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Deep computing for the life sciencesVol. 40, No. 2, 2001
Order No. G321-0141 |
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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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Papers may be viewed by clicking on the title of interest |
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Message from the Vice President, Life Sciences Solutions |
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Caroline A. Kovac |
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Preface |
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John J. Ritsko and Marilyn L. Bates |
p. 247 |
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Deep computing for the life sciences |
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W. C. Swope |
p. 248 |
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Computational challenges in structural and functional genomics |
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T. Head-Gordon and J. C. Wooley |
p. 265 |
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Computational protein folding: From lattice to all-atom |
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Y. Duan and P. A. Kollman |
p. 297 |
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Blue Gene: A vision for protein science using a petaflop supercomputer |
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IBM Blue Gene team |
p. 310 |
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Load balancing of molecular dynamics simulation with NWChem |
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T. P. Straatsma and J. A. McCammon |
p. 328 |
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Mapping, modeling, and visual exploration of structure-function relationships in the heart |
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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 |
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Large-scale virtual screening for discovering leads in the postgenomic era |
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B. Waszkowycz, T. D. J. Perkins, R. A. Sykes, and J. Li |
p. 360 |
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Functional classification of proteins by pattern discovery and top-down clustering of primary sequences |
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A. H. Liu and A. Califano |
p. 379 |
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Intelligent decision support for protein crystal growth |
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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 |
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Convergent evolution of protein structure prediction and computer chess tournaments: CASP, Kasparov, and CAFASP |
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N. Siew and D. Fischer |
p. 410 |
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New techniques for extracting features from protein sequences |
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J. T. L. Wang, Q. Ma, D. Shasha, and C. H. Wu |
p. 426 |
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Fastfinger: A study into the use of compressed residue pair separation matrices for protein sequence comparison |
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B. Robson |
p. 442 |
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A high-throughput distributed DNA sequence analysis and database system |
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J. T. Inman, H. R. Flores, G. D. May, J. W. Weller, and C. J. Bell |
p. 464 |
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DiscoveryLink: A system for integrated access to life sciences data sources |
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L. M. Haas, P. M. Schwarz, P. Kodali, E. Kotlar, J. E. Rice, and W. C. Swope |
p. 489 |
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K2/Kleisli and GUS: Experiments in integrated access to genomic data sources |
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S. B. Davidson, J. Crabtree, B. P. Brunk, J. Schug, V. Tannen, G. C. Overton, and C. J. Stoeckert, Jr. |
p. 512 |
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Transparent access to multiple bioinformatics information sources |
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C. A. Goble, R. Stevens, G. Ng, S. Bechhofer, N. W. Paton, P. G. Baker, M. Peim, and A. Brass |
p. 532 |
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GeneX: An Open Source gene expression database and integrated tool set |
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H. Mangalam, J. Stewart, J. Zhou, K. Schlauch, M. Waugh, G. Chen, A. D. Farmer, G. Colello, and J. W. Weller |
p. 552 |
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An integration platform for heterogeneous bioinformatics software components |
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A. C. Siepel, A. N. Tolopko, A. D. Farmer, P. A. Steadman, F. D. Schilkey, B. D. Perry, and W. D. Beavis |
p. 570 |
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The GeneMine system for genome/proteome annotation and collaborative data mining |
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C. Lee and K. Irizarry |
p. 592 |
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