targeting due to oversimplified models of the human body).

SimWalk II. HPA staff are implementing a parallel version of the SimWalk program used by the Department of Medical Genetics to study the genetic component of diseases.

Prodigies. HPA staff are working with the IUB Chemistry Department to migrate the Prodigies package onto AVIDD. This package does protein analysis, based upon new instruments developed locally. The migration will make it to handle larger genome and increase the throughput.

Global analysis of arthropod evolution. This project addressed the question, whether arthropods with six legs (insects and their relatives) constitute a single evolutionary family. A team led by University Information Technology Services, the Indiana University Center for Genomics and Bioinformatics, and the High Performance Computing Center of the University of Stuttgart won a prestigious High Performance Computing Grand Challenge award SC2003, the premiere annual international supercomputing conference. This project took top honors in the category of "Most Geographically Distributed Application."

Merlin. HPA staff have expanded Merlin, a sparse tree implementation of gene flow in pedigree analysis, from a 32-bit package to a 64-bit package to accommodate larger trees.

MCNP5 and MCNPX. HPA staff installed, tested and assisted in the use of MCNP5 and MCNPX, Monte Carlo particle transport code for use in shielding designs by the Midwest Proton Therapy Center.

Simwalk. Genetics and pedigrees HPA has optimized the serial (single processor) version of the Simwalk program, used by the Department of Medical Genetics to study the genetic components of diseases (such as alcoholism). This decreased the time required to complete an analysis by 70%. HPA staff then increased the maximum number of affected descended from the pedigree founders in non-parametric linkage analysis from 20 to 30.

CRIMap HPA worked with the Medical Genetics Department to extend the capabilities of a supercomputer version of CRIMap.

SHELX This program, used by the Department of Molecular Biology to compute protein structure, has been ported to the Research SP and AVIDD cluster.

RegRegion HPA staff have implemented a parallel version of a code used by the IUB Department of Biology to simulate the evolution of the modular structure of a two-function regulatory region of a locus, before and after duplication.

INGEN IT Core room MSB 223 has been renovated for use by INGEN researchers.

GeneIndex. HPA has worked with the Center for Genomics and Bioinformatics to create a new software application. GeneIndex indexes and matches patterns in DNA sequences, and is used in inference of amino acid sequences.

NBPack. implemented and optimized a serial version of a code based upon an advanced data structure, being used by the Center for Cell and Virus Theory to study processes occurring over many different scales of space and time.

fastDNAml. HPA staff have implemented a parallel version of this code, used by the Department of Biology and the School of Informatics to compute most likely phylogenies, and has ported it to multiple environments.

PerfectMatch Working with the Department of Medicine's Biostatistics Division, the IT core is working to improve detection of weak signals in microarray data.

Extracting genetic information from MEDLINE. Based on trie data structure, we are working with the Biochemistry Department and the Computer Science Department to extract gene information in MEDLINE database. This part will eventually be incorporated into the BioMap application.

Publications by HPA Staff

Pavlis, G. L., P. Wang, F.L. Vernon, "Array Processing of Large Aperture Seismic Arrays with Generalized Cross-Correlation" (Invited talk to special session on signal processing of the meeting of the American Geophysical Union), Dec 2005

Ellisman, M., M. Brady, D. Hart, F.P. Lin, M. Muller, L. Smarr, "The Emerging Role of Biogrids", Communications of the ACM, 47:11, 2004.

Horowitz, C. J., M. A. Perez-Garcia, D. K. Berry, J. Piekarewicz, "Dynamical response of the nuclear pasta in neutron star crusts", Physical Review C 72, 035801 (2005)

Horowitz, C. J., M. A. Perez-Garcia, J. Carriere, D. K. Berry, J. Piekarewicz, "Nonuniform neutron-rich matter and coherent neutrino scattering", Physical Review C 70, 065806 (2004)

Stewart, C.A. R. Keller, R. Repasky, M. Hess, D. Hart, M. Mueller, R. Sheppard, U. Woessner, M. Aumueller, Huian Li, D.K. Berry, J. Colbourne, "A global grid for analysis of arthropod evolution", in: R. Buyya (ed.) Proceedings: Fifth IEEE/ACM International Workshop on Grid Computing, pp. 328-337, Pittsburgh, PA 2004.

Stewart, C.A., D. Hart, R.W. Sheppard, H. Li, R. Cruise, V. Moskvin, L. Papiez, Parallel computing in biomedical research and the search for peta-scale biomedical applications, pp. 719-716 In: G.R. Joubert, W.E. Nagel, F.J. Peters, and W.V. Walter (eds). Parallel computing: software technology, algorithms, architectures & applicaitons. Advances in Parallel Computing Vol. 13. Elsevier, Oxford. 2004.

Zina Ben Miled, Jin Liu, Omran Bukhres, Huian Li, J. Martin, C. Balagopalakrishna, Robert Oppelt, Use and Maintenance of Histograms for Large Scientific Database Access Planning: A Case Study of a Pharmaceutical Data Repository, Intelligent Information Systems, Vol 23-2, pp. 145-178, September, 2004.

Wang P., Turner G., Simms S., Hart D., Papakhian M., and Stewart A. C., "1 TFLOPS Achieved with a Geographically Distributed Linux Cluster", Part 4, Cluster and Grid Computing, High Performance Computing: Paradigm and Infrastructure, John Wiley & Sons, 2004

Wang P., Turner G., Lauer A. D., Allen M., Simms S., Hart D., Papakhian M., and Stewart A. C.,  "LINPACK Performance on a Geographically Distributed Linux Cluster", Proceedings of the 18th  International Parallel and Distributed Processing Symposium, IPDPS 2004, Santa Fe, New Mexico, April  26-30, 2004

Kamal Kumar, Mathew J. Palakal, Snehasis Mukhopadhyay, Mathew J. Stephens, Huian Li, "BioMap: Toward the Development of a Knowledge Base of Biomedical Literature," 19th Annual ACM Symposium on Applied Computing, Cyprus, March 14 -17, 2004

Stewart, C.A., R. Repasky, J. Colbourne, D. Hart, D. K. Berry, R. Sheppard, E. Wernert, M. Papakhian, J. N. Huffman. "Global analysis of arthropod evolution", Proceedings of I-Light Applications Workshop, 9 March 2004, Indianapolis, IN.

