Orchestration of multiscale model for computational oncology

Cancer is a challenging disease that involves multiple types of biological interactions in different time and space scales. Often computational modelling has been facing problems that, in the current technology level, is impracticable to represent in a single space-time continuum. To handle this sort of problems, complex orchestrations of multiscale models is frequently done. PRIMAGE is a large EU project that aims to support personalized childhood cancer diagnosis and prognosis. The goal is to do so predicting the growth of the solid tumour using multiscale in-silico technologies. The project proposes an open cloud-based platform to support decision making in the clinical management of paediatric cancers. The orchestration of predictive models is in general complex and would require a software framework that support and facilitate such task. The present work, proposes the development of an updated framework, referred herein as the VPH-HFv3, as a part of the PRIMAGE project. This framework, a complete re-writing with respect to the previous versions, aims to orchestrate several models, which are in concurrent development, using an architecture as simple as possible, easy to maintain and with high reusability. This sort of problem generally requires unfeasible execution times. To overcome this problem was developed a strategy of particularisation, which maps the upper-scale model results into a smaller number and homogenisation which does the inverse way and analysed the accuracy of this approach.

Deployment of a data analysis workflow of the ATLAS experiment on HPC systems

LHC experiments produce an enormous amount of data, estimated of the order of a few PetaBytes per year. Data management takes place using the Worldwide LHC Computing Grid (WLCG) grid infrastructure, both for storage and processing operations. However, in recent years, many more resources are available on High Performance Computing (HPC) farms, which generally have many computing nodes with a high number of processors. Large collaborations are working to use these resources in the most efficient way, compatibly with the constraints imposed by computing models (data distributed on the Grid, authentication, software dependencies, etc.). The aim of this thesis project is to develop a software framework that allows users to process a typical data analysis workflow of the ATLAS experiment on HPC systems. The developed analysis framework shall be deployed on the computing resources of the Open Physics Hub project and on the CINECA Marconi100 cluster, in view of the switch-on of the Leonardo supercomputer, foreseen in 2023.

GUIsurfer: A Reverse Engineering Framework for User Interface Software

GUIsurfer: A Reverse Engineering Framework for User Interface Software

HEP-Frame: A software engineered framework to aid the development and efficient multicore execution of scientific code

This work was supported by FCT (Fundação para a Ciência e Tecnologia) within Project Scope (UID/CEC/00319/2013), by LIP (Laboratório de Instrumentação e Física Experimental de Partículas) and by Project Search-ON2 (NORTE-07-0162- FEDER-000086), co-funded by the North Portugal Regional Operational Programme (ON.2 - O Novo Norte), under the National Strategic Reference Framework, through the European Regional Development Fund.

evaluation framework for software test processes

Magdeburg, Univ., Fak. für Informatik, Diss., 2009

Framework of quality measurement in CASE tool based software development

Magdeburg, Univ., Fak. für Informatik, Diss., 2010

Software Process Modeling with Eclipse Process Framework

The software development industry is constantly evolving. The rise of the agile methodologies in the late 1990s, and new development tools and technologies require growing attention for everybody working within this industry. The organizations have, however, had a mixture of various processes and different process languages since a standard software development process language has not been available. A promising process meta-model called Software & Systems Process Engineering Meta- Model (SPEM) 2.0 has been released recently. This is applied by tools such as Eclipse Process Framework Composer, which is designed for implementing and maintaining processes and method content. Its aim is to support a broad variety of project types and development styles. This thesis presents the concepts of software processes, models, traditional and agile approaches, method engineering, and software process improvement. Some of the most well-known methodologies (RUP, OpenUP, OpenMethod, XP and Scrum) are also introduced with a comparison provided between them. The main focus is on the Eclipse Process Framework and SPEM 2.0, their capabilities, usage and modeling. As a proof of concept, I present a case study of modeling OpenMethod with EPF Composer and SPEM 2.0. The results show that the new meta-model and tool have made it possible to easily manage method content, publish versions with customized content, and connect project tools (such as MS Project) with the process content. The software process modeling also acts as a process improvement activity.

