Integrative data mining: the new direction in bioinformatics

Biological research is becoming increasingly database driven, motivated, in part, by the advent of large-scale functional genomics and proteomics experiments such as those comprehensively measuring gene expression. These provide a wealth of information on each of the thousands of proteins encoded by a genome. Consequently, a challenge in bioinformatics is integrating databases to connect this disparate information as well as performing large-scale studies to collectively analyze many different data sets. This approach represents a paradigm shift away from traditional single-gene biology, and it often involves statistical analyses focusing on the occurrence of particular features (e.g., folds, functions, interactions, pseudogenes, or localization) in a large population of proteins. Moreover, the explicit application of machine learning techniques can be used to discover trends and patterns in the underlying data. In this article, we give several examples of these techniques in a genomic context: clustering methods to organize microarray expression data, support vector machines to predict protein function, Bayesian networks to predict subcellular localization, and decision trees to optimize target selection for high-throughput proteomics     

Review of "Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications" (Hu, X. and Pan, Y., Eds.; 2007) [Book Reviews]

This book, part of the Wiley series on Bioinformatics: Computational Techniques and Engineering, includes 16 chapters and 355 pages. It has extensive references on each chapter and an overall index. More than 50 authors contribute to the text, which is largely written as a series of research papers that are combined in book format. There are chapters on protein secondary-structure prediction, protein-protein interaction, protein identification, RNA secondary structure visualization, drug activity comparisons, cancer classification with microarray data, and cancer survival based on gene expression data. Other topics covered include data representation, storage, and access; text mining; and cluster analysis. The book is well written and edited. It is a worthwhile read for any bioinformatician and fulfills its stated objective of presenting cutting-edge research topics.     

Gene expression microarrays

Molecular biology and genetics have advanced a lot in recent years, thanks to technological advances in this field. Now, the focus in genomic research is shifting from "structural genomics" (sequencing) towards "functional genomics" (using the sequences to understand gene function). The author discusses the principle of the microarray technique, target labelling and hybridization, data analysis and management, unsupervised and supervised analysis, application of microarrays and their future, cancer research and toxicology     

Functional proteomics with biolinguistic methods

In this article, new algorithms for comparative proteomics using extensions of n-gram analysis are described. Results demonstrate that these algorithms are more sensitive than those currently available for both genomics and proteomics analysis, enabling a more accurate portrayal of similarity of gene function. The algorithms allow the comparison of protein sequences using biochemical properties that enable the protein molecules to fold and perform the necessary functions. The algorithms described are amenable to parallelization with effective domain database partitioning. This makes them an attractive alternative for searching protein databases by developing high-speed, functionally partitioned searches.     

Enabling proteomics discovery through visual analysis. The peptide permutation and protein prediction tool.

Proteins play a key role in cellular processes, making proteomics central to understanding systems biology. MS techniques provide a means to observe entire proteomes at a global level. Yet, high-throughput MS proteomics techniques generate data faster than it can currently be analyzed. The success of proteomics depends on high-throughput experimental techniques coupled with sophisticated visual analysis and data-mining methods. Visual analysis has been applied successfully in a number of fields plagued with huge, complex data sets and will likely be an important tool in proteomics discovery. PQuad, a novel visualization of MS proteomics data, provides powerful analysis capabilities that support a number of proteomic data applications. In particular, PQuad supports differential proteomics by simplifying the comparison of peptide sets from different experimental conditions as well as different protein identification or confidence scoring techniques. Finally, PQuad supports data validation and quality control by providing a variety of resolutions for huge amounts of data to reveal errors undetected by other methods.     

Mixed Models: Theory and Applications [Book Review]

This book can be roughly divided in three parts. In the first part (comprising the first eight chapters) the author lays out the foundation for the mixed effects model. The second part of the book (comprised by Chapter 9) discusses methods of model diagnostics and influential analysis, whereby influence is the equivalent of sensitivity analysis, in that they both aim to determine the effect of a small (or infinitesimal) perturbation over data or a model. The third part of the book deals with applications, with Chapter 10 covering tumor growth, and Chapters 11 and 12 covering statistical shape and image analysis. The book is written in a way that will satisfy both a statistician and a computer scientist. Helpful summary points are provided at the end of each chapter. In addition, the book cites a vast range of references, which make it possible for anyone wanting further information on any subject. One gripe is that the book does not include exercises at the end of each chapter, which could have been ideal if one were to adopt it for a graduate-level course.     

