الصفحة 1
الصفحة 1
New Algorithms for Macromolecular Simulation
Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.
Networks : From Biology to Theory
The concept of a network emerges as a powerful and stimulating research paradigm in mathematics, physics and computer science, and demonstrates a very lively interaction between experimental findings, simulation studies, and theoretical investigations that then in turn lead to new experimental questions. This volume explores this concept in full and features contributions from a truly global set of contributors.
Intelligence and security informatics : Biosurveillance ; 2nd NSF Workshop, BioSurveillance 2007, New Brunswick, NJ, USA, May 22, 2007, Proceedings
The 2007 NSF BioSurveillance Workshop (BioSurveillance 2007) was built on the success of the first NSF BioSurveillance Workshop, hosted by the University of Arizona’s NSF BioPortal Center in March 2006.
Implementation and Application of Automata ; Vol. 4094 ; 11th International Conference, CIAA 2006, Taipei, Taiwan, August 21-23, 2006, Proceedings
This book constitutes the refereed proceedings of the 11th International Conference on Implementation and Application of Automata, CIAA 2006, held in Taipei, Taiwan, in August 2006.
Grid computing in life science ; 1st International Workshop on Life Science Grid, LSGRID 2004 Kanazawa, Japan, May 31-June 1, 2004, Revised Selected and Invited Papers
Researchers in the ?eld of life sciences rely increasingly on information te- nology to extract and manage relevant knowledge. The complex computational and data management needs of life science research make Grid technologies an attractive support solution. However, many important issues must be addressed before the Life Science Grid becomes commonplace. The 1st International Life Science Grid Workshop (LSGRID 2004) was held in Kanazawa Japan, May 31–June 1, 2004. This workshop focused on life s- ence applications of grid systems especially for bionetwork research and systems biology which require heterogeneous data integration from genome to phenome, mathematical modeling and simulation from molecular to population levels, and high-performance computing including parallel processing, special hardware and grid computing.
Frontiers of high performance computing and networking – ISPA 2006 workshops ; ISPA 2006 International workshops FHPCN, XHPC, S-GRACE, GridGIS, HPC-GTP, PDCE, ParDMCom, WOMP, ISDF, and UPWN, Sorrento, Italy, December 4 -7, 2006, Proceedings
This book constitutes the refereed joint proceedings of ten internationl workshops held in conjunction with the 4th International Symposium on Parallel and Distributed Processing and Applications, ISPA 2006, held in Sorrento, Italy in December 2006 (see LNCS 4330). Topics addressed are frontiers of high performance computing and networking (FHPCN 2006), XEN in HPC cluster and grid computing environments (XHPC 2006), semantic grid applications in computing and engineering (S-GRACE 2006), fertilization of grid computing and geographic information system (GridGIS 2006), high performance computing in genomic proteomic and transcriptomic (HPC-GTP 2006), parallel and distributed computing in engineering (PDCE 2006), parallel and distributed multimedia computing (ParDMCom 2006), middleware performance (WOMP 2006), information security and digital forensics (ISDF 2006), and ubiquitous processing for wireless networks (UPWN 2006).
Ergodic Dynamics : From Basic Theory to Applications
This textbook provides a broad introduction to the fields of dynamical systems and ergodic theory. Motivated by examples throughout, the author offers readers an approachable entry-point to the dynamics of ergodic systems. Modern and classical applications complement the theory on topics ranging from financial fraud to virus dynamics, offering numerous avenues for further inquiry. Starting with several simple examples of dynamical systems, the book begins by establishing the basics of measurable dynamical systems, attractors, and the ergodic theorems. From here, chapters are modular and can be selected according to interest. Highlights include the Perron–Frobenius theorem, which is presented with proof and applications that include Google PageRank. An in-depth exploration of invariant measures includes ratio sets and type III measurable dynamical systems using the von Neumann factor classification. Topological and measure theoretic entropy are illustrated and compared in detail, with an algorithmic application of entropy used to study the papillomavirus genome. A chapter on complex dynamics introduces Julia sets and proves their ergodicity for certain maps. Cellular automata are explored as a series of case studies in one and two dimensions, including Conway’s Game of Life and latent infections of HIV. Other chapters discuss mixing properties, shift spaces, and toral automorphisms.