The Design of a Software Lifecycle Management Framework to a Configuration Management System

Keeping track of software assets and managing software installations in IT environments can be a hard endeavor, especially when the size and diversity of the environment grows. How to install and uninstall software efficiently and cost effectively? Are there too few or too many software licenses purchased? If installed, is the software actually in use? Software Asset Management (SAM) is a process that involves managing and optimizing the purchase, deployment, maintenance, utilization, and disposal of software applications within an organization. This master’s thesis describes a special Software Lifecycle Management Framework to provide solutions to the multitude of challenges within SAM. The main objectives when designing the framework was to provide a set of tools to control the software assets during their entire lifecycle while trying to minimize the costs related to owning and managing them.

Application of the scrum framework in non-software project management

Scrum is an agile project management approach that has been widely practiced in the software development projects. It has proven to increase quality, productivity, customer satisfaction, transparency and team morale among other benefits from its implementation. The concept of scrum is based on the concepts of incremental innovation strategies, lean manufacturing, kaizen, iterative development and so on and is usually contrasted with the linear development models such as the waterfall method in the software industry. The traditional approaches to project management such as the waterfall method imply intensive upfront planning and approval of the entire project. These sort of approaches work well in the well-defined stable environments where all the specifications of the project are known in the beginning. However, in the uncertain environments when a project requires continuous development and incorporation of new requirements, they do not tend to work well. The scrum framework was inspiraed by Nonaka’s article about new product developement and was later adopted by software development practitioners. This research explores conditions for and benefits of the application of scrum framework beyond software development projects. There are currently a few case studies on the scrum implementation in non-software projects, but there is a noticeable trend of it in the scrum practitioners’ community. The research is based on the real-life context multiple case study analysis of three different non-software projects. The results of the research showed that in order to succeed within scrum projects need to satisfy certain conditions – necessary and sufficient. Among them the key factors are uncertainty of the project environment, not well defined outcomes, commitment of the scrum teams and management support. The top advantages of scrum implementation identified in the present research include improved transparency, accountability, team morale, communications, cooperation and collaboration. Further researches are advised to be carried out in order to validate these findings on a larger sample and to focus on more specific areas of scrum project management implementation.

Development of an Ecology-Oriented Software-Defined Networking Framework

ICT contributed to about 0.83 GtCO2 emissions where the 37% comes from the telecoms infrastructures. At the same time, the increasing cost of energy has been hindering the industry in providing more affordable services for the users. One of the sources of these problems is said to be the rigidity of the current network infrastructures which limits innovations in the network. SDN (Software Defined Network) has emerged as one of the prominent solutions with its idea of abstraction, visibility, and programmability in the network. Nevertheless, there are still significant efforts needed to actually utilize it to create a more energy and environmentally friendly network. In this paper, we suggested and developed a platform for developing ecology-related SDN applications. The main approach we take in realizing this goal is by maximizing the abstractions provided by OpenFlow and to expose RESTful interfaces to modules which enable energy saving in the network. While OpenFlow is made to be the standard for SDN protocol, there are still some mechanisms not defined in its specification such as settings related to Quality of Service (QoS). To solve this, we created REST interfaces for setting of QoS in the switches which can maximize network utilization. We also created a module for minimizing the required network resources in delivering packets across the network. This is achieved by utilizing redundant links when it is needed, but disabling them when the load in the network decreases. The usage of multi paths in a network is also evaluated for its benefit in terms of transfer rate improvement and energy savings. Hopefully, the developed framework can be beneficial for developers in creating applications for supporting environmentally friendly network infrastructures.

