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10th IEEE Working Conference on Source Code Analysis and Manipulation (SCAM)

作者： Zeller, Andreas Saarland Univ Comp Sci Saarbrucken Germany

ISBN: (纸本)9780769541785

Models-abstract and simple descriptions of some artifact-are the backbone of all software engineering activities. While writing models is hard, existing code can serve as a source for abstract descriptions of how software behaves. To infer correct usage, code analysis needs usage examples, though;the more, the better. We have built a lightweight parser that efficiently extracts API usage models from source code-models that can then be used to detect anomalies. Applied on the 200 million lines of code of the Gentoo Linux distribution, we would extract more than 15 million API constraints, encoding and abstracting the "wisdom of Linux code".

关键词： API usage model extraction Linux Linux code abstract descriptions application program interfaces code analysis data mining language independent parsing lightweight parsing mining models mining specifications program compilers software engineering software engineering activities source code

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Mercury: Enabling Remote Procedure Call for High-Performance Computing

Mercury: Enabling Remote Procedure Call for High-Performance...

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15th IEEE International Conference on Cluster Computing (CLUSTER)

作者： Soumagne, Jerome Kimpe, Dries Zounmevo, Judicael Chaarawi, Mohamad Koziol, Quincey Afsahi, Ahmad Ross, Robert HDF Grp Champaign IL 61820 USA Argonne Natl Lab Argonne IL 60439 USA Queens Univ Kingston ON K7L 3N6 Canada

ISBN: (纸本)9781479908981

Remote procedure call (RPC) is a technique that has been largely adopted by distributed services. This technique, now more and more used in the context of high-performance computing (HPC), allows the execution of routines to be delegated to remote nodes, which can be set aside and dedicated to specific tasks. However, existing RPC frameworks assume a socket-based network interface (usually on top of TCP/IP), which is not appropriate for HPC systems, because this API does not typically map well to the native network transport used on those systems, resulting in lower network performance. In addition, existing RPC frameworks often do not support handling large data arguments, such as those found in read or write calls. We present in this paper an asynchronous RPC interface, called Mercury, specifically designed for use in HPC systems. The interface allows asynchronous transfer of parameters and execution requests and provides direct support of large data arguments. Mercury is generic in order to allow any function call to be shipped. Additionally, the network implementation is abstracted, allowing easy porting to future systems and efficient use of existing native transport mechanisms.

关键词： application program interfaces data handling parallel processing remote procedure calls

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ACUA: API Change and Usage Auditor 14

ACUA: API Change and Usage Auditor

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14th IEEE International Working Conference on Source Code Analysis and Manipulation (SCAM)

作者： Wu, Wei Adams, Bram Gueheneuc, Yann-Gael Antoniol, Giuliano Ecole Polytech DGIGL Montreal PQ H3C 3A7 Canada

ISBN: (纸本)9780769553047

Modern software uses frameworks through their application programming interfaces (APIs). Framework APIs may change while frameworks evolve. Client programs have to upgrade to new releases of frameworks if security vulnerabilities are discovered in the used releases. Patching security vulnerabilities can be delayed by non-security-related API changes when the frameworks used by client programs are not up to date. Keeping frameworks updated can reduce the reaction time to patch security leaks. Client program upgrades are not cost-free, developers need to understand the API usages in client programs and API changes between framework releases before conduct upgrading tasks. In this paper, we propose a tool ACUA to generate reports containing detailed API change and usage information by analyzing the binary code of both frameworks and clients programs written in Java. Developers can use the API change and usage reports generated by ACUA to estimate the work load and decide when to starting upgrading client programs based on the estimation.

关键词： Java application program interfaces safety-critical software source code (software) ACUA API Change-and-Usage Auditor application programming interfaces binary code analysis client program upgrade framework release nonsecurity-related API changes reaction time reduction security leakage patching security vulnerabilities software usage framework work load estimation Abstracts Analytical models Contracts Data models Detection algorithms Security Software API change and usage Software maintenance framework API evolution application programming interfaces Java Java programming language Frameworks safety-critical software Detection algorithms Software maintenance data models API contract AXIAL POWER INDICATOR American Petroleum Institute Security hole ANALYSIS MODELS customers

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fAST: Flattening Abstract Syntax Trees for Efficiency 19

fAST: Flattening Abstract Syntax Trees for Efficiency

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IEEE/ACM 41st International Conference on Software Engineering - Software Engineering in Practice (ICSE-SEIP)

作者： Yu, Yijun Open Univ Sch Comp & Commun Milton Keynes Bucks England

ISBN: (纸本)9781728117645

Frequently source code analysis tools need to exchange internal representations of abstract syntax trees (AST) with each other. Conveniently, and intuitively, the externalised representations are in the form of hierarchical trees. We argue, counter-intuitively, that hierarchical representation is not the most efficient way for source analysis tools to exchange parsed AST. In this work, we propose to speed up AST parsing whilst preserving the equivalence of hierarchies in binary forms: (1) AST could be saved as a flat one-dimensional array where pointers to tree nodes are converted into integer offsets, and (2) such flattened AST are more efficient to access by programming tools through the generated application programming interfaces (API). In programming language-agnostic evaluations, we show that parsing flattened AST becomes 100x faster than in textual form AST on a benchmark of open-source projects of 6 different programming languages.

