Decision Support Models for Composing and Navigating through e-Learning Objects

Libraries of learning objects may serve as basis for deriving course offerings that are customized to the needs of different learning communities or even individuals. Several ways of organizing this course composition process are discussed. Course composition needs a clear understanding of the dependencies between the learning objects. Therefore we discuss the metadata for object relationships proposed in different standardization projects and especially those suggested in the Dublin Core Metadata Initiative. Based on these metadata we construct adjacency matrices and graphs. We show how Gozinto-type computations can be used to determine direct and indirect prerequisites for certain learning objects. The metadata may also be used to define integer programming models which can be applied to support the instructor in formulating his specifications for selecting objects or which allow a computer agent to automatically select learning objects. Such decision models could also be helpful for a learner navigating through a library of learning objects. We also sketch a graph-based procedure for manual or automatic sequencing of the learning objects.

The sequence comparison index: A novel method for comparing proteins and proteomes

Historically morphological features were used as the primary means to classify organisms. However, the age of molecular genetics has allowed us to approach this field from the perspective of the organism's genetic code. Early work used highly conserved sequences, such as ribosomal RNA. The increasing number of complete genomes in the public data repositories provides the opportunity to look not only at a single gene, but at organisms' entire parts list. ^ Here the Sequence Comparison Index (SCI) and the Organism Comparison Index (OCI), algorithms and methods to compare proteins and proteomes, are presented. The complete proteomes of 104 sequenced organisms were compared. Over 280 million full Smith-Waterman alignments were performed on sequence pairs which had a reasonable expectation of being related. From these alignments a whole proteome phylogenetic tree was constructed. This method was also used to compare the small subunit (SSU) rRNA from each organism and a tree constructed from these results. The SSU rRNA tree by the SCI/OCI method looks very much like accepted SSU rRNA trees from sources such as the Ribosomal Database Project, thus validating the method. The SCI/OCI proteome tree showed a number of small but significant differences when compared to the SSU rRNA tree and proteome trees constructed by other methods. Horizontal gene transfer does not appear to affect the SCI/OCI trees until the transferred genes make up a large portion of the proteome. ^ As part of this work, the Database of Related Local Alignments (DaRLA) was created and contains over 81 million rows of sequence alignment information. DaRLA, while primarily used to build the whole proteome trees, can also be applied shared gene content analysis, gene order analysis, and creating individual protein trees. ^ Finally, the standard BLAST method for analyzing shared gene content was compared to the SCI method using 4 spirochetes. The SCI system performed flawlessly, finding all proteins from one organism against itself and finding all the ribosomal proteins between organisms. The BLAST system missed some proteins from its respective organism and failed to detect small ribosomal proteins between organisms. ^

On Understanding How Developers Use the Spotter Search Tool

Analyzing how software engineers use the Integrated Development Environment (IDE) is essential to better understanding how engineers carry out their daily tasks. Spotter is a code search engine for the Pharo programming language. Since its inception, Spotter has been rapidly and broadly adopted within the Pharo community. However, little is known about how practitioners employ Spotter to search and navigate within the Pharo code base. This paper evaluates how software engineers use Spotter in practice. To achieve this, we remotely gather user actions called events. These events are then visually rendered using an adequate navigation tool chain. Sequences of events are represented using a visual alphabet. We found a number of usage patterns and identified underused Spotter features. Such findings are essential for improving Spotter.

Reusable Knowledge-based Components for Building Software Applications: A Knowledge Modelling Approach

In computer science, different types of reusable components for building software applications were proposed as a direct consequence of the emergence of new software programming paradigms. The success of these components for building applications depends on factors such as the flexibility in their combination or the facility for their selection in centralised or distributed environments such as internet. In this article, we propose a general type of reusable component, called primitive of representation, inspired by a knowledge-based approach that can promote reusability. The proposal can be understood as a generalisation of existing partial solutions that is applicable to both software and knowledge engineering for the development of hybrid applications that integrate conventional and knowledge based techniques. The article presents the structure and use of the component and describes our recent experience in the development of real-world applications based on this approach.

Some issues in analysis and specialization of modular ciao-prolog programs

Separating programs into modules is a well-known technique which has proven very useful in program development and maintenance. Starting by introducing a number of possible scenarios, in this paper we study different issues which appear when developing analysis and specialization techniques for modular logic programming. We discuss a number of design alternatives and their consequences for the different scenarios considered and describe where applicable the decisions made in the Ciao system analyzer and specializer. In our discussion we use the module system of Ciao Prolog. This is both for concreteness and because Ciao Prolog is a second-generation Prolog system which has been designed with global analysis and specialization in mind, and which has a strict module system. The aim of this work is not to provide a theoretical basis on modular analysis and specialization, but rather to discuss some interesting practical issues.