A unified framework for the comprehension of software's time dimension

Les logiciels sont de plus en plus complexes et leur développement est souvent fait par des équipes dispersées et changeantes. Par ailleurs, de nos jours, la majorité des logiciels sont recyclés au lieu d’être développés à partir de zéro. La tâche de compréhension, inhérente aux tâches de maintenance, consiste à analyser plusieurs dimensions du logiciel en parallèle. La dimension temps intervient à deux niveaux dans le logiciel : il change durant son évolution et durant son exécution. Ces changements prennent un sens particulier quand ils sont analysés avec d’autres dimensions du logiciel. L’analyse de données multidimensionnelles est un problème difficile à résoudre. Cependant, certaines méthodes permettent de contourner cette difficulté. Ainsi, les approches semi-automatiques, comme la visualisation du logiciel, permettent à l’usager d’intervenir durant l’analyse pour explorer et guider la recherche d’informations. Dans une première étape de la thèse, nous appliquons des techniques de visualisation pour mieux comprendre la dynamique des logiciels pendant l’évolution et l’exécution. Les changements dans le temps sont représentés par des heat maps. Ainsi, nous utilisons la même représentation graphique pour visualiser les changements pendant l’évolution et ceux pendant l’exécution. Une autre catégorie d’approches, qui permettent de comprendre certains aspects dynamiques du logiciel, concerne l’utilisation d’heuristiques. Dans une seconde étape de la thèse, nous nous intéressons à l’identification des phases pendant l’évolution ou pendant l’exécution en utilisant la même approche. Dans ce contexte, la prémisse est qu’il existe une cohérence inhérente dans les évènements, qui permet d’isoler des sous-ensembles comme des phases. Cette hypothèse de cohérence est ensuite définie spécifiquement pour les évènements de changements de code (évolution) ou de changements d’état (exécution). L’objectif de la thèse est d’étudier l’unification de ces deux dimensions du temps que sont l’évolution et l’exécution. Ceci s’inscrit dans notre volonté de rapprocher les deux domaines de recherche qui s’intéressent à une même catégorie de problèmes, mais selon deux perspectives différentes.

A compositional framework for hardware/software co-design

We describe a compositional framework, together with its supporting toolset, for hardware/software co-design. Our framework is an integration of a formal approach within a traditional design flow. The formal approach is based on Interval Temporal Logic and its executable subset, Tempura. Refinement is the key element in our framework because it will derive from a single formal specification of the system the software and hardware parts of the implementation, while preserving all properties of the system specification. During refinement simulation is used to choose the appropriate refinement rules, which are applied automatically in the HOL system. The framework is illustrated with two case studies. The work presented is part of a UK collaborative research project between the Software Technology Research Laboratory at the De Montfort University and the Oxford University Computing Laboratory.

Framework orientado a objetos para projeto de hardware e software embarcados para sistemas tempo-real

A crescente complexidade dos sistemas tempo-real embarcados demanda novas metodologias e ferramentas para gerenciar os problemas de projeto, análise, integração e validação de sistemas complexos. Este trabalho aborda o tema co-projeto de sistemas tempo-real embarcados, propondo estratégias para a integração das fases iniciais de modelagem de um sistema tempo-real embarcado com as fases subseqüentes do projeto, como a implementação do software e do hardware. É proposto um framework orientado a objetos que permite a criação de modelos orientados a objetos de sistemas tempo-real embarcados, utilizando conceitos temporais similares aos propostos em UML-RT (ou mais especificamente no UML Profile for Schedulability, Performance and Time). É proposta uma estratégia de mapeamento dos requisitos temporais dos diagramas UMLRT para uma interface de programação (API) baseada na “Especificação Tempo-Real para Java” (Real-Time Specification for Java ou RTSJ), a qual pode ser executada tanto em software – em programas RTSJ executando em máquinas virtuais Java (JVM) tempo-real – ou em hardware – em processadores Java Tempo-Real. Para permitir o mapeamento para hardware são propostas extensões tempo-real ao processador Java FemtoJava, desenvolvido no âmbito de dissertações de mestrado e projetos de pesquisa no PPGC, criando-se um novo processador tempo-real denominado de RT-FemtoJava. Dentre as extensões propostas ao processador FemtoJava destaca-se a inclusão de um relógio de tempo-real e o suporte a instruções para alocação e manipulação de objetos. Os conceitos propostos foram validados no âmbito de estudos de caso, sendo os resultados obtidos descritos na presente dissertação.

Hermes: um software-modem ADSL baseado no framework Ptolemy II

Esta dissertação tem como objetivo principal apresentar a implementação de um software-modem ADSL totalmente escrito em Java, utilizando o framework Ptolemy II, denominado de Hermes (de "A Handy Experimental Software Modem System"). Um software-modem é útil em ocasiões onde se precisem executar testes e simulações de sistemas de comunicação com um número grande de modens e quando os parâmetros desses sistemas precisem ser modificados com um alto grau de liberdade. Além disso, um software-modem possui características que tornam mais fácil a tarefa de acrescentar, eliminar, validar e analisar funções e algoritmos de processamento de sinais e de telecomunicações. Testes e simulações foram realizados para analisar a funcionalidade do Hermes, utilizando, inclusive, o Tracespan, um equipamento para análise não-intrusiva de redes DSL. A partir dos resultados obtidos em conjunto com o Tracespan, foi possível validar com sucesso as funções do Hermes.