Roles and requirements for a research microarray database

DNA microarrays, which allow for the parallel analysis of thousands of genes, have become the most popular functional genomic tool in use today. Substantial data sets are currently being produced by researchers in both the public and the private sector. Proceeding at a significantly slower rate than its complement, microarray data generation, the analysis of microarray data is a true bottleneck for research. The situation will only become more serious in the future, as DNA microarray technology becomes less expensive and projects increase both in number and in size. Clearly, in order to realize the full promise of microarray technology, bioinformatics solutions must evolve. The research microarray database is a crucial step in the evolution of bioinformatics software for modern genomic-scale science. The role of the research microarray database is to support microarray data analysis in the context of a collaborative research environment. At the current stage of microarray research, there are four principal requirements a microarray research database should satisfy. It must be able to store microarray data, store the annotation of the data, store a detailed record of the tasks performed while working with the data, and support research collaboration. Each of the four requirements presents challenges of its own. In conclusion, relational database management systems (DBMSs) have been under active, intensive development for over 20 years. In these two decades, the challenges and issues discussed here have been addressed by the designers of relational database engines. State-of-the-art security features are built into every major DMBS, allowing users to share data safely in a multi-user environment, such as the Internet. Advanced concurrency control ensures data integrity and consistency. A DBMS is the ideal solution for the Internet-connected world of research and data analysis.     

Key challenges in proteomics and proteoinformatics

In this article, a survey on experimental and computational approaches related to proteomics is presented. Considered broadly, proteomics includes: techniques for identifying proteins in a sample, detecting posttranslational modifications (changes to proteins after translation), predicting the structure and function of proteins from sequence data, and integrating information about protein sequences from different databases. The paper focuses on the ways in which recent biological findings complicate the mapping from genes to RNA to protein. The authors argue that the challenges encountered in proteomics provide a valuable lesson on the complexity of life itself, as live organisms always contradict oversimplified models of biological information flow. In this overview, a snapshot of contemporary issues in proteomics is shown.     

Theory (Instantaneous Power Theory and Applications to Power Conditioning; Akagi, H. et al; 2007 [Book Review]

This new book presents a deep review of various power theories and shows how the instantaneous active and reactive power theory provides an important basic knowledge for understanding and designing active filters for power conditioning. The book consists of six chapters covering the following topics and more: instantaneous power theory; shunt active filters; hybrid and series active filters; and combined series and shunt power conditioners. The book is easy to read and each chapter ends with a summary and list of references. The book perfectly fills the gap on the power electronics book market. It is an extremely attractive reference book for research and development engineers who are interested in design of modern active power filters and conditioners as well as flexible ac transmission systems. It can also be recommended for advanced senior-level courses as well as for undergraduate courses.     

Enabling proteomics discovery through visual analysis

This article presents the motivation for developing visual analysis tools for proteomic data and demonstrates their application to proteomics research with a visualization tool named Peptide Permutation and Protein Prediction, or PQuad, a functioning visual analytic tool for the study of systems biology, is in operation at the Pacific Northwest National Laboratory (PNNL). PQuad supports the exploration of proteins identified by proteomic techniques in the context of supplemental biological information. In particular, PQuad supports differential proteomics by simplifying the comparison of peptide sets from different experimental conditions as well as different proteins identification or confidence scoring techniques. Finally, PQuad supports data validation and quality control by providing a variety of resolutions for huge amounts of data to reveal errors undetected by other methods.     

图书馆计算机编目系统种次号数据库的建立

种次号数据库与计算机编目及书目流通等工作关系紧密 ,它的正确与否直接影响书目数据、馆藏流通的准确性。本文介绍了种次号数据库的建立过程     

Sustainable Energy: Choosing Among Options [Book Review]

This book was written by five professors at the Massachusetts Institute of Technology as the textbook for a course of the same name. The early chapters provide tools for measuring the sustainability, usefulness, and economics of different energy-generating methods. The guts of the book are the eight chapters on specific technologies: fossil fuels; nuclear power; biomass; geothermal; hydro-power; solar; tidal; and wind sources. The parallel formats of each section make comparisons easy. The last third of the book covers both an array of energy issues other than pure generation as well as further efforts to provide context and tools for evaluating information. The text covers an astonishingly broad range of topics. Despite not having fuller coverage of some topics, the depth brought to many subjects is impressive. The book is an excellent reference tool.     

