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作者： Ali Masoudi-Nejad Susumu Goto Takashi R. Endo Minoru Kanehisa

Kyoto Encyclopedia of Genes and Genomes (KEGG) is a bioinformatics resource for understanding biological function from a genomic perspective. It is a multispecies, integrated resource consisting of genomic, chemical, and network information, with cross-references to numerous outside databases and containing a complete set of building blocks (genes and molecules) and wiring diagrams (biological pathways) to represent cellular functions. KEGG consists of a suite of databases: PATHWAY, GENES/Sequence Similarity Database (SSDB), Biomolecular Relations in Information Transmission and Expression (BRITE), and LIGAND, which is a composite database of COMPOUND, DRUG, GLYCAN, REACTION, REPAIR, and ENZYME. Two new databases have been recently added to KEGG: DGENES (for draft genomes) and EGENES (for expressed-sequence tag [EST] data). EGENES is a knowledge base system for efficient analysis of organism-specific ESTs, including publicly available plant ESTs. EGENES links the genomic information with higher order functional information in a single database. The genomic information stored in EGENES is a collection of EST contigs, produced by assembling the public ESTs. In this chapter, we will introduce KEGG and discuss its importance for the plant research community by focusing on EGENES. Because all the resources in KEGG follow the same architecture and design, an appraisal of EGENES should give readers an idea of the available information stored in KEGG and how to use them efficiently. less

关键词： EST Assembly Genomics Microarray Sequence Assembly GenBank programming language Arabidopsis thaliana Lotus corniculatus Medicago truncatula Populus tremula Populus balsamifera Solanum lycopersicum Oryza sativa Japonica Group Zea mays Physcomitrella patens Oryza sativa Brassica napus Citrus Glycine max Lactuca sativa Solanum tuberosum Triticum aestivum Saccharum officinarum transcriptome analysis functional annotation Plant metabolic pathway plant EST clustering gene index EGENES

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Construction of

Construction of

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作者： Jang B. Rampal Peter J. Coassin Robert S. Matson

The concept of DNA arrays was first introduced in the early 1980s, by Sir Edwin Southern. Since then, many research institutions and biotechnology companies have investigated the potential use of arrays in fields ranging from genetic diagnostics to forensics investigations. A 64-channel automated chemical delivery system, known as the Southern Array Maker, which synthesizes oligonucleotides directly onto an aminated polypropylene substrate has been constructed. Many different arrays have been synthesized for the purpose of detecting single point mutations, which might be either indicators of, or directly responsible for, many different types of genetic diseases and cancers. These include cystic fibrosis, H-ras, K-ras, and other mutations. In addition to the synthesized arrays, we are also looking into various alternative methods of producing both highand low-density DNA arrays. This chapter is intended to demonstrate the synthesis of oligoarrays by in situ method using standard phosphoramidite chemistry. Phosphoramidate linkage to the aminated polypropylene is quite stable under oligo cleavage and deprotection conditions. Oligonucleotide density is approx 3 pmole or 1012 molecules/mm2. less

关键词： PCR X-ray Photoelectron Spectroscopy Oligonucleotide Synthesis Reversed-phase HPLC Ultraviolet-visible Spectrophotometry Capillary Electrophoresis (CE) HPLC Image Analysis Microarray programming language hybridization solid-phase synthesis phosphoramidite chemistry oligoarrays probe density

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Lectin Microarrays for Glycoprotein Analysis

Lectin Microarrays for Glycoprotein Analysis

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作者： Kanoelani T. Pilobello Lara K. Mahal

Glycosylation is one of the most common posttranslational modifications, with more than half of all known proteins thought to be glycoproteins. Alterations in glycosylation play a role in a diverse set of biological phenomena including tumor cell metastasis, intracellular communication, and inflammation. The complexity of glycosylation at the molecular level and the lack of rapid analytical tools complicate the study of glycan function. We have recently developed a lectin microarray for the high-throughput analysis of glycosylation. Lectins are carbohydrate-binding proteins that have been used for decades as a detection method for glycans. By placing the lectins in a microarray format and using standard microarray printing and scanning technology, we have created a simple yet powerful technique for glycan profiling. less

关键词： Microarray Dialysis Data analysis Python programming language Bos taurus Lotus tetragonolobus Lens culinaris Glycine max Solanum tuberosum Triticum array glycomics carbohydrate analysis glycan profiling

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XML for Data Representation and Model Specification in Neuroscience

XML for Data Representation and Model Specification in Neuro...

