Abstract

Abstract
Prolog affords concise, elegant, and clean solutions for many interesting problems, but is not immune to the software engineering challenges of large-scale application development. Code modularization, using modules or objects, is a key feature to keep projects manageable. Since most literature, instruction, and practice focus exclusively on object-oriented languages derived from imperative languages, objects are perceived as alien to logic programming while modules are considered a natural fit. Logtalk is an object-oriented logic programming language that can use most Prolog implementations as a back-end compiler. Logtalk objects are about code encapsulation and reuse, providing an alternative to Prolog module systems, and enabling natural solutions for a wide range of problems that would be awkward to solve using modules. This talk presents the Logtalk design goals, followed by a tutorial on Logtalk programming and some application examples. The talk ends with a discussion on the problems and benefits of developing Logtalk as a portable Prolog application. © 2009 Springer Berlin Heidelberg.

Abstract
This paper presents a survey of programming patterns for Logtalk parametric objects. A parametric object is an object whose identifier is a compound term containing logical variables. These variables play the role of object parameters. Object predicates can be coded to depend on the parameter values. Parametric objects are a common feature of some other object-oriented logic programming languages and Prolog object-oriented extensions. Logtalk extends the usefulness of parametric objects by introducing the concept of object proxies. An object proxy is a compound term that can be interpreted as a possible instantiation of the identifier of a parametric object. Object proxies, when represented as predicate facts, allow application memory footprint to be minimized while still taking full advantage of Logtalk object-oriented features for representing and reasoning with taxonomic knowledge. © 2011 Springer-Verlag Berlin Heidelberg.

Abstract
This paper identifies potential security loopholes in the implementation of support for meta-predicates Closing these loopholes depends on three conditions: a clear distinction between closures and goals, support for an extended meta-predicate directive that allows the specification of closures, and the availability of the call/2-N family of built-in meta-predicates. These conditions provide the basis for a set of simple safety rules that allows meta-predicates to be securely supported. These safety rules are currently implemented by Logtalk, all object-oriented logic programming language, and may also be applied in the context of Prolog predicate-based module systems. Experimental results illustrate how these rules can prevent several security problems, including accidental or malicious changes to the original meta-predicate arguments and bypassing of predicate scope rules and predicate scope directives.

Abstract
This paper presents the logic programming concept of thread-based competitive or-parallelism, which combines the original idea of competitive or-parallelism with committed-choice nondeterminism and speculative threading. In thread-based competitive or-parallelism, an explicit; disjunction of subgoals is interpreted as a set of concurrent alternatives, each running in its own thread. The individual subgoals usually correspond to predicates implementing different procedures that, depending on the problem specifics, are expected to either fail or succeed with different performance levels. The subgoals compete for providing an answer and the first successful subgoal leads to the termination of the remaining ones. We discuss the implementation of thread-based competitive or-parallelism in the context of Logtalk, an object-oriented logic programming language, and present experimental results.

Abstract
The analysis of considerable numbers of DNA sequences is largely dependent on the development of simple software tools for automatically process the genetic data deposited on public databases. However, there are some difficulties in the automation process due to diverse synonyms being used as qualifiers for genes and some inconsistencies in gene locations between related Primate species, this fact happening even in the carefully curated database RefSeq. Here, we present mtDNA GeneEXtractor, a Windows based computer tool developed for the extraction of information for particular gene/regions from mammal mitochondrial DNA sequences deposited under GenBank format. The tool was quite efficient in retrieving organized information for comparative mtDNA gene/region diversity analyses when tested for the evaluation of transition/transversion ratios in humans and between Primates. Taking phylogenetic information into account to avoid redundancy due to ancestry-sharing, the transition/transversion ratios in the 13 protein-coding genes had a mean value of 12.46 for Primates (from 6.46 in ND2 to 17.04 in COX1) and higher (34.74) but more heterogeneous (ranging from 17.30 in ND5 to 74.39 in ND4) in a worldwide human database. The similar patterns of transition/transversion ratios in all positions and in only four fold degenerate positions show no evidence for selection in the 13 mtDNA protein-coding genes.