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作者： Shahar Alon Eli Eisenberg

Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite for this editing process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Indeed, tens of editing sites were found in miRNAs, some of which change the miRNA binding specificity. Here, we describe a protocol for the identification of RNA editing sites in mature miRNAs using deep sequencing data. less

关键词： Deep Sequencing Genomics Statistical Calculation Bowtie Illumina Sequencing programming language Mus musculus Bioinformatics miRNA A-to-I editing

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A bottom-up approach to verifiable embedded system information flow security

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IET INFORMATION SECURITY 2014年第1期8卷 12-17页

作者： Mu, Dejun Hu, Wei Mao, Baolei Ma, Bo Northwestern Polytech Univ Sch Automat Xian 710072 Peoples R China

With the wide deployment of embedded systems and constant increase in their inter-connections, embedded systems tend to be confronted with attacks through security holes that are hard to predict using typical security measures such as access control or data encryption. To eliminate these security holes, embedded security should be accounted for during the design phase from all abstraction levels with effective measures taken to prevent unintended interference between different system components caused by harmful flows of information. This study proposes a bottom-up approach to designing verifiably information flow secure embedded systems. The proposed method enables tight information flow controls by monitoring all flows of information from the level of Boolean gates. It lays a solid foundation to information flow security in the underlying hardware and exposes the ability to prove security properties to all abstraction levels in the entire system stack. With substantial amounts of modifications made to the instruction set architecture, operating system, programming language and input/output architecture, the target system can be designed to be verifiably information flow secure.

关键词： embedded systems formal verification instruction sets operating systems (computers) security of data bottom up approach verifiable embedded system information flow security security holes access control data encryption information flow controls instruction set architecture operating system programming language input-output architecture

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Algol in France: From Universal Project to Embedded Culture

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IEEE ANNALS OF THE HISTORY OF COMPUTING 2014年第4期36卷 6-25页

作者： Mounier-Kuhn, Pierre CNRS F-75700 Paris France Univ Paris 04 F-75230 Paris 05 France

This article focuses on Algol as a research agenda and a decisive step in the building of a new scientific community. It provides an analysis of the main French actors involved in the global Algol endeavor-small groups of computer scientists who participated in its evolution, within academic laboratories, R&D departments of computer companies, user organizations, or learned societies.

关键词： Algol Bull Computer languages computer science Europe France History history of computing IBM industrial research learned society Mathematics Plan Calcul programming programming language Research and development Software engineering

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Serving many at once: How a database approach can create unity in dynamical ecosystem modelling

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ENVIRONMENTAL MODELLING & SOFTWARE 2014年第0期61卷 266-273页

作者： Mooij, Wolf M. Brederveld, Robert J. de Klein, Jeroen J. M. DeAngelis, Don L. Downing, Andrea S. Faber, Michiel Gerla, Daan J. Hipsey, Matthew R. 't Hoen, Jochem Janse, Jan H. Janssen, Annette B. G. Jeuken, Michel Kooi, Bob W. Lischke, Betty Petzoldt, Thomas Postma, Leo Schep, Sebastiaan A. Scholten, Huub Teurlincx, Sven Thiange, Christophe Trolle, Dennis van Dam, Anne A. van Gerven, Luuk P. A. van Nes, Egbert H. Kuiper, Jan J. Netherlands Inst Ecol NIOO KNAW Dept Aquat Ecol NL-6700 AB Wageningen Netherlands Wageningen Univ Dept Environm Sci Aquat Ecol & Water Qual Management Grp NL-6700 AA Wageningen Netherlands Witteveen Bos NL-7400 AV Deventer Netherlands Univ Miami USGS Biol Resources Div Coral Gables FL 33124 USA Univ Miami Dept Biol Coral Gables FL 33124 USA Stockholm Univ Dept Syst Ecol S-10691 Stockholm Sweden Inst Marine Resource & Ecosyst Studies IMARES Dept Ecosyst NL-1790 AD Den Burg Netherlands Univ Western Australia Sch Earth & Environm Crawley WA 6009 Australia Netherlands Environm Assessment Agcy PBL NL-3720 AH Bilthoven Netherlands Deltares NL-2600 MH Delft Netherlands Vrije Univ Amsterdam Fac Earth & Life Sci Dept Theoret Biol NL-1081 HV Amsterdam Netherlands Univ Potsdam Inst Biochem & Biol Dept Ecol & Ecosyst Modelling D-14469 Potsdam Germany Tech Univ Dresden Fac Environm Sci Inst Hydrobiol D-01062 Dresden Germany Wageningen Univ Dept Social Sci Informat Technol Grp NL-6700 EW Wageningen Netherlands Aarhus Univ Dept Biosci DK-8600 Silkeborg Denmark UNESCO IHE Inst Water Educ NL-2601 DA Delft Netherlands Royal Netherlands Inst Sea Res NIOZ Dept Ecosyst Studies NL-4400 AC Yerseke Netherlands

Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be run. To create an instance of the model, the information in the database is translated and augmented with the language and platform specifics. This process is automated so that a new instance can be created each time the database is updated. We describe the approach using the simple Lotka-Volterra model and the complex ecosystem model for shallow lakes PCLake, which we automatically implement in the frameworks OSIRIS, GRIND for MATLAB, ACSL, R, DUFLOW and DELWAQ. A clear advantage of working in a database is the overview it provides. The simplicity of the approach only adds to its elegance. (C) 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-SA license (http://***/licenses/by-nc-sa/3.0/).

关键词： Modelling framework programming language Differential equation Community-based modelling Database approach to modelling DATM

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Enhancing R with Advanced Compilation Tools and Methods

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STATISTICAL SCIENCE 2014年第2期29卷 181-200页

作者： Lang, Duncan Temple Univ Calif Davis Dept Stat Davis CA 95616 USA

I describe an approach to compiling common idioms in R code directly to native machine code and illustrate it with several examples. Not only can this yield significant performance gains, but it allows us to use new approaches to computing in R. Importantly, the compilation requires no changes to R itself, but is done entirely via R packages. This allows others to experiment with different compilation strategies and even to define new domain-specific languages within R We use the Low-Level Virtual Machine (LLVM) compiler toolkit to create the native code and perform sophisticated optimizations on the code. By adopting this widely used software within R, we leverage its ability to generate code for different platforms such as CPUs and GPUs, and will continue to benefit from its ongoing development. This approach potentially allows us to develop high-level R code that is also fast, that can be compiled to work with different data representations and sources, and that could even be run outside of R. The approach aims to both provide a compiler for a limited subset of the R language and also to enable R programmers to write other compilers. This is another approach to help us write high-level descriptions of what we want to compute, not how.

关键词： programming language efficient computation compilation extensible compiler toolkit

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A Domain-specific language to Facilitate Software Defined Radio Parallel Executable Patterns Deployment on Heterogeneous Architectures

A Domain-specific Language to Facilitate Software Defined Ra...

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33rd IEEE International Performance, Computing, and Communications Conference (IPCCC)

作者： Mohapi, Lerato J. Winberg, Simon Inggs, Michael Univ Cape Town Radar Remote Sensing Grp Dept Elect Engn ZA-7925 Cape Town South Africa

ISBN: (纸本)9781479975754

In this paper, we present a domain-specific language, referred to as OptiSDR, that matches high level digital signal processing (DSP) routines for software defined radio (SDR) to their generic parallel executable patterns targeted to heterogeneous computing architectures (HCAs). These HCAs includes a combination of hybrid GPU-CPU and DSP-FPGA architectures that are programmed using different programming paradigms such as C/C++, CUDA, OpenCL, and/or VHDL. OptiSDR presents an intuitive single high-level source code and near specification-level approach for optimization and facilitation of HCAs. OptiSDR uses an optimized embedded domain-specific language (DSL) compiler framework called Delite. Our focus is on the programming language expressiveness for parallel programming and optimization of typical DSP algorithms for deployment on SDR HCAs. We demonstrate the capability of OptiSDR to express the solution to the issues of parallel DSP low-level implementation complexities in the closest way to the original parallel programming of SDR systems. This paper will achieve these by focusing on three generic parallel executable patterns suitable for DSP routines such as cross-correlation, convolution in FIR filter based Hilbert transformers, and fast Fourier transforms for spectral analysis. This paper concludes with a performance analysis using DSP algorithms that tests automatically generated code against hand-crafted solutions.

