Tools for Search Tree Visualization: The APT Tool

The control part of the execution of a constraint logic program can be conceptually shown as a search-tree, where nodes correspond to calis, and whose branches represent conjunctions and disjunctions. This tree represents the search space traversed by the program, and has also a direct relationship with the amount of work performed by the program. The nodes of the tree can be used to display information regarding the state and origin of instantiation of the variables involved in each cali. This depiction can also be used for the enumeration process. These are the features implemented in APT, a tool which runs constraint logic programs while depicting a (modified) search-tree, keeping at the same time information about the state of the variables at every moment in the execution. This information can be used to replay the execution at will, both forwards and backwards in time. These views can be abstracted when the size of the execution requires it. The search-tree view is used as a framework onto which constraint-level visualizations (such as those presented in the following chapter) can be attached

An overview of the ciao multiparadigm language and program development environment and its design philosophy

We describe some of the novel aspects and motivations behind the design and implementation of the Ciao multiparadigm programming system. An important aspect of Ciao is that it provides the programmer with a large number of useful features from different programming paradigms and styles, and that the use of each of these features can be turned on and off at will for each program module. Thus, a given module may be using e.g. higher order functions and constraints, while another module may be using objects, predicates, and concurrency. Furthermore, the language is designed to be extensible in a simple and modular way. Another important aspect of Ciao is its programming environment, which provides a powerful preprocessor (with an associated assertion language) capable of statically finding non-trivial bugs, verifying that programs comply with specifications, and performing many types of program optimizations. Such optimizations produce code that is highly competitive with other dynamic languages or, when the highest levéis of optimization are used, even that of static languages, all while retaining the interactive development environment of a dynamic language. The environment also includes a powerful auto-documenter. The paper provides an informal overview of the language and program development environment. It aims at illustrating the design philosophy rather than at being exhaustive, which would be impossible in the format of a paper, pointing instead to the existing literature on the system

Visualization designs for constraint logic programming

We address the design and implementation of visual paradigms for observing the execution of constraint logic programs, aiming at debugging, tuning and optimization, and teaching. We focus on the display of data in CLP executions, where representation for constrained variables and for the constrains themselves are seeked. Two tools, VIFID and TRIFID, exemplifying the devised depictions, have been implemented, and are used to showcase the usefulness of the visualizations developed

TOR: modular search with hookable disjunction

Horn Clause Programs have a natural exhaustive depth-first procedural semantics. However, for many programs this semantics is ineffective. In order to compute useful solutions, one needs the ability to modify the search method that explores the alternative execution branches. Tor, a well-defined hook into Prolog disjunction, provides this ability. It is light-weight thanks to its library approach and efficient because it is based on program transformation. Tor is general enough to mimic search-modifying predicates like ECLiPSe's search/6. Moreover, Tor supports modular composition of search methods and other hooks. The Tor library is already provided and used as an add-on to SWI-Prolog.publisher: Elsevier articletitle: Tor: Modular search with hookable disjunction journaltitle: Science of Computer Programming articlelink: http://dx.doi.org/10.1016/j.scico.2013.05.008 content_type: article copyright: Copyright © 2013 Elsevier B.V. All rights reserved.status: publishe

The JStar language philosophy

This paper introduces the JStar parallel programming language, which is a Java-based declarative language aimed at discouraging sequential programming, en-couraging massively parallel programming, and giving the compiler and runtime maximum freedom to try alternative parallelisation strategies. We describe the execution semantics and runtime support of the language, several optimisations and parallelism strategies, with some benchmark results

Implementation of an event driven scheme for visualizing parallel execution of logic programs

This article presents in an informal way some early results on the design of a series of paradigms for visualization of the parallel execution of logic programs. The results presented here refer to the visualization of or-parallelism, as in MUSE and Aurora, deterministic dependent and-parallelism, as in Andorra-I, and independent and-parallelism as in &-Prolog. A tool has been implemented for this purpose and has been interfaced with these systems. Results are presented showing the visualization of executions from these systems and the usefulness of the resulting tool is briefly discussed

Some paradigms for visualizing parallel execution of logic programs

This paper addresses the design of visual paradigms for observing the parallel execution of logic programs. First, an intuitive method is proposed for arriving at the design of a paradigm and its implementation as a tool for a given model of parallelism. This method is based on stepwise reñnement starting from the deñnition of basic notions such as events and observables and some precedence relationships among events which hold for the given model of parallelism. The method is then applied to several types of parallel execution models for logic programs (Orparallelism, Determinate Dependent And parallelism, Restricted and-parallelism) for which visualization paradigms are designed. Finally, VisAndOr, a tool which implements all of these paradigms is presented, together with a discussion of its usefulness through examples

The PARSE Programming Paradigm. Part I: Software Development Methodology. Part II: Software Development Support Tools

The programming methodology of PARSE (parallel software environment), a software environment being developed for reconfigurable non-shared memory parallel computers, is described. This environment will consist of an integrated collection of language interfaces, automatic and semi-automatic debugging and analysis tools, and operating system —all of which are made more flexible by the use of a knowledge-based implementation for the tools that make up PARSE. The programming paradigm supports the user freely choosing among three basic approaches /abstractions for programming a parallel machine: logic-based descriptive, sequential-control procedural, and parallel-control procedural programming. All of these result in efficient parallel execution. The current work discusses the methodology underlying PARSE, whereas the companion paper, “The PARSE Programming Paradigm — II: Software Development Support Tools,” details each of the component tools

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