12,275 research outputs found
Transforming specifications of observable behaviour into programs
A methodology for deriving programs from specifications of observable
behaviour is described. The class of processes to which this methodology
is applicable includes those whose state changes are fully definable by labelled
transition systems, for example communicating processes without
internal state changes. A logic program representation of such labelled
transition systems is proposed, interpreters based on path searching techniques
are defined, and the use of partial evaluation techniques to derive
the executable programs is described
A C++-embedded Domain-Specific Language for programming the MORA soft processor array
MORA is a novel platform for high-level FPGA programming of streaming vector and matrix operations, aimed at multimedia applications. It consists of soft array of pipelined low-complexity SIMD processors-in-memory (PIM). We present a Domain-Specific Language (DSL) for high-level programming of the MORA soft processor array. The DSL is embedded in C++, providing designers with a familiar language framework and the ability to compile designs using a standard compiler for functional testing before generating the FPGA bitstream using the MORA toolchain. The paper discusses the MORA-C++ DSL and the compilation route into the assembly for the MORA machine and provides examples to illustrate the programming model and performance
Type-driven automated program transformations and cost modelling for optimising streaming programs on FPGAs
In this paper we present a novel approach to program optimisation based on compiler-based type-driven program transformations and a fast and accurate cost/performance model for the target architecture. We target streaming programs for the problem domain of scientific computing, such as numerical weather prediction. We present our theoretical framework for type-driven program transformation, our target high-level language and intermediate representation languages and the cost model and demonstrate the effectiveness of our approach by comparison with a commercial toolchain
Logics for Unranked Trees: An Overview
Labeled unranked trees are used as a model of XML documents, and logical
languages for them have been studied actively over the past several years. Such
logics have different purposes: some are better suited for extracting data,
some for expressing navigational properties, and some make it easy to relate
complex properties of trees to the existence of tree automata for those
properties. Furthermore, logics differ significantly in their model-checking
properties, their automata models, and their behavior on ordered and unordered
trees. In this paper we present a survey of logics for unranked trees
An Introduction to Programming for Bioscientists: A Python-based Primer
Computing has revolutionized the biological sciences over the past several
decades, such that virtually all contemporary research in the biosciences
utilizes computer programs. The computational advances have come on many
fronts, spurred by fundamental developments in hardware, software, and
algorithms. These advances have influenced, and even engendered, a phenomenal
array of bioscience fields, including molecular evolution and bioinformatics;
genome-, proteome-, transcriptome- and metabolome-wide experimental studies;
structural genomics; and atomistic simulations of cellular-scale molecular
assemblies as large as ribosomes and intact viruses. In short, much of
post-genomic biology is increasingly becoming a form of computational biology.
The ability to design and write computer programs is among the most
indispensable skills that a modern researcher can cultivate. Python has become
a popular programming language in the biosciences, largely because (i) its
straightforward semantics and clean syntax make it a readily accessible first
language; (ii) it is expressive and well-suited to object-oriented programming,
as well as other modern paradigms; and (iii) the many available libraries and
third-party toolkits extend the functionality of the core language into
virtually every biological domain (sequence and structure analyses,
phylogenomics, workflow management systems, etc.). This primer offers a basic
introduction to coding, via Python, and it includes concrete examples and
exercises to illustrate the language's usage and capabilities; the main text
culminates with a final project in structural bioinformatics. A suite of
Supplemental Chapters is also provided. Starting with basic concepts, such as
that of a 'variable', the Chapters methodically advance the reader to the point
of writing a graphical user interface to compute the Hamming distance between
two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables,
numerous exercises, and 19 pages of Supporting Information; currently in
press at PLOS Computational Biolog
Soft Concurrent Constraint Programming
Soft constraints extend classical constraints to represent multiple
consistency levels, and thus provide a way to express preferences, fuzziness,
and uncertainty. While there are many soft constraint solving formalisms, even
distributed ones, by now there seems to be no concurrent programming framework
where soft constraints can be handled. In this paper we show how the classical
concurrent constraint (cc) programming framework can work with soft
constraints, and we also propose an extension of cc languages which can use
soft constraints to prune and direct the search for a solution. We believe that
this new programming paradigm, called soft cc (scc), can be also very useful in
many web-related scenarios. In fact, the language level allows web agents to
express their interaction and negotiation protocols, and also to post their
requests in terms of preferences, and the underlying soft constraint solver can
find an agreement among the agents even if their requests are incompatible.Comment: 25 pages, 4 figures, submitted to the ACM Transactions on
Computational Logic (TOCL), zipped file
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