关键词： FIR filters Hilbert transforms convolution fast Fourier transforms parallel programming program compilers programming languages signal processing software radio spectral analysis telecommunication computing DSL compiler framework DSP algorithms DSP routines DSP-FPGA architectures Delite FIR filter OptiSDR SDR HCA cross-correlation digital signal processing domain-specific language heterogeneous computing architectures high-level source code hybrid GPU-CPU parallel executable patterns deployment programming language programming paradigms software defined radio Computer architecture DSL Digital signal processing Finite impulse response filters Graphics processing units programming

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Bit-Error Injection for Software Developers

Bit-Error Injection for Software Developers

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Software Evolution Week / IEEE Conference on Software Maintenance, Reengineering, and Reverse Engineering (CSMR-WCRE)

作者： Heing-Becker, Marcel Kamph, Timo Schupp, Sibylle Hamburg Univ Technol TUHH Inst Software Syst Hamburg Germany

ISBN: (纸本)9781479937523

This paper presents FITIn, a bit-error injection tool designed for evaluating software-implemented hardware fault tolerance (SIHFT) mechanisms. Like most bit-error injection tools, FITIn injects faults at run time into the binary of a program. Unlike previous bit-error injection tools, FITIn allows a software developer to control the targets of injection campaigns at the level of a higher programming language rather than assembler. FITIn is implemented as a Valgrind plugin and has been tested for C programs. We present its architecture, demonstrate its functioning using examples from three benchmarks (Dhrystone, STAMP, and CoreMark), provide performance figures, and discuss general limitations of the approach.

关键词： C language fault tolerant computing program testing software tools C programs FITIn SIHFT Valgrind plugin assembler bit-error injection tool injection campaigns programming language software developer software developers software-implemented hardware fault tolerance mechanisms Benchmark testing Elevators Hardware Registers Robustness Software

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A programming language for composable DNA circuits

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JOURNAL OF THE ROYAL SOCIETY INTERFACE 2009年第sup4期6卷 S419-S436页

作者： Phillips, Andrew Cardelli, Luca Microsoft Res Cambridge CB3 0FB England

Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their automatic compilation to nucleotide sequences. We present a programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.

关键词： DNA computing circuits programming language compositional

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Domain-Specific languages for Embedded Systems Portable Software Development 16

Domain-Specific Languages for Embedded Systems Portable Soft...

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16th FRUCT Conference of Open-Innovations-Association

作者： Ivanova, Vera Sedov, Boris Sheynin, Yuriy Syschikov, Alexey St Petersburg State Univ Aerosp Instrumentat St Petersburg Russia

ISBN: (纸本)9785757704890

In this paper we present a new method of Domain Specific language development for a portable software development for embedded systems. Domain Specific languages allow to involve domain experts apart with programmers in embedded software development. We propose a visual programming approach and methods for coarse-grained programming. In a combination with a method for domain specific languages development it allows rapid building of an infrastructure for selected domains programming. Coarse-grained approach provides abilities for easy targeting of developed program to various target platforms and configurations.

关键词： embedded systems programming languages software engineering visual programming coarse-grained programming domain specific language development embedded software development portable software development programming language DSL Domain specific languages Embedded systems programming Unified modeling language Visualization Embedded systems visual programming Computer programming languages Software design computer software UML programming digital subscriber lines Software engineering application-specific language Visualization

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Programmable enforcement framework of information flow policies 15

Programmable enforcement framework of information flow polic...

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15th Italian Conference on Theoretical Computer Science, ICTCS 2014

作者： Ngo, Minh Massacci, Fabio University of Trento Italy

We propose a programmable framework that can be easily instantiated to enforce a large variety of information flow properties. Our framework is based on the idea of secure multi-execution in which multiple instances of the controlled program are executed in parallel. The information flow property of choice can be obtained by simply implementing programs that control parallel executions. We present the architecture of the enforcement mechanism and its instantiations for non-interference (NI) (from Devriese and Piessens), non-deducibility (ND) (from Sutherland) and some properties proposed by Mantel, such as removal of inputs (RI) and deletion of inputs (DI), and demonstrate formally soundness and precision of enforcement for these properties.

关键词： Non-Deducibility Non-Interference Possibilistic information flow properties programming language Secure multi execution

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