Current mammographic screeningfor breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Bec...
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The following topics are dealt with: genomics; transcriptomes; proteomics; applied bioinformatics; data mining; ontology; comparative genomics; evolution and phylogenetics; functional genomics; high performance comput...
The following topics are dealt with: genomics; transcriptomes; proteomics; applied bioinformatics; data mining; ontology; comparative genomics; evolution and phylogenetics; functional genomics; high performance computing; pathways network systems biology; pattern recognition; promoter analysis; protein structure analysis; and sequence alignment.
Heterogeneous administrative domains, operating systems (OS), and libraries make it difficult for computational scientists to fully utilize metacomputers and grids. Dealing with the presence or absence of features on,...
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ISBN:
(纸本)9780955301827
Heterogeneous administrative domains, operating systems (OS), and libraries make it difficult for computational scientists to fully utilize metacomputers and grids. Dealing with the presence or absence of features on, say, different clusters, adds complexity. How can a user or high-performance computing (HPC) application abstract out the heterogeneity? One possible solution is to use a virtual machine (VM) environment that supports guest operating systems and virtual disks. But, over the decades, VMs have sometimes suffered from performance overheads and limited platforms on which they can run. Through a simple quantitative study, we show that recent improvements in software and hardware support reduces the overheads for HPC applications (e.g., GROMACS, BLAST, HMMer) to under 6% for compute-intensive jobs, but 9.7% or higher for more I/O-intensive jobs, on our x86-based platform. We also argue for qualitative and pragmatic benefits of using VMs for HPC, including ease of deployment, improved functionality, and the ability to run jobs on more systems than would normally be accessible. While not perfect, VMs are emerging as a pragmatic tool in HPC.
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the most important currently outstanding q...
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ISBN:
(纸本)9781595937063
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry and medicine. A wide range of biologically interesting phenomena, however, occur over time scales on the order of a millisecond-about three orders of magnitude beyond the duration of the longest current MD simulations. In this paper, we describe a massively parallel machine called Anton, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems. The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized high-speed communication network. Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation. The remainder of the simulation algorithm is executed by a programmable portion of each chip that achieves a substantial degree of parallelism while preserving the flexibility necessary to accommodate anticipated advances in physical models and simulation methods.
This work proposes a fuzzy multimodal technique capable of guaranteeing the desired level of security while keeping under control the high costs typically associated to some biometric authentication devices. Specifica...
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This work proposes a fuzzy multimodal technique capable of guaranteeing the desired level of security while keeping under control the high costs typically associated to some biometric authentication devices. Specifically we describe a fuzzy controller choosing within a palette of authentication techniques to continuously check and confirm its trust in the identity of a user.
This talk will trace the growing influence of fundamental ideas from computer science on the nature of research in a number of scientific fields. There is a growing awareness that information processing lies at the he...
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This talk will trace the growing influence of fundamental ideas from computer science on the nature of research in a number of scientific fields. There is a growing awareness that information processing lies at the heart of the processes studied in fields as diverse as quantum mechanics, statistical physics, nanotechnology, neuroscience, linguistics, economics and sociology. Increasingly, mathematical models in these fields are expressed in algorithmic languages and describe algorithmic processes. The speaker will briefly describe connections between quantum computing and the foundations of quantum mechanics, and between statistical mechanics and phase transitions in computation. He will indicate how the growth of the Web has created new phenomena to be investigated by sociologists and economists. He will then focus in greater detail on computational molecular biology, where the view of living cells as complex information processing systems has become the dominant paradigm, and will discuss specific algorithmic problems arising in the sequencing of genomes, the comparative analysis of the resulting genomic sequences, the modeling of networks of interacting proteins, and the associations between genetic variation and disease.
This talk will trace the growing influence of fundamental ideas from computer science on the nature of research in a number of scientific fields. There is a growing awareness that information processing lies at the he...
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This talk will trace the growing influence of fundamental ideas from computer science on the nature of research in a number of scientific fields. There is a growing awareness that information processing lies at the heart of the processes studied in fields as diverse as quantum mechanics, statistical physics, nanotechnology, neuroscience, linguistics, economics and sociology. Increasingly, mathematical models in these fields are expressed in algorithmic languages and describe algorithmic processes. The speaker will briefly describe connections between quantum computing and the foundations of quantum mechanics, and between statistical mechanics and phase transitions in computation. He will indicate how the growth of the Web has created new phenomena to be investigated by sociologists and economists. He will then focus in greater detail on computational molecular biology, where the view of living cells as complex information processing systems has become the dominant paradigm, and will discuss specific algorithmic problems arising in the sequencing of genomes, the comparative analysis of the resulting genomic sequences, the modeling of networks of interacting proteins, and the associations between genetic variation and disease.
Innovations in computational biology such as high throughput genomic technologies have resulted in numerous large databases containing genomic information which are being annotated with terms from the gene ontology to...
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Innovations in computational biology such as high throughput genomic technologies have resulted in numerous large databases containing genomic information which are being annotated with terms from the gene ontology to ensure consistency of the referenced biological concepts. These annotations are being used in determining the similarity between genes and gene products, an important task in post-genomics study. This paper presents an investigation of similarity measures between annotated objects with a focus on the domain of computational biology and the gene ontology. A framework for experimenting with and developing new similarity measures between annotated objects in other domains is discussed in the context of the querying with ontological terminologies and their annotations (QUOTA) system currently being developed.
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