关键词： application program interfaces program compilers program diagnostics programming languages source code (software) trees (mathematics) application programming interfaces analysis programme compilers Computer programming Languages AST tree nodes Internal representations syntax open source

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A Parallel Algorithm for the Best k-mismatches Alignment Problem

A Parallel Algorithm for the Best <i>k</i>-mismatches Alignm...

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22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP)

作者： Del Fabbro, Cristian Tardivo, Fabio Policriti, Alberto Inst Appl Genom Udine Italy Univ Udine I-33100 Udine Italy

ISBN: (纸本)9781479927289

We propose a parallel algorithm that solves the best k-mismatches alignment problem against a genomic reference using the "one sequence/multiple processes" paradigm and distributed memory. Our proposal is designed to take advantage of a computing cluster using MPI (Message Passing Interface) for communication. Our solution distributes the reference among different nodes and each sequence is processed concurrently by different nodes. When a (putative) best solution is found, the successful process propagates the information to other nodes, reducing search space and saving computation time. The distributed algorithm was developed in C++ and optimized for the PLX and FERMI supercomputers, but it is compatible with every OpenMPI-based cluster. It was included in the ERNE (Extended Randomized Numerical alignEr) package, whose aim is to provide an all-inclusive set of tools for short reads alignment and cleaning. ERNE is free software, distributed under the Open Source License (GPL V3) and can be downloaded at: http://***. The algorithm described in this work is implemented in the ERNE-PMAP and ERNE-PBS5 programs, the former designed to align DNA and RNA sequences, while the latter is optimized for bisulphite-treated sequences.

关键词： C++ language DNA RNA application program interfaces bioinformatics distributed memory systems message passing parallel algorithms public domain software software packages C++ programming DNA sequence alignment ERNE-PBS5 programs ERNE-PMAP programs Extended Randomized Numerical aligner package FERMI supercomputers GPL V3 MPI OpenMPI-based cluster PLX supercomputers RNA sequence alignment best k-mismatches alignment problem bisulphite-treated sequences computation time computing cluster distributed algorithm distributed memory free software message passing interface one sequence-multiple processes paradigm open source license parallel algorithm search space reduction Bioinformatics Clustering algorithms DNA Genomics Next generation networking Sequential analysis Software bs-seq erne mpi parallel sequence alignment

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An Improved Parallel Differential Evolution Approach for Protein Structure Prediction Using Both 2D and 3D Off-lattice Models

An Improved Parallel Differential Evolution Approach for Pro...

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IEEE Symposium on Differential Evolution (SDE)

作者： Kalegari, Diego H. Lopes, Heitor S. Univ Tecnol Fed Parana Bioinformat Lab Curitiba Parana Brazil

ISBN: (纸本)9781467358736

Protein structure prediction (PSP) is a well-known problem in bioinformatics. Identifying protein native conformations makes it possible to predict its function within the organism. Knowing this also helps the development of new drugs and the comprehension of some biological mechanisms. During years some techniques have been developed for this purpose but, due to their high cost, it is necessary to use simplified models of protein structures. However, even the simplest models, with low biological plausibility, are excessively complex from the computational point of view. This paper reports the application of Differential Evolution (DE) to solve the PSP problem using a Toy Model (also known as the AB Model) in both 2D and 3D to represent the protein structure. This work presents two different versions of the DE algorithm (basic and adaptive) using a parallel architecture (master-slave) based on Message Passing Interface in a cluster. Some special operators for DE were developed: explosion and mirror mutation. All tests executed in this work used four benchmark sequences, ranging from 13 to 55 amino acids. The results for both parallel DE algorithms using both 2D and 3D models were compared with other works in the literature. The DE algorithm achieved excellent results. Overall results encourage further research towards the use of knowledge-based operators to improve further the performance of DE.

关键词： application program interfaces bioinformatics lattice theory message passing parallel algorithms proteins

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Early Experience on the Blue Gene/Q Supercomputing System

Early Experience on the Blue Gene/Q Supercomputing System

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IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS)

作者： Morozov, Vitali Kumaran, Kalyan Vishwanath, Venkatram Meng, Jiayuan Papka, Michael E. Argonne Natl Lab Argonne IL 60439 USA

ISBN: (纸本)9780769549712

The Argonne Leadership Computing Facility (ALCF) is home to Mira, a 10 PF Blue Gene/Q (BG/Q) system. The BG/Q system is the third generation in Blue Gene architecture from IBM and like its predecessors combines system-on-chip technology with a proprietary interconnect (5-D torus). Each compute node has 16 augmented PowerPC A2 processor cores with support for simultaneous multithreading, 4-wide double precision SIMD, and different data prefetching mechanisms. Mira offers several new opportunities for tuning and scaling scientific applications. This paper discusses our early experience with a subset of micro-benchmarks, MPI benchmarks, and a variety of science and engineering applications running at ALCF. Both performance and power are studied and results on BG/Q is compared with its predecessor BG/P. Several lessons gleaned from tuning applications on the BG/Q architecture for better performance and scalability are shared.

