Delno avtomatizirana rekonstrukcija in dokumentiranje metod razvoja programske opreme

Software development is a complex and creative process. In contrast to a typical business process it tends to be more dynamic and dependent on a number of circumstances. Empirical studies show that companies still don’t document their development practices, or if they do, these are not up-to-date and do not reflect how they really develop software. On the other hand, various supporting tools such as issue tracking system, revision control system, document management system, etc. are used by developers and project managers during their work, capturing a vast body of knowledge about how a software development process has been performed. The main objective of this dissertation is to propose an approach that can help companies in documenting their real development practice. Comparing to existing approaches that require substantial effort on the side of project members, our approach extracts information on development practice directly from software repositories. Five companies have been studied to identify information that can be retrieved from software repositories. Based on this, an approach to reconstruct development practice has been developed. The approach has been evaluated on a real software repository shared by an additional company. The results confirm that software repository information suffice for the reconstruction of various aspects of development process, i.e. disciplines, activities, user roles, and artifacts.Razvoj programske opreme je kompleksen in ustvarjalen proces. V primerjavi s tipičnim poslovnim procesom je bolj dinamičen in odvisen od številnih okoliščin. Empirične študije kažejo, da podjetja še vedno ne dokumentirajo svoje razvojne prakse, če pa že, le-te ne vzdržujejo in posledično ne odražajo, kako dejansko razvijajo programsko opremo. Po drugi strani pa razvijalci in vodje projektov med svojim delom uporabljajo različna podporna orodja, kot so sistem za sledenje zahtevkom, sistem za nadzor verzij, sistem za upravljanje dokumentov, itd., ki zajamejo veliko znanja o tem, kako je bil izveden proces razvoja programske opreme. Glavni cilj pričujoče disertacije je predlagati pristop, ki lahko pomaga podjetjem pri dokumentiranju njihove dejanske razvojne prakse. V primerjavi z obstoječimi pristopi, ki zahtevajo veliko napora na strani članov projekta, naš pristop rekonstruira informacije o razvojni praksi neposredno iz programskih repozitorijev. Na podlagi podatkov petih podjetij so bile identificirane informacije, ki jih je mogoče pridobiti iz programskih repozitorijev. Na podlagi tega je bil razvit pristop za rekonstrukcijo razvojne prakse. Pristop je bil evalviran na resničnem programskem repozitoriju, ki ga je zagotovilo dodatno podjetje. Rezultati potrjujejo, da informacije iz programskih repozitorijev zadostujejo za rekonstrukcijo različnih vidikov razvojnega procesa, tj. disciplin, aktivnosti, uporabniških vlog in artefaktov

Accessing 3D Data

The issue of access and discoverability is not simply a matter of permissions and availability. To identify, locate, retrieve, and reuse 3D materials requires consideration of a multiplicity of content types, as well as community and financial investment to resolve challenges related to usability, interoperability, sustainability, and equity. This chapter will cover modes, audiences, assets and decision points, technology requirements, and limitations impacting access, as well as providing recommendations for next steps

Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species

Metabolic network reconstructions have become an important tool for probing cellular metabolism in the field of systems biology. They are used as tools for quantitative prediction but also as scaffolds for further knowledge contextualization. The yeast Saccharomyces cerevisiae was one of the first organisms for which a genome-scale metabolic model (GEM) was reconstructed, in 2003, and since then 45 metabolic models have been developed for a wide variety of relevant yeasts species. A systematic evaluation of these models revealed that-despite this long modeling history-the sequential process of tracing model files, setting them up for basic simulation purposes and comparing them across species and even different versions, is still not a generalizable task. These findings call the yeast modeling community to comply to standard practices on model development and sharing in order to make GEMs accessible and useful for a wider public

Application of Semantics to Solve Problems in Life Sciences

Fecha de lectura de Tesis: 10 de diciembre de 2018La cantidad de información que se genera en la Web se ha incrementado en los últimos años. La mayor parte de esta información se encuentra accesible en texto, siendo el ser humano el principal usuario de la Web. Sin embargo, a pesar de todos los avances producidos en el área del procesamiento del lenguaje natural, los ordenadores tienen problemas para procesar esta información textual. En este cotexto, existen dominios de aplicación en los que se están publicando grandes cantidades de información disponible como datos estructurados como en el área de las Ciencias de la Vida. El análisis de estos datos es de vital importancia no sólo para el avance de la ciencia, sino para producir avances en el ámbito de la salud. Sin embargo, estos datos están localizados en diferentes repositorios y almacenados en diferentes formatos que hacen difícil su integración. En este contexto, el paradigma de los Datos Vinculados como una tecnología que incluye la aplicación de algunos estándares propuestos por la comunidad W3C tales como HTTP URIs, los estándares RDF y OWL. Haciendo uso de esta tecnología, se ha desarrollado esta tesis doctoral basada en cubrir los siguientes objetivos principales: 1) promover el uso de los datos vinculados por parte de la comunidad de usuarios del ámbito de las Ciencias de la Vida 2) facilitar el diseño de consultas SPARQL mediante el descubrimiento del modelo subyacente en los repositorios RDF 3) crear un entorno colaborativo que facilite el consumo de Datos Vinculados por usuarios finales, 4) desarrollar un algoritmo que, de forma automática, permita descubrir el modelo semántico en OWL de un repositorio RDF, 5) desarrollar una representación en OWL de ICD-10-CM llamada Dione que ofrezca una metodología automática para la clasificación de enfermedades de pacientes y su posterior validación haciendo uso de un razonador OWL

Prism: the Development of an Online Repository for Information Security Education Resources

The goal of this study was to develop, implement and evaluate an online system that would allow intuitive sharing and retrieval of information security (IS) education materials, and a corresponding taxonomic system relevant to common contexts in which IS concepts are taught. After determining initial requirements, popular open-source content management systems were evaluated. The most suitable solution was customized, and implemented as the Public Repository for Information Security Material (PRISM) website. An initial organizational taxonomy was developed, and the repository was populated with resources from several sources. Evaluations of PRISM suggest that core functionalities have been suitably designed and implemented, have provided guidance regarding the next phase of development, and have affirmed the scientific value of the PRISM design artifact