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Catalyzing Inquiry at the Interface of Computing and Biology (2005) / Chapter Skim
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B Challenge Problems in Bioinformatics and Computational Biology from Other Reports
Pages 429-436

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From page 429...
... Improve multiresolution structure prediction 5. Combine classical molecular dynamics simulations with quantum chemical forces 6.
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From page 430...
... Data management · Data modeling and data structure design · Query algorithms, especially across heterogeneous data types · Data server communication, especially peer-to-peer replication · Distributed memory management and process management B.4 WORKSHOP ON NEXT-GENERATION BIOLOGY: THE ROLE OF NEXT-GENERATION COMPUTING (Shankar Subramaniam and John Wooley) 4 Exemplar Challenges for Bioinformatics and Computational Biology 1.
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From page 431...
... Precise, predictive model of RNA splicing/alternative splicing: ability to predict the splicing pattern of any primary transcript 3. Precise, quantitative models of signal transduction pathways:ability to predict cellular response to external stimuli 4.
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From page 432...
... Integrating Earth and human systems 11. A knowledge server for planetary management Research Across Domains: Data · Information management -- human evolution continued · Exponential increase in data and information across domains · Access to information across domains -- as or more important than the information itself · Integration of data across knowledge domains · Apply analytical tools across knowledge domains · Modeling of complex systems · Simulation of phenomena -- descriptive science becomes predictive science Research Across Domains: People · Share data across disciplines · Build and use analytical and modeling tools across disciplines · Work in collaborative, cross-domain groups Research Across Domains: Time · Real-time data access, integration, and analysis · Real-time modeling and effects prediction · Real-time dissemination of research results · Real-time testing by research community · Real-time policy discussions · Real-time policy decisions 8S.
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From page 433...
... restoration of hearing, coarse vision, and locomotion (via both paralyzed and artificial limbs) All of these applications make use of: · Three-dimensional models · Increasingly refined grids and increasing levels of tissue discrimination · Anatomically realistic models · Special-purpose hardware for visualization · Distributed computing techniques.
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From page 434...
... Development of open source, multiscale modality informatics toolkits B.12 THE DEPARTMENT OF ENERGY'S GENOMES TO LIFE PROGRAM12 21st Century Biology Requiring "Biocomp" Tools 1. Population models, symbiosis, and stability 2.
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From page 435...
... Stochastic simulation of cell signaling pathways 9. Complex dynamics of cell cycle regulation 10.
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Key Terms

  • molecular biomedicine
  • structure prediction
  • computational biology
  • data mining
  • biomedical computing

  • mechanistic understanding
  • cell signaling
  • protein folding
  • knowledge domains
  • predictive model

  • metabolic pathways
  • teraflop computing
  • ieee circuits
  • image analysis
  • protein func

  • chemical species
  • improve multiresolution
  • artificial limbs
  • john wooley
  • drug discovery

  • teraflop technologies
  • model networks
  • clinical decision
  • relevant time
  • investigate integral

  • neural nets
  • disease outbreak
  • policy discussions
  • simulation modeling
  • stochastic simulation


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