The ciao module system: A new module system for prolog

Ciao Prolog incorporates a module system which allows sepárate compilation and sensible creation of standalone executables. We describe some of the main aspects of the Ciao modular compiler, ciaoc, which takes advantage of the characteristics of the Ciao Prolog module system to automatically perform sepárate and incremental compilation and efficiently build small, standalone executables with competitive run-time performance, ciaoc can also detect statically a larger number of programming errors. We also present a generic code processing library for handling modular programs, which provides an important part of the functionality of ciaoc. This library allows the development of program analysis and transformation tools in a way that is to some extent orthogonal to the details of module system design, and has been used in the implementation of ciaoc and other Ciao system tools. We also describe the different types of executables which can be generated by the Ciao compiler, which offer different tradeoffs between executable size, startup time, and portability, depending, among other factors, on the linking regime used (static, dynamic, lazy, etc.). Finally, we provide experimental data which illustrate these tradeoffs.

The ciao modular, standalone compiler and its generic program processing library

Ciao Prolog incorporates a module system which allows sepárate compilation and sensible creation of standalone executables. We describe some of the main aspects of the Ciao modular compiler, ciaoc, which takes advantage of the characteristics of the Ciao Prolog module system to automatically perform sepárate and incremental compilation and efficiently build small, standalone executables with competitive run-time performance, ciaoc can also detect statically a larger number of programming errors. We also present a generic code processing library for handling modular programs, which provides an important part of the functionality of ciaoc. This library allows the development of program analysis and transformation tools in a way that is to some extent orthogonal to the details of module system design, and has been used in the implementation of ciaoc and other Ciao system tools. We also describe the different types of executables which can be generated by the Ciao compiler, which offer different tradeoffs between executable size, startup time, and portability, depending, among other factors, on the linking regime used (static, dynamic, lazy, etc.). Finally, we provide experimental data which illustrate these tradeoffs.

A system for automatically generating documentation for (C)LP programs

We describe lpdoc, a tool which generates documentation manuals automatically from one or more logic program source files, written in ISO-Prolog, Ciao, and other (C)LP languages. It is particularly useful for documenting library modules, for which it automatically generates a rich description of the module interface. However, it can also be used quite successfully to document full applications. A fundamental advantage of using lpdoc is that it helps maintaining a true correspondence between the program and its documentation, and also identifying precisely to what version of the program a given printed manual corresponds. The quality of the documentation generated can be greatly enhanced by including within the program text assertions (declarations with types, modes, etc.) for the predicates in the program, and machine-readable comments. One of the main novelties of lpdoc is that these assertions and comments are written using the Ciao system assertion language, which is also the language of communication between the compiler and the user and between the components of the compiler. This allows a significant synergy among specification, documentation, optimization, etc. A simple compatibility library allows conventional (C)LP systems to ignore these assertions and comments and treat normally programs documented in this way. The documentation can be generated in many formats including texinfo, dvi, ps, pdf, info, html/css, Unix nroff/man, Windows help, etc., and can include bibliographic citations and images. lpdoc can also generate “man” pages (Unix man page format), nicely formatted plain ascii “readme” files, installation scripts useful when the manuals are included in software distributions, brief descriptions in html/css or info formats suitable for inclusion in on-line indices of manuals, and even complete WWW and info sites containing on-line catalogs of documents and software distributions. The lpdoc manual, all other Ciao system manuals, and parts of this paper are generated by lpdoc.

Supporting End-User Development through a New Composition Model: An Empirical Study

End-user development (EUD) is much hyped, and its impact has outstripped even the most optimistic forecasts. Even so, the vision of end users programming their own solutions has not yet materialized. This will continue to be so unless we in both industry and the research community set ourselves the ambitious challenge of devising end to end an end-user application development model for developing a new age of EUD tools. We have embarked on this venture, and this paper presents the main insights and outcomes of our research and development efforts as part of a number of successful EU research projects. Our proposal not only aims to reshape software engineering to meet the needs of EUD but also to refashion its components as solution building blocks instead of programs and software developments. This way, end users will really be empowered to build solutions based on artefacts akin to their expertise and understanding of ideal solutions

A card Game Description Language

We present initial research regarding a system capable of generating novel card games. We furthermore propose a method for com- putationally analysing existing games of the same genre. Ultimately, we present a formalisation of card game rules, and a context-free grammar G cardgame capable of expressing the rules of a large variety of card games. Example derivations are given for the poker variant Texashold?em , Blackjack and UNO. Stochastic simulations are used both to verify the implementation of these well-known games, and to evaluate the results of new game rules derived from the grammar. In future work, this grammar will be used to evolve completely novel card games using a grammar- guided genetic program.

