High Performance Biocomputation

By Abarbanel, Henry

Book Id: WPLBN0000096807
Format Type: PDF eBook:
File Size: 2.05 MB
Reproduction Date: 2008

Title:	High Performance Biocomputation
Author:	Abarbanel, Henry
Volume:
Language:	English
Subject:	Government publications, Legislation., Government Printing Office (U.S.)
Collections:	Government Library Collection
Historic Publication Date:
Publisher:	Government Printing Office


Citation APA MLA Chicago Abarbanel, B. H. (n.d.). High Performance Biocomputation. Retrieved from http://self.gutenberg.org/

Excerpt
Excerpt: This section summarizes the conclusions and recommendations of the 2004 JASON summer study commissioned by the Department of Energy (DOE) to explore the opportunities and challenges presented by applying advanced computational power and methodology to problems in the biological sciences. JASON was tasked to investigate the current suite of computationally intensive problems as well as potential future endeavors. JASON was also tasked to consider how advanced computational capability and capacity could best be brought to bear on bioscience problems and to explore how different computing approaches such as Grid computing, supercomputing, cluster computing or custom architectures might map onto interesting biological problems.

Table of Contents
Contents 1 EXECUTIVE SUMMARY 1 2 INTRODUCTION 9 2.1 The Landscape of Computational Biology . . . . . . . . . . . 10 2.2 Character of Computational Resources . . . . . . . . . . . . . 13 2.3 Grand challenges . . . . . . . . . . . . . . . . . . . . . . . . . 16 3 MOLECULAR BIOPHYSICS 19 3.1 Imaging of Biomolecular Structure . . . . . . . . . . . . . . . 20 3.2 Large-scalemolecular-based simulations in biology . . . . . . . 22 3.3 Protein Folding . . . . . . . . . . . . . . . . . . . . . . . . . . 30 3.4 A Potential Grand Challenge - The Digital Ribosome . . . . . 35 3.5 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 4 GENOMICS 43 4.1 Sequence Data Collection . . . . . . . . . . . . . . . . . . . . 43 4.2 Computational Challenges . . . . . . . . . . . . . . . . . . . . 46 4.2.1 DNA read overlap recognition and genome assembly . . 46 4.2.2 Phylogenetic tree reconstruction . . . . . . . . . . . . . 46 4.2.3 Cross-species genome comparisons . . . . . . . . . . . . 47 4.2.4 Data Integration . . . . . . . . . . . . . . . . . . . . . 48 4.3 A Potential Grand Challenge - Ur-Shrew . . . . . . . . . . . . 49 5 NEUROSCIENCE 55 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 5.2 A Potential Grand Challenge — The Digital Retina . . . . . . . 59 6 SYSTEMS BIOLOGY 65 6.1 The Validity of the Circuit Approach . . . . . . . . . . . . . . 68 6.2 A Possible Grand Challenge: Bacterial Chemotaxis . . . . . . 74 7 CONCLUSIONS AND RECOMMENDATIONS 75 7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 7.2 Findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 7.3 Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . 78 A APPENDIX: Briefers 81