. "B Challenge Problems in Bioinformatics and Computational Biology from Other Reports." Catalyzing Inquiry at the Interface of Computing and Biology. Washington, DC: The National Academies Press, 2005.
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Catalyzing Inquiry at the Interface of Computing and Biology
B.3WORKSHOP ON MODELING OF BIOLOGICAL SYSTEMS (Peter Kollman and Simon Levin)3
Challenging Issues That Span All Areas of Modeling Systems
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
Structure-function relationships
Large and small nucleic acids
Proteins
Membrane systems
General macromolecular assemblies
CeIlular, tissue, organismal systems
Ecological and evolutionary systems
Image analysis and visualization
Image interpretation and data fusion
Inverse problems
Two-, three- and higher-dimensional visualization and virtual reality
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
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.4WORKSHOP ON NEXT-GENERATION BIOLOGY: THE ROLE OF NEXT-GENERATION COMPUTING (Shankar Subramaniam and John Wooley)4
Exemplar Challenges for Bioinformatics and Computational Biology
Full genome-genome comparisons
Rapid assessment of polymorphic genetic variations
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.