Distributed, High-Performance and Grid Computing in Computational Biology ; International Workshop, GCCB 2006, International Workshop, GCCB 2006, Eilat, Israel, January 21, 2007, Proceedings
Modern computational biology and bioinformatics are characterized by large and complex structured data and by applications requiring considerable computing resources, such as processing units, storage elements and software programs. In addition, these disciplines are intrinsically geographically distributed in terms of their instruments, communities and computing resources. Tackling the computational challenges in computational biology and bioinformatics increasingly requires high-end and distributed computing infrastructures, systems and tools.
Distributed and parallel computing ; 6th International conference on algorithms and architectures for parallel processing, ICA3PP, Melbourne, Australia, October 2-3, 2005, Proceedings
There are many applications that require parallel and distributed processing to allow complicated engineering, business and research problems to be solved in a reasonable time. Parallel and distributed processing is able to improve company profit, lower costs of design, production, and deployment of new technologies, and create better business environments. The major lesson learned by car and aircraft engineers, drug manufacturers, genome researchers and other specialist is that a computer system is a very powerful tool that is able to help them solving even more complicated problems. That has led computing specialists to new computer system architecture and exploiting parallel computers, clusters of clusters, and distributed systems in the form of grids.
Data Mining in Bioinformatics
8. 1. 1 Protein Subcellular Location The life sciences have entered the post-genome era where the focus of biological research has shifted from genome sequences to protein functionality. Withwhole-genomedraftsofmouseandhumaninhand,scientistsareputting more and more e?ort into obtaining information about the entire proteome in a given cell type. The properties of a protein include its amino acid sequences, its expression levels under various developmental stages and in di?erent tissues, its3Dstructure and activesites,its functionalandstructural binding partners, and its subcellular location. Protein subcellular location is important for understanding protein function inside the cell. For example, the observation that the product of a gene is localized in mitochondria will support the hypothesis that this protein or gene is involved in energy metabolism. Proteins localized in the cytoskeleton are probably involved in intracellular tra?cking and support.
Data Mining for Biomedical Applications ; PAKDD 2006 Workshop, BioDM 2006, Singapore, April 9, 2006, Proceedings
This book constitutes the refereed proceedings of the International Workshop on Data Mining for Biomedical Applications, BioDM 2006, held in Singapore in conjunction with the 10th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2006). The 14 revised full papers presented together with 1 keynote talks were carefully reviewed and selected from 35 submissions. The papers are organized in topical sections on protein-protein interactions, database and search, bio data clustering, and in-silico diagnosis.
Data Integration in the Life Sciences ; Vol. 4075 ; 3rd International Workshop, DILS 2006, Hinxton, UK, July 20-22, 2006, Proceedings
Data management and data integration are fundamental problems in the life sciences. Advances in molecular biology and molecular medicine are almost u- versallyunderpinned by enormouse?orts in data management,data integration, automatic data quality assurance, and computational data analysis. Many hot topics in the life sciences, such as systems biology, personalized medicine, and pharmacogenomics, critically depend on integrating data sets and applications producedby di?erent experimentalmethods, in di?erent researchgroups,andat di?erent levels of granularity.
Data Integration in the Life Sciences ; 4th International Workshop, DILS 2007, Philadelphia, PA, USA, June 27-29, 2007, Proceedings
it cover a wide spectrum of theoretical and practical issues including scienti?c work?ows, - notation in data integration, mapping and matching techniques, and modeling of life science data. It presenting research on new models, methods, or algorithms and 6 papers presenting imp- mentation of systems or experience with systems in practice.
Computational Life Sciences ; Vol. 4216 ; 2nd International Symposium, CompLife 2006, Cambridge, UK, September 27-29, 2006, Proceedings
This book constitutes the refereed proceedings of the Second International Symposium on Computational Life Sciences, CompLife 2006. The papers are organized in topical sections on genomics, data mining, molecular simulation, molecular informatics, systems biology, biological networks/metabolism, and computational neuroscience.