Wernert, E. A., D. K. Berry, J. N. Huffman, C. A. Stewart, "Tree3D - A System for Temporal and Comparative Analysis of Phylogenetic Trees." Proceedings of IEEE Information Visualization 2003, Seattle, WA, October 2003.

Stewart, C.A., Repasky, R., Hart, D., Papakhian, M., Shankar, A., Wernert,E., Arenson, A., and G. Bernbom, "Advanced Information Technology Support For Life Sciences Research." Proceedings of SIGUCCS 2003, San Antonio, TX.

Stewart, C.A., Repasky, R., Hart, D., Papakhian, M., Shankar, A., Wernert,E., Arenson, A., and G. Bernbom. 2003, "Advanced Information Technology Support For Life Sciences Research. " Presented at SIGUCCS 2003, Sept. 21-24, San Antonio, TX.

Hart, D., Grover, D., Liggett, M., Repasky, R., Shields, C., Simms, S., Sweeny, A., and Wang, P, "Distributed Parallel Computing Using Windows Desktop Systems." Proceedings of CLADE 2003, June 20-27, 2003, Seattle, WA.

Pickett, B. K., A. C. Mejia, R. H. Durisen, P. M. Cassen, D. K. Berry, R. P. Link, "The thermal regulation of gravitational instabilities in protoplanetary disks", The Astrophysical Journal, 590:1060-1080, June 20, 2003

Cruise, R.B., Papiez, L.S, "Integral Equation Formulation of a Mixed Diffusion-Jump Model of Elastic Scattering." Nuclear Mathematical and Computational Sciences: A Century in Review, A Century Anew, Gatlinburg, Tennessee, April 6-11, 2003, on CD-ROM, American Nuclear Society, LaGrange Park, IL.

Cruise, R.B., Sheppard, R.W, Moskvin, V.P., "Parallelization of the Penelope Monte Carlo Particle Transport Simulation Package." Nuclear Mathematical and Computational Sciences: A Century in Review, A Century Anew, Gatlinburg, Tennessee, April 6-11, 2003, on CD-ROM, American Nuclear Society, LaGrange Park, IL.

Stewart, C., Hart, D., Berry, D.K., Olsen, G.J., Wernert, E., Fischer, W., "Parallel implementation and performance of fastDNAml - a program for maximum likelihood phylogenetic inference." Proceedings of SC2001. Denver, Colorado, November 2001.

Stewart C., Peebles C.S., Papakhian, M., Samuel, J., Hart, D., Simms, S., "High Performance Computing: Delivering Valuable and Valued Services at Colleges and Universities." Proceedings of SIGUCCS 2001. Portland, Oregon, October 2001.

Presentations by HPA Staff

Gopu A., Grover D., Hart. D, Repasky R., Rinkovsky J., Simms S., Sweeny A., Wang P., " HYDRA: Using Windows Desktop Systems in Distributed Parallel Computing", Booth presentation, Super Computing '05 Conference, Seattle, WA, Nov 18 2005. (Download latest version of presentation)

Gopu A., Grover D., Hart. D, Repasky R., Rinkovsky J., Simms S., Sweeny A., Wang P., " HYDRA: Using Windows Desktop Systems in Distributed Parallel Computing", Workshop presentation, GGF15-CampusGrids, Boston, MA, Oct 2 2005.

Pavlis, G. L., P. Wang, F.L.Vernon, Array Processing of Large Aperture Seismic Arrays with Generalized Cross-Correlation (Invited talk to Special Session on Signal Processing of the American Geophysical Union, Dec. 2005.

Horowitz, C. J., M. A. Perez-Garcia, J. Carriere, D. K. Berry, J. Piekarewicz, "Computer simulation of neutron rich matter using the MDGRAPE-2", presentation at the IU booth at SC2005, Seattle, WA, Nov 14-18, 2005

Berry D. K., "Computer simulation of neutron rich matter using the MDGRAPE-2", NSF TeraGrid Site Visit meeting, May 23, 2005.

Hart, D., High Performance Computing Support at IU, Center for Genomics and Bioinformatics Roundtable, February 3, 2005.

Stewart, C.A., R. Repasky, J. Colbourne, D. Hart, D.K. Berry, R. Sheppard, E. Wernert, M. Papakhian, J.N. Huffman, Global analysis of arthropod evolution. 2nd I-light Symposium, 9 March 2004.

Stewart C., Turner G., Wang P., Hart D., Simms S., Lauer D., Papakhian M., Allen M., Squyres J., and Lumstaine A., "1 Tflops Achieved with Distributed Linux Cluster", poster, SC2003, Phoenix, Arizona, Nov  15-21, 2003

Robert Cruise, "Adaptive Monte Carlo Methods," Department of Radiation Oncology Colloquium, IU School of Medicine, June 14, 2002.

Olsen, G. J., R. Repasky, W. Fischer, D. C. Hart, D. K. Berry, C. A. Stewart, "Parallel implementation of fastDNAml, a program for maximum likelihood estimation of phylogenetic trees", poster, First SIAM Conference on the Life Sciences, Boston, MA, March 6-8, 2002