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FOOD: An Intermediate Model for Automated Refactoring

FOOD: An Intermediate Model for Automated Refactoring

引用

5th International Conference on Software Methodologies, Tools and Techniques (SoMeT 2006)

作者： Juillerat, Nicolas Hirsbrunner, Beat Univ Fribourg Dept Comp Sci CH-1700 Fribourg Switzerland

ISBN: (纸本)9781586036737

As big software projects grow, there is an increasing need of cleaning up or restructuring the existing code. This problem can be addressed by using refactorings, which are small semantics-preserving code transformations. Many refactorings have been automated in existing development environments to help the developer in this process. Most implementations are currently based on the abstract syntax tree. Unfortunately, this model, which was first designed for the compilation process, does not provide all the abstractions that are required for complex refactorings such as extracting a method. In this paper, the FOOD model is introduced and described. Based entirely on graphs, this model is targeted to the implementation of complex code transformations by providing the necessary abstractions. The "extract method" refactoring is applied on the FOOD model as a concrete example. Then a comparison with existing models such as abstract syntax trees is made.

关键词： Refactoring FOOD Model Extract Method programming language Graph

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A language-based approach to service deployment

A language-based approach to service deployment

引用

IEEE Services Computing Workshops

作者： Wang, Xiaoning Li, Wei Liu, Hong Xu, Zhiwei Chinese Acad Sci Inst Comp Technol Res Ctr Grid & Serv Comp Beijing 100080 Peoples R China Chinese Acad Sci Grad Sch Beijing 100039 Peoples R China

ISBN: (纸本)0769526705

This paper presents a language-based approach to service deployment. The language is called Abacus, which is a service-oriented programming language for grid applications. In Abacus, a service is abstracted as a basic language construct, and service deployment is expressed by a deployment statement. This approach allows an Abacus application to automatically deploy a service at runtime without any configuration information. This paper compares the development detail in the Abacus environment with that in the manual deployment environment, and evaluates our deployment approach accordingly. On the one hand, this approach frees maintainers from annoying deployment work at low-level, which helps to enhance the productivity in building grid applications. On the other hand, this approach allows services to be deployed according to the application logic, helping to improve the utilization and the management of various grid resources.

关键词： grid computing service-oriented service deployment programming language grid application

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Biomolecular screening of formylpeptide receptor ligands with a sensitive, quantitative, high-throughput flow cytometry platform

Biomolecular screening of formylpeptide receptor ligands wit...

引用

作者： Bruce S Edwards Susan M Young Tudor I Oprea Cristian G Bologa Eric R Prossnitz Larry A Sklar

The formylpeptide receptor (FPR) family of G protein–coupled receptors contributes to the localization and activation of tissue-damaging leukocytes at sites of chronic inflammation. Here we describe a high-throughput flow cytometry screening approach that has successfully identified multiple families of previously unknown FPR ligands. The assay detects active structures that block the binding of a fluorescent ligand to membrane FPR of intact cells, thus detecting both agonists and antagonists. It is homogeneous in that assay reagents are added in sequence and the wells are subsequently analyzed without intervening wash steps. Microplate wells are routinely processed at a rate of 40 wells per minute, requiring a volume of only 2 μl to be sampled from each. This screening approach has recently been extended to identify a high-affinity, selective agonist for the intracellular estrogen-binding G protein–coupled receptor GPR30. With the development of appropriate assay reagents, it may be generally adaptable to a wide range of receptors. The total time required for the assay ranges between 1.5 and 2.5 h. The time required for flow cytometry analysis of a 96-well plate at the end of the procedure is less than 2.5 min. By comparison, manual processing of 96 samples will typically require 40–50 min, and a fast commercial automated sampler processes 96-well plates in less than 15 min, requiring the aspiration of 22 μl per sample for an analysis volume of 2 μl. less

关键词： Flow Cytometry Crystallization Statistical Calculation Cell And Tissue Culture Data analysis programming language Homo sapiens U-937

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The Stanford Microarray Database

The Stanford Microarray Database

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作者： Jeremy Gollub Catherine A. Ball Gavin Sherlock

The Stanford Microarray Database (SMD) is a DNA microarray research database that provides a large amount of data for public use. This chapter describes the use of the primary tools for searching, browsing, retrieving, and analyzing data available for SMD. With this introduction, researchers and students will be able to examine and analyze a large body of gene expression and other experiments. Additional tools for depositing, annotating, sharing, and analyzing data, available only to registered users, are also described. SMD is available for installation as a local database. less

关键词： Microarray Gene Expression Profiling Nucleic Acid Microarray Functional Enrichment Statistical Calculation Data analysis programming language DNA cDNA gene expression clustering database repository

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Unrestrictive identification of post-translational modifications through peptide mass spectrometry

Unrestrictive identification of post-translational modificat...

