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Deep computing for the life sciences

Vol. 40, No. 2, 2001

Order No. G321-0141

Knowledge gained from the sequencing of the human genome promises to change our lives. Powerful computing techniques have been used to acquire the knowledge gained so far, and still more powerful techniques will be required to fulfill the promises of genetically based drug design, medical diagnosis and treatment, and agricultural applications, among others. This issue of the IBM Systems Journal—and the companion issue of the IBM Journal of Research and Development—is devoted to papers on deep computing for life sciences. Included in this issue are papers that address associated biological, computational, and informational challenges.
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Message from the Vice President, Life Sciences Solutions Caroline A. Kovac
Preface John J. Ritsko and Marilyn L. Bates p. 247
Deep computing for the life sciences W. C. Swope p. 248
Computational challenges in structural and functional genomics T. Head-Gordon and J. C. Wooley p. 265
Computational protein folding: From lattice to all-atom Y. Duan and P. A. Kollman p. 297
Blue Gene: A vision for protein science using a petaflop supercomputer IBM Blue Gene team p. 310
Load balancing of molecular dynamics simulation with NWChem T. P. Straatsma and J. A. McCammon p. 328
Mapping, modeling, and visual exploration of structure-function relationships in the heart R. L. Winslow, D. F. Scollan, J. L. Greenstein, C. K. Yung, W. Baumgartner, Jr., G. Bhanot, D. L. Gresh, and B. E. Rogowitz p. 342
Large-scale virtual screening for discovering leads in the postgenomic era B. Waszkowycz, T. D. J. Perkins, R. A. Sykes, and J. Li p. 360
Functional classification of proteins by pattern discovery and top-down clustering of primary sequences A. H. Liu and A. Califano p. 379
Intelligent decision support for protein crystal growth I. Jurisica, P. Rogers, J. I. Glasgow, S. Fortier, J. R. Luft, J. R. Wolfley, M. A. Bianca, D. R. Weeks, and G. T. DeTitta p. 394
Convergent evolution of protein structure prediction and computer chess tournaments: CASP, Kasparov, and CAFASP N. Siew and D. Fischer p. 410
New techniques for extracting features from protein sequences J. T. L. Wang, Q. Ma, D. Shasha, and C. H. Wu p. 426
Fastfinger: A study into the use of compressed residue pair separation matrices for protein sequence comparison B. Robson p. 442
A high-throughput distributed DNA sequence analysis and database system J. T. Inman, H. R. Flores, G. D. May, J. W. Weller, and C. J. Bell p. 464
DiscoveryLink: A system for integrated access to life sciences data sources L. M. Haas, P. M. Schwarz, P. Kodali, E. Kotlar, J. E. Rice, and W. C. Swope p. 489
K2/Kleisli and GUS: Experiments in integrated access to genomic data sources S. B. Davidson, J. Crabtree, B. P. Brunk, J. Schug, V. Tannen, G. C. Overton, and C. J. Stoeckert, Jr. p. 512
Transparent access to multiple bioinformatics information sources C. A. Goble, R. Stevens, G. Ng, S. Bechhofer, N. W. Paton, P. G. Baker, M. Peim, and A. Brass p. 532
GeneX: An Open Source gene expression database and integrated tool set H. Mangalam, J. Stewart, J. Zhou, K. Schlauch, M. Waugh, G. Chen, A. D. Farmer, G. Colello, and J. W. Weller p. 552
An integration platform for heterogeneous bioinformatics software components A. C. Siepel, A. N. Tolopko, A. D. Farmer, P. A. Steadman, F. D. Schilkey, B. D. Perry, and W. D. Beavis p. 570
The GeneMine system for genome/proteome annotation and collaborative data mining C. Lee and K. Irizarry p. 592