Power converters and amplifiers (review of "Pulse-Width Modulated DC-DC Power Converters" by Kazimierczuk, M.K.; 2008) [Book news]

This book is a comprehensive textbook in the areas of electrical, electronics, and telecommunications engineering. It consists of 17 chapters and two appendices. Some of the topics covered include: buck PWM DC-DC converters; boost PWM DC-DC converters; buck-boost-PWM DC-DC converters; half-bridge and full-bridge converters; push-pull PWM DC-DC converters; open-loop small-signal characteristics of boost converters for CCM; current-mode control of boost converters; silicon and silicon carbide power diodes; and soft-switching DC-DC converters. Appendix A is an introduction to SPICE and Appendix B provides an introduction to MATLAB. Answers to problems and the index are also included at the end of the book. The book is recommended for senior undergraduate and graduate students but also for practicing engineers working with switch-mode power supplies, within applications such as computers, telecommunications, industrial electronic systems, automobile electronics, medical equipment, radars, and aerospace power technology.     

Jitter at High Speed (review of "Jitter, Noise, and Signal Integrity at High-Speed" by Mike Peng Li) [Book Reviews]

This book is an outgrowth of the work its author has done in the past 15 years in the areas of jitter and jitter analysis. It covers the basics of random processes and jitter and builds on these up to systems and testing. While the book places an emphasis on basic probability theory and the mathematics of jitter, there are no problems to aid this book as a text. Despite some flaws with reference and topic coverage, the book largely succeeds at providing one source for jitter information and serves as useful reference.     

Mathematical Handbook for Electrical Engineers [Book Review]

This book consists of three parts. Part I contains the most widely used fundamental mathematical definitions, laws, and rules that are used to solve the majority of electrical engineering problems. Part II contains solved examples in four different areas of electrical engineering: circuits and devices; antennas and propagation; waveforms and signal processing; and stochastic radio engineering. The majority of the problems fall in the later category. Part III contains reference data on all sorts of mathematical expressions. Engineers, especially electrical engineers who work with mathematical problems either on a regular basis or infrequently, would find this book to be a useful resource for setting up and solving problems.     

Introduction to Physical Polymer Science, 4th Edition [Book Review]

This is a classic reference text that has been updated and revised to include some recent developments in polymer science, including topics on nanocomposites, DNA and proteins, and glass transition of nano-thin film plastics. Although the coverage of the new topics does not do them justice, the strength of this book remains in the fundamentals. Some of the topics covered include: the basic structure of common polymers; chain structure; molecular weights; concentrated solutions; the amorphous state; the crystalline state; glass transition; cross-linking; and polymer blends. The text is well written, and there are many illustrations, photographs, graphs and tables. The book is easy to follow and understand and is highly recommended as a basic text on polymer science or as a textbook for undergraduate studies. It could also be used by engineers and scientists working in the filed who need a good book on fundamentals.     

Medical Device Design for Six Sigma: A Road Map for Safety and Effectiveness (El-Haik, B.S. and Mekki, K.S.; 2008) [Book reviews]

The intent of this book is to provide an in-depth treatment of design for six sigma (DFSS) and related technologies to assist in safe, efficacious medical device design. The book consists of 20 chapters, each beginning with an overview of the material to be covered and ending with the summary statements relevant to that material. Appendixes cover terminology, references, and necessary statistical tables. This book, written by two authors with a large amount of DFSS experience, is overly intense for most undergraduates. This book is therefore recommended for early-level graduate courses in medical device design or as a reference text.     

Smart electrical energy networks [review of Power Electronics in Smart Electrical Energy Networks (Strzelecki, R. and Benysek, G.; 2008)] [Book News]

The major aim of this book, a monograph written by an international team of authors, is to present the features, solutions, and applications of the power electronics arrangements likely to be useful in smart electrical energy networks. The book is organized into 12 chapters and includes the following topics: principles of electrical power control; an overview of power electronics converters and controls; quality problems in smart networks; high frequency AC power distribution platforms; integration of distributed generation with electrical power systems; active power quality controllers; and grid integration of wind energy systems, among other topics. The book includes numerous practical examples and very good illustrations that highlight the discussed topics. Each chapter begins with an introduction and is supplemented with a summary and list of references at the end. The book can be used a s a reference for advanced senior-level courses.     

Modeling and characterization of RF and microwave power FETs [book review]

This book provides a coherent review of the advanced state of power FET modeling and characterization. It covers the topics of device construction, model selection, device measurement, and model validation in sufficient detail to be truly useful. Although not designed as a university text, the book contains enough math and fundamental to serve as a foundation for a course. This is a well-written and useful text.     

Biomaterials--The Intersection of Biology and Materials Science (Temenoff, J.S. et al.; 2008) [Book reviews]

This book is divided into two subject areas. The first seven chapters discuss materials science, whereas the last seven chapters discuss biological response. The characterization and regulatory issues are included throughout the book as appropriate. This is an excellent book for students in the biomedical engineering curriculum and also an excellent reference for practicing engineers, providing explanation of many intricacies of biomaterials and sufficient background material to make the subject understandable.