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作者： Stephen Tanner Pavel A Pevzner Vineet Bafna

Proteins are post-translationally modified in vivo as part of cellular regulation and signaling, and undergo further chemical modifications during laboratory processing. Even relatively simple protein samples may carry a wide range of modifications. Peptide tandem mass spectrometry provides a way to study these events. We present a protocol for computational identification of post-translational modifications (PTMs) and the sites where they occur. The protocol performs an unrestrictive search, and requires no prior knowledge of what modifications are present in the sample. We present a largely automated procedure for PTM discovery, and provide a guide for analysis of PTM annotations. This protocol requires you to type out several commands, so you may wish to enlist the help of a colleague familiar with the computer's command-line interface. A typical MS run of up to 25,000 scans can be searched and analyzed in 3 h. less

关键词： Mass Spectrometry Tandem Mass Spectrometry Database Search Python programming language

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WormBase

WormBase

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作者： Todd W. Harris Lincoln D. Stein

WormBase is a comprehensive repository for information on Caenorhabditis elegans and related nematodes. Although the primary web-based interface of WormBase (http://***/ ) is familiar to most C. elegans researchers, WormBase also offers powerful data-mining features for addressing questions of comparative genomics, genome structure, and evolution. In this chapter, we focus on data mining at WormBase through the use of flexible web interfaces, custom queries, and scripts. The intended audience includes users wishing to query the database beyond the confines of the web interface or fetch data en masse. No knowledge of programming is necessary or assumed, although users with intermediate skills in the Perl scripting language will be able to utilize additional data-mining approaches. less

关键词： Data Mining Genomics Genome Visualization RNA Interference Microarray programming language Caenorhabditis elegans bioinformatics WormBase AceDB AcePerl

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Reverse engineering cellular networks

Reverse engineering cellular networks

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作者： Adam A Margolin Kai Wang Wei Keat Lim Manjunath Kustagi Ilya Nemenman Andrea Califano

We describe a computational protocol for the ARACNE algorithm, an information-theoretic method for identifying transcriptional interactions between gene products using microarray expression profile data. Similar to other algorithms, ARACNE predicts potential functional associations among genes, or novel functions for uncharacterized genes, by identifying statistical dependencies between gene products. However, based on biochemical validation, literature searches and DNA binding site enrichment analysis, ARACNE has also proven effective in identifying bona fide transcriptional targets, even in complex mammalian networks. Thus we envision that predictions made by ARACNE, especially when supplemented with prior knowledge or additional data sources, can provide appropriate hypotheses for the further investigation of cellular networks. While the examples in this protocol use only gene expression profile data, the algorithm's theoretical basis readily extends to a variety of other high-throughput measurements, such as pathway-specific or genome-wide proteomics, microRNA and metabolomics data. As these data become readily available, we expect that ARACNE might prove increasingly useful in elucidating the underlying interaction models. For a microarray data set containing ∼10,000 probes, reconstructing the network around a single probe completes in several minutes using a desktop computer with a Pentium 4 processor. Reconstructing a genome-wide network generally requires a computational cluster, especially if the recommended bootstrapping procedure is used. less

关键词： Microarray Proteomics Metabolomics Statistical Calculation Statistical Inference Flow Cytometry Data analysis programming language

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Toward horizontal integration of anthropoid robotic control systems

Toward horizontal integration of anthropoid robotic control ...

引用

3rd International Conference on Computing, Communications and Control Technologies

作者： Frenger, Paul Working Hypothesis Inc Houston TX 77282 USA

ISBN: (纸本)9789806560468

There has been a recent proliferation of high quality anthropoid robots. Unfortunately, the control systems of these machines share very little in terms of computer software, hardware, or system data. In this paper, the author takes the position that horizontal (inter-institution) integration of anthropoid control systems is essential to efficient production of future advanced robots. He reviews several existing designs, then discusses techniques for achieving systems convergence. He proposes the creation of a generally accepted, high quality, reusable anthropoid robot control platform, with organizational support to promulgate it.

关键词： artificial intelligence artificial neural network ASIC embedded system FPGA inference engine machine learning operating system robot programming language simulated emotions

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NSL - A network security oriented language

NSL - A network security oriented language

引用

Conference on Network Architectures, Management and Applications II

作者： Li, WM Li, ZT Huazhong Univ Sci & Technol Coll Comp Wuhan 430074 Peoples R China

ISBN: (纸本)0819455806

The wide use of network improves security risks, but the traditional network security tools are single-functional and they are difficult to extend and manage. These security tools can't fulfill the need of users. The paper presents a network security oriented language: NSL (Network Security language). The language provides a common abstract layer of all kinds of security application. It can be used to construct multifunctional, distributed and extendable security applications, satisfying various and emergent security requirements. The paper describes its network oriented structures, features and three security mechanisms. The NSL interpreter implementation is also analyzed by the performance test. At last, the paper puts forward improving work which will be done in the future.

关键词： network security programming language interpreter optimization

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Towards general purpose, high level, software languages

Towards general purpose, high level, software languages

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1st European Conference on Model Driven Architecture - Foundations and Applications

作者： Kleppe, A Klasse Objecten Netherlands

ISBN: (纸本)3540300260

A highly significant benefit of MDA is that it raises the level of abstraction at which the soft-ware developer is able to work. However, the languages available to the developer have not seen much change in the last decade. Modeling languages offer high level concepts, but the pre-dominant modeling language (UML) offers too little expressive power to be able to specify a system completely. Meanwhile, the level of abstraction of most programming language con-cepts is the same as 10 to 15 years ago. Although transformation tools may to some extent bridge the gap between modeling and programming languages, in practice the developer still needs to do both modeling and programming. This means switching between the two levels of abstractions, which is difficult for most people. We argue that a general purpose, high level, software language is necessary to get MDA adopted. This language will enable any developer to focus on the problem at hand while the supporting tools - transformation tools or generators- take care of the nitty gritty details. This paper introduces an early version of such a language, which brings together a number of powerful concepts from various sources: UML, OCL, design patterns, existing programming languages, and eventually aspectoriented languages.

关键词： modeling language programming language UML OCL design patterns domain specific languages MDA model transformations

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