关键词： IBM computers application program interfaces multi-threading parallel machines system-on-chip

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Data model for biopart datasheets

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Engineering Biology 2018年第1期2卷 7-18页

作者： De Murieta, Iñaki Sainz Bultelle, Matthieu Kitney, Richard I. Department of Bioengineering Imperial College London LondonSW7 2AZ United Kingdom

This study introduces a new data model, based on the DICOM-SB (see glossary of terms for definition of acronyms) standard for synthetic biology, that is capable of describing/incorporating the data, metadata and ancillary information from detailed characterisation experiments - to present DNA components (bioparts) in datasheets. The data model offers a standardised mechanism to associate bioparts with data and information about component performance - in a particular biological context (or a range of contexts, e.g. chassis). The data model includes the raw, experimental data for each characterisation run, and the protocol details needed to reliably reproduce the experiment. In addition, it provides metrics (e.g. relative promoter units, synthesis/growth rates etc.) that constitute the main content of a biopart datasheet. The data model has been developed to directly link to DICOM-SB, but also to be compatible with existing data standards, e.g. SBOL and SBML. It has been implemented within the latest version of the API that enables access to the SynBIS information system. The work should contribute significantly to the current standardisation effort in synthetic biology. The standard data model for datasheets is seen as a necessary step towards effective interoperability between part repositories, and between repositories and BioCAD applications.

关键词： CAD DNA molecular biophysics meta data data acquisition application program interfaces biology computing biopart datasheets DICOM-SB synthetic biology metadata ancillary information detailed characterisation experiments DNA components standardised mechanism component performance biological context data acquisition phase-of-characterization experimental protocol details relative promoter units synthesis-growth rates data standards SBOL SBML API SynBIS information system standard data model BioCAD applications

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Three-dimensional positioning from Google street view panoramas

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IET IMAGE PROCESSING 2013年第3期7卷 229-239页

作者： Tsai, Victor J. D. Chang, Chun-Ting Natl Chung Hsing Univ Dept Civil Engn Taichung 40227 Taiwan

Location-based services (LBS) on web-based maps and images have come into real-time since Google launched its street view imaging services in 2007. This research employs Google Maps API and Web Service, GAE for JAVA, AJAX, Proj4js, cascading style sheets and HyperText markup language in developing a platform for accessing the orientation parameters of Google street view (GSV) panoramas in order to determine the three-dimensional (3D) position of points of interest (POIs) by intersection between two nearby GSV images and to validate the 3D position of a GSV panorama by resection from three known POIs. Extracted 3D positional information of the features are then packed in keyhole markup language format and stored in GAE Servlet for future LBS applications integrated with Google Maps and Google Earth. Experimental results from two tests on intersection and one test on resection of GSV panoramas in National Chung Hsing University campus were examined with error reports and source analyses. With automatic conjugate image-matching capability, the developed system is suitable for volumetric data collection in establishing web-based LBS applications integrated with GSV panoramas and Google Maps/Earth in which positional accuracy is not primarily concerned.

关键词： application program interfaces geographic information systems hypermedia markup languages Java mobile computing Web services social networking (online) three-dimensional positioning Google street view panoramas location-based services LBS Web-based maps Google Maps API Web service GAE JAVA AJAX Proj4js HyperText markup language points of interest POI GSV images National Chung Hsing University application program interfaces geographic information systems hypermedia markup languages Java mobile computing Web services social networking (online) three-dimensional positioning Google street view panoramas location-based services LBS Web-based maps Google Maps API Web service GAE JAVA AJAX Proj4js HyperText markup language points of interest POI GSV images National Chung Hsing University

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Deploying the Robot application programming Interface Delegate via Second-Generation IP-over-DTN

Deploying the Robot Application Programming Interface Delega...

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IEEE Aerospace Conference

作者： Tsao, Philip Torres, Jay Schoolcraft, Joshua Mittman, David CALTECH Jet Prop Lab Pasadena CA 91109 USA

ISBN: (纸本)9781467318112

The Robot application programmer Interface Delegate (RAPID) is a pipeline designed for telerobotic operations in the Human Exploration Technology (HET) program. As human spaceflight missions become more ambitious and far reaching (for example, long duration operations on board ISS or around near-Earth asteroids), traditional telerobotic technology becomes expensive, unwieldy and difficult to scale. We present a RAPID deployment architecture that leverages the advantages of COT S internetworking infrastructure while enjoying many of the benefits of space-optimized Delay/Disruption Tolerant Network (DTN) technology. DTNTAP is a multi-platform second-generation IP over DTN implementation with performance and usability improvements over its predecessor. Selected results from functional and performance tests are presented and new capabilities are described.

关键词： IP networks aerospace robotics application program interfaces control engineering computing delay tolerant networks space communication links telerobotics

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