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作者： Sharon M. Crook Fred W. Howell

EXtensible Markup language (XML) technology provides an ideal representation for the complex structure of models and neuroscience data, as it is an open file format and provides a language-independent method for storing arbitrarily complex structured information. XML is composed of text and tags that explicitly describe the structure and semantics of the content of the document. In this chapter, we describe some of the common uses of XML in neuroscience, with case studies in representing neuroscience data and defining model descriptions based on examples from NeuroML. The specific methods that we discuss include (1) reading and writing XML from applications, (2) exporting XML from databases, (3) using XML standards to represent neuronal morphology data, (4) using XML to represent experimental metadata, and (5) creating new XML specifications for models. less

关键词： Data Mining Electrophysiology programming language Data analysis XML MorphML NeuroML neuronal morphology neuroinformatics

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Statistical Methods for Identifying Differentially Expressed Gene Combinations

Statistical Methods for Identifying Differentially Expressed...

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作者： Yen-Yi Ho Leslie Cope Marcel Dettling Giovanni Parmigiani

Identification of coordinate gene expression changes across phenotypes or biological conditions is the basis of the ability to decode the role of gene expression regulatory networks. Statistically, the identification of these changes can be viewed as a search for groups (most typically pairs) of genes whose expression provides better phenotype discrimination when considered jointly than when considered individually. Such groups are defined as being jointly differentially expressed. In this chapter several approaches for identifying jointly differentially expressed groups of genes are reviewed of compared on a set of simulations. less

关键词： Microarray Statistical Calculation programming language correlation entropy High-order interactions liquid correlation joint differential expression

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Sequence Handling by Sequence Analysis Toolbox v1.0

Sequence Handling by Sequence Analysis Toolbox v1.0

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作者： Christian Ravnsborg Ingrell Rune Matthiesen Ole Nørregaard Jensen

The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl inositol-anchored proteins. less

关键词： Sequence Analysis Mass Spectrometry High-Throughput Sequencing Structure Prediction Tandem Mass Spectrometry Swiss-Prot Expasy programming language Isoelectric point hydropathicity index transmembrane segments glycosylphosphatidyl inositol-anchored proteins

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XL:: an XML programming language for Web service specification and composition

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COMPUTER NETWORKS-THE INTERNATIONAL JOURNAL OF COMPUTER AND TELECOMMUNICATIONS NETWORKING 2003年第5期42卷 641-660页

作者： Florescu, D Grünhagen, A Kossmann, D XQRL Inc Palo Alto CA 94301 USA Tech Univ Munich D-85747 Garching Germany

We present an XML programming language designed for the implementation of Web services. XL is portable and fully compliant with W3C standards such as XQuery, XML Protocol, and XML Schema. One of the key features of XL is that it allows programmers to concentrate on the logic of their application. XL provides high level and declarative constructs for actions which are typically carried out in the implementation of a Web service;e.g., logging, error handling, retry of actions, workload management, events, etc. Issues such as performance tuning (e.g., caching, horizontal partitioning, etc.) should be carried out automatically by an implementation of the language. This way, the productivity of the programmers, the ability of evolution of the programs, and the chances to achieve good performance are substantially enhanced. (C) 2003 Elsevier Science B.V. All rights reserved.