MIA - a free and open source software for gray scale medical image analysis

Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. Conclusion In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed.

Reachability-based acyclicity analysis by Abstract Interpretation

In programming languages with dynamic use of memory, such as Java, knowing that a reference variable x points to an acyclic data structure is valuable for the analysis of termination and resource usage (e.g., execution time or memory consumption). For instance, this information guarantees that the depth of the data structure to which x points is greater than the depth of the data structure pointed to by x.f for any field f of x. This, in turn, allows bounding the number of iterations of a loop which traverses the structure by its depth, which is essential in order to prove the termination or infer the resource usage of the loop. The present paper provides an Abstract-Interpretation-based formalization of a static analysis for inferring acyclicity, which works on the reduced product of two abstract domains: reachability, which models the property that the location pointed to by a variable w can be reached by dereferencing another variable v (in this case, v is said to reach w); and cyclicity, modeling the property that v can point to a cyclic data structure. The analysis is proven to be sound and optimal with respect to the chosen abstraction.

Modelado y Comparación de Colecciones en la Web Semántica

En esta tesis se estudia la representación, modelado y comparación de colecciones mediante el uso de ontologías en el ámbito de la Web Semántica. Las colecciones, entendidas como agrupaciones de objetos o elementos con entidad propia, son construcciones que aparecen frecuentemente en prácticamente todos los dominios del mundo real, y por tanto, es imprescindible disponer de conceptualizaciones de estas estructuras abstractas y de representaciones de estas conceptualizaciones en los sistemas informáticos, que definan adecuadamente su semántica. Mientras que en muchos ámbitos de la Informática y la Inteligencia Artificial, como por ejemplo la programación, las bases de datos o la recuperación de información, las colecciones han sido ampliamente estudiadas y se han desarrollado representaciones que responden a multitud de conceptualizaciones, en el ámbito de la Web Semántica, sin embargo, su estudio ha sido bastante limitado. De hecho hasta la fecha existen pocas propuestas de representación de colecciones mediante ontologías, y las que hay sólo cubren algunos tipos de colecciones y presentan importantes limitaciones. Esto impide la representación adecuada de colecciones y dificulta otras tareas comunes como la comparación de colecciones, algo crítico en operaciones habituales como las búsquedas semánticas o el enlazado de datos en la Web Semántica. Para solventar este problema esta tesis hace una propuesta de modelización de colecciones basada en una nueva clasificación de colecciones de acuerdo a sus características estructurales (homogeneidad, unicidad, orden y cardinalidad). Esta clasificación permite definir una taxonomía con hasta 16 tipos de colecciones distintas. Entre otras ventajas, esta nueva clasificación permite aprovechar la semántica de las propiedades estructurales de cada tipo de colección para realizar comparaciones utilizando las funciones de similitud y disimilitud más apropiadas. De este modo, la tesis desarrolla además un nuevo catálogo de funciones de similitud para las distintas colecciones, donde se han recogido las funciones de (di)similitud más conocidas y también algunas nuevas. Esta propuesta se ha implementado mediante dos ontologías paralelas, la ontología E-Collections, que representa los distintos tipos de colecciones de la taxonomía y su axiomática, y la ontología SIMEON (Similarity Measures Ontology) que representa los tipos de funciones de (di)similitud para cada tipo de colección. Gracias a estas ontologías, para comparar dos colecciones, una vez representadas como instancias de la clase más apropiada de la ontología E-Collections, automáticamente se sabe qué funciones de (di)similitud de la ontología SIMEON pueden utilizarse para su comparación. Abstract This thesis studies the representation, modeling and comparison of collections in the Semantic Web using ontologies. Collections, understood as groups of objects or elements with their own identities, are constructions that appear frequently in almost all areas of the real world. Therefore, it is essential to have conceptualizations of these abstract structures and representations of these conceptualizations in computer systems, that define their semantic properly. While in many areas of Computer Science and Artificial Intelligence, such as Programming, Databases or Information Retrieval, the collections have been extensively studied and there are representations that match many conceptualizations, in the field Semantic Web, however, their study has been quite limited. In fact, there are few representations of collections using ontologies so far, and they only cover some types of collections and have important limitations. This hinders a proper representation of collections and other common tasks like comparing collections, something critical in usual operations such as semantic search or linking data on the Semantic Web. To solve this problem this thesis makes a proposal for modelling collections based on a new classification of collections according to their structural characteristics (homogeneity, uniqueness, order and cardinality). This classification allows to define a taxonomy with up to 16 different types of collections. Among other advantages, this new classification can leverage the semantics of the structural properties of each type of collection to make comparisons using the most appropriate (dis)similarity functions. Thus, the thesis also develops a new catalog of similarity functions for the different types of collections. This catalog contains the most common (dis)similarity functions as well as new ones. This proposal is implemented through two parallel ontologies, the E-Collections ontology that represents the different types of collections in the taxonomy and their axiomatic, and the SIMEON ontology (Similarity Measures Ontology) that represents the types of (dis)similarity functions for each type of collection. Thanks to these ontologies, to compare two collections, once represented as instances of the appropriate class of E-Collections ontology, we can know automatically which (dis)similarity functions of the SIMEON ontology are suitable for the comparison. Finally, the feasibility and usefulness of this modeling and comparison of collections proposal is proved in the field of oenology, applying both E-Collections and SIMEON ontologies to the representation and comparison of wines with the E-Baco ontology.