Computational Life Sciences ; Vol. 3695 ; 1st International Symposium, CompLife 2005, Konstanz, Germany, September 25-27, 2005, Proceedings
This book constitutes the refereed proceedings of the First International Symposium on Computational Life Sciences, CompLife 2005, held in Konstanz, Germany in September 2005. The integration of knowledge in the life sciences is continuing apace with ev- increasingimportancebeing placedoncomputer-basedmethodsofdata capture, analysis, and knowledge representation. Today, our many di?erent sciences are providing us with a sea of information: it is the handling of this in?ux that is becoming a key discovery and regulatory question. The solutions to these problems will result in advancements to all of the involved sciences and will be highly in?uential both in the selection of the areas scientists seek to investigate and also on their success. For this to happen, it is crucial to establish an open and lively exchange between computer scientists, biologists, and chemists. To encourage precisely this type of exchange, crossing the borders of the sciences, we organized the 1st Symposium on Computational Life Science in Konstanz, Germany(September 25 27,2005).
Computational intelligence and bioinformatics ; International conference on intelligent computing, ICIC 2006, Kunming, China, August 16-19, 2006, Proceedings, Part III
The International Conference on Intelligent Computing (ICIC) was formed to provide an annual forum dedicated to the emerging and challenging topics in artificial intelligence, machine learning, bioinformatics, and computational biology, etc. It aims to bring together researchers and practitioners from both academia and industry to share ideas, problems and solutions related to the multifaceted aspects of intelligent computing.the theme for this conference was “Emerging Intelligent Computing Technology and Applications”. Papers related to this theme were especially solicited, including theories, methodologies, and applications in science and technology.
Computational Discovery of Scientific Knowledge : Introduction, Techniques, and Applications in Environmental and Life Sciences
Advances in technology have enabled the collection of data from scientific observations, simulations, and experiments at an ever-increasing pace. For the scientist and engineer to benefit from these enhanced data collecting capabilities, it is becoming clear that semi-automated data analysis techniques must be applied to find the useful information in the data. Computational scientific discovery methods can be used to this end: they focus on applying computational methods to automate scientific activities, such as finding laws from observational data. In contrast to mining scientific data, which focuses on building highly predictive models, computational scientific discovery puts a strong emphasis on discovering knowledge represented in formalisms used by scientists and engineers, such as numeric equations and reaction pathways. This state-of-the-art survey provides an introduction to computational approaches to the discovery of scientific knowledge and gives an overview of recent advances in this area, including techniques and applications in environmental and life sciences.
Combinatorial pattern matching ; Vol.4009) ; 17th Annual Symposium, CPM 2006, Barcelona, Spain, July 5-7, 2006, Proceedings
The book presents 33 revised full papers together with 3 invited talks, organized in topical sections on data structures, indexing data structures, probabilistic and algebraic techniques, applications in molecular biology, string matching, data compression, and dynamic programming
Combinatorial pattern matching ; Vol. 3537 ; 16th Annual Symposium, CPM 2005, Jeju Island, Korea, June 19-22, 2005, Proceedings
This volume presents the proceedings of The 16th Annual Symposium on Combinatorial Pattern Matching was heldon Jeju Island, Korea on June 19–22, 2005. the Program Committee accepted 37 of the submissionsto be presented at the conference. This collection of papers offers original research contributionsin combinatorial pattern matching and its applications.In addition to the selected papers
Combinatorial pattern matching ; 18th Annual Symposium, CPM 2007, London, Canada, July 9-11, 2007, Proceedings
This book presented original research contri- tions on computational pattern matching and analysis, data compression and compressed text processing, sufix arrays and trees, and computational biology. Combinatorial Pattern Matching addresses issues of searching and matching strings and more complicated patterns such as trees, regular expressions, graphs, point sets, and arrays.The goal is to derive non-trivial combinatorial properties of such structures and to exploit these properties in order to either achieve superior performance for the corresponding computational problems or pinpoint conditions under which searches cannot be performed eficiently.