关键词： XML Web service programming language

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programming with exceptions in JCilk

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SCIENCE OF COMPUTER programming 2006年第2期63卷 147-171页

作者： Danaher, John S. Lee, I. -Ting Angelina Leiserson, Charles E. MIT Comp Sci & Artificial Intelligence Lab Cambridge MA 02139 USA

JCilk extends the serial subset of the Java language by importing the fork-join primitives spawn and sync from the Cilk multithreaded language, thereby providing call-return semantics for multithreaded subcomputations. In addition, JCilk transparently integrates Java's exception handling with multithreading by extending the semantics of Java's try and catch constructs, but without adding new keywords. This extension is "faithful" in that it obeys Java's ordinary serial semantics when executed on a single processor. When executed in parallel, however, an exception thrown by a JCilk computation causes its sibling computations to abort, which yields a clean semantics in which the enclosing cilk try block need only handle a single exception. The exception semantics of JCilk allows programs with speculative computations to be programmed easily. Speculation is essential in order to parallelize programs such as branch-and-bound or heuristic search. We show how JCilk's linguistic mechanisms can be used to program the "queens" puzzle and a parallel alpha-beta search. We have implemented JCilk's semantic model in a prototype compiler and runtime system, called JCilk-1. The compiler implements continuations in a novel fashion by introducing goto statements into Java. The JCilk-1 runtime system shadows the dynamic hierarchy of cilk try blocks using a "try tree", allowing the system to chase down side computations that must be aborted. Performance studies indicate that JCilk's exception mechanism incurs minimal overhead, contributing at most a few percent on top of the cost for a spawn/return. (c) 2006 Elsevier B.V. All rights reserved.

关键词： multithreading parallel computing programming language runtime system posix thread Cilk fork-join JVM Java exception handling bytecode semisynchronous atomicity speculative computing

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Applying software development lifecycles in teaching introductory programming courses

Applying software development lifecycles in teaching introdu...

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19th Conference on Software Engineering Education and Training

作者： Rahman, Syed M. Juell, Paul L. N Dakota State Univ Dept Comp Sci Fargo ND 58105 USA

ISBN: (纸本)0769525571

In this paper, we introduce a new software development method that emphasizes software testing cycles and makes a cultural change in program development. In our approach, students follow the software lifecycles to develop their programs;specifically, a student who is to write a program begins by writing a test suite and completes other development cycles. Students in programming courses usually develop "toy" programs that are superficially tested, graded, and eventually discarded Generally, students are not worried about the quality or maintenance of their products. We believe this style of teaching programming courses leaves students unprepared for developing reliable software. Industry leaders also claimed that more than 50% of a software project's budget was spent on activities related to improving software quality. They stated the reason was the inadequate attention paid to software quality in the development phase. Our approach integrates into the existing programming courses without changing the course contents, syllabus, policies, or loads, and our model improves the students' program quality, in terms of black-box testing. Students indicated that our method helped them in understanding the problems and writing the programs, made the code easier to debug, and improved the students' code reliability and quality.

关键词： software development method programming language software testing software quality software cost

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An interactive computer model for coriolis demonstrations

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Journal of Geoscience Education 2006年第1期54卷 54-60页

作者： Urbano, Lensyl D. Houhgton, Jennifer L. Department of Earth Sciences University of Memphis Memphis TN 38111 United States

The coriolis effect can be a difficult concept for students to understand, particularly in large classes where the effectiveness of physical demonstrations is limited by visibility. We developed a fully interactive computer visualization aimed at introductory undergraduate and precollege students based on the physical demonstration of a marble rolling across a turntable. The marble's velocity, turntable angular velocity and direction, and friction between the marble and the surface can be controlled to allow significant instructional flexibility. Pre and post demonstration student surveys indicate that the application improved student understanding of the coriolis effect, and the use of this type of demonstration was favorably received by the students. This program is written in the free, open-source Python programming language, specifically with the VPython module, which makes three-dimensional, physically-based, real-time visualizations efficiently programmable for geoscience demonstrations by non-professional programmers.

关键词： .three-dimensional demonstrations Friction frames angular Interactive Computer coriolis effect physical demonstration turntable marble velocity programming language VPython pressure gradient

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