Avances tecnológicos y obsolescencia programada

El objetivo seguido en este proyecto fin de carrera, ha sido el análisis de la evolución general de la tecnología, tanto electrónica, como en Telecomunicaciones e Informática, desde sus inicios hasta la actualidad, realizando un estudio sobre cómo esos avances han mejorado, incluso cambiado nuestra vida cotidiana y cómo a consecuencia de la conversión de muchos de estos productos tecnológicos en objeto de consumo masivo, la propia dinámica económico-comercial ha llevado a las empresas a la programación del fin del su vida útil con el objeto de incrementar su demanda y, consiguientemente, la producción. Se trata de lo que se conoce desde hace décadas como Obsolescencia Programada. Para realizar este documento se ha realizado un breve repaso por los acontecimientos históricos que promovieron el inicio de esta práctica, así como también nos ha llevado a realizar mención de todos esos aparatos tecnológicos que han sufrido una mayor evolución y por tanto son los más propensos a que se instauren en ellos, debido a cómo influyen dichos cambios en los consumidores. Otro de los aspectos más importantes que rodean a la Obsolescencia Programada, es cómo influye en el comportamiento de la sociedad, creando en ella actitudes consumistas, que precisamente son las que alimentan que el ciclo económico siga basándose en incluir esta práctica desde el diseño del producto, puesto que a mayor consumo, mayor producción, y por tanto, supone un aumento de beneficios para el fabricante. Aunque, lo que para algunos supone un amplio margen de rentabilidad, existen otros componentes de la ecuación que no salen tan bien parados, como pueden ser los países del tercer mundo que están siendo poblados de basura electrónica, y en general el medio ambiente y los recursos de los que hoy disponemos, que no son ilimitados, y que están viéndose gravemente afectados por la inserción de esta práctica. Como cierre de este análisis, se repasarán algunas de las técnicas empleadas en algunos de los productos más utilizados hoy en día y las conclusiones a las que se han llevado después de analizar todos estos puntos del tema. ABSTRACT. The main goal followed in this final project has been analyzing the overall evolution of technology, both electronics and telecommunications. Also, computer science; from beginning to present it has been realized some studies about these advances have improved our daily life, even changing our routine, and turn us massive consumers of all technological products on the market. This dynamic economic and commercial has led companies to programming the end of its useful life in order to increase demand, and consequently, the production. This is known as Obsolescence. To make this document has been made a brief review through historical events that promoted the opening of this practice, and also led us to make mention all these technological devices have undergone further evolution and therefore more likely to establish them, because these changes affect consumers. Another important aspect around planned obsolescence is how to influence in society’s behavior, creating consumerist attitudes, which are precisely those feed the economic cycle continues to be based on including this practice from product design, because increased consumption and production. Therefore, this fact increases profits for the manufacturer. Although, for some people suppose a wide margin of profitability, there are other components do not have such luck; for example, third World countries have been filled with e-waste and the environment, in general, and resources available today which are not unlimited, and who are seriously affected by the inclusion of this practice. To close this analysis, we will review a few techniques used in some products most widely used today, and the conclusions that have been made after analyzing all these points of the topic.

Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets

An integrated understanding of molecular and developmental biology must consider the large number of molecular species involved and the low concentrations of many species in vivo. Quantitative stochastic models of molecular interaction networks can be expressed as stochastic Petri nets (SPNs), a mathematical formalism developed in computer science. Existing software can be used to define molecular interaction networks as SPNs and solve such models for the probability distributions of molecular species. This approach allows biologists to focus on the content of models and their interpretation, rather than their implementation. The standardized format of SPNs also facilitates the replication, extension, and transfer of models between researchers. A simple chemical system is presented to demonstrate the link between stochastic models of molecular interactions and SPNs. The approach is illustrated with examples of models of genetic and biochemical phenomena where the UltraSAN package is used to present results from numerical analysis and the outcome of simulations.