B.3 WORKSHOP ON MODELING OF BIOLOGICAL SYSTEMS (Peter Kollman and Simon Levin)3

Challenging Issues That Span All Areas of Modeling Systems
  1. Integrating data and developing models of complex systems across multiple spatial and temporal scales

    • Scale relations and coupling

    • Temporal complexity and coding

    • Parameter estimation and treatment of uncertainty

    • Statistical analysis and data mining

    • Simulation modeling and prediction

  1. Structure-function relationships

    • Large and small nucleic acids

    • Proteins

    • Membrane systems

    • General macromolecular assemblies

    • CeIlular, tissue, organismal systems

    • Ecological and evolutionary systems

  1. Image analysis and visualization

    • Image interpretation and data fusion

    • Inverse problems

    • Two-, three- and higher-dimensional visualization and virtual reality

  1. Basic mathematical issues

    • Formalisms for spatial and temporal encoding

    • Complex geometry

    • Relationships between network architecture and dynamics

    • Combinatorial complexity

    • Theory for systems that combine stochastic and nonlinear effects often in partially distributed systems

  1. 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. Full genome-genome comparisons

  2. Rapid assessment of polymorphic genetic variations

3  

“Modeling of Biological Systems,” P. Kollman and S. Levin (chairs), a workshop at the National Science Foundation, March 14 and 15, 1996, available at http://www.resnet.wm.edu/~jxshix/math490/Modeling%20of%20Biological%20Systems.htm.

4  

S. Subramaniam and J. Wooley, DOE-NSF-NIH 1998 Workshop on Next-Generation Biology: The Role of Next Generation Computing, available at http://cbcg.lbl.gov/ssi-csb/nextGenBioWS.html.



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