From software extensions to product lines of dataflow programs

Abstract Dataflow programs are widely used. Each program is a directed graph where nodes are computations and edges indicate the flow of data. In prior work, we reverse-engineered legacy dataflow programs by deriving their optimized implementations from a simple specification graph using graph transformations called refinements and optimizations. In MDE-speak, our derivations were PIM-to-PSM mappings. In this paper, we show how extensions complement refinements, optimizations, and PIM-to-PSM derivations to make the process of reverse engineering complex legacy dataflow programs tractable. We explain how optional functionality in transformations can be encoded, thereby enabling us to encode product lines of transformations as well as product lines of dataflow programs. We describe the implementation of extensions in the ReFlO tool and present two non-trivial case studies as evidence of our work’s generality

A integração do Building Information Modeling (BIM) num projeto de reabilitação

Dissertação de mestrado integrado em Engenharia Civil

Current Challenges in Modeling Cellular Metabolism

Mathematical and computational models play an essential role in understanding the cellular metabolism. They are used as platforms to integrate current knowledge on a biological system and to systematically test and predict the effect of manipulations to such systems. The recent advances in genome sequencing techniques have facilitated the reconstruction of genome-scale metabolic networks for a wide variety of organisms from microbes to human cells. These models have been successfully used in multiple biotechnological applications. Despite these advancements, modeling cellular metabolism still presents many challenges. The aim of this Research Topic is not only to expose and consolidate the state-of-the-art in metabolic modeling approaches, but also to push this frontier beyond the current edge through the introduction of innovative solutions. The articles presented in this e-book address some of the main challenges in the field, including the integration of different modeling formalisms, the integration of heterogeneous data sources into metabolic models, explicit representation of other biological processes during phenotype simulation, and standardization efforts in the representation of metabolic models and simulation results.

A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.

Índice Digital Regional 2014

O objetivo subjacente a toda a investigação que deu origem ao Índice Digital Regional (IDR), inserida num projeto de doutoramento, ia no sentido da “compreensão da realidade da Sociedade da Informação nas sete regiões NUTs II portuguesas, comparando-as e contrastando-as”. À semelhança do que acontece em grande parte dos indicadores de desenvolvimento, em que as assimetrias regionais são uma evidência verificada há várias décadas, importava perceber até que ponto o desenvolvimento da Sociedade da Informação em Portugal está a ser desencadeado sem ter ou não em atenção os valores da equidade, da coesão nacional e da solidariedade regional. Este artigo analisa os resultados do IDR recalculado com os dados estatísticos mais recentes.

Hazard assessment of storm events for the battery, New York

The environmental and socio-economic importance of coastal areas is widely recognized, but at present these areas face severe weaknesses and high-risk situations. The increased demand and growing human occupation of coastal zones have greatly contributed to exacerbating such weaknesses. Today, throughout the world, in all countries with coastal regions, episodes of waves overtopping and coastal flooding are frequent. These episodes are usually responsible for property losses and often put human lives at risk. The floods are caused by coastal storms primarily due to the action of very strong winds. The propagation of these storms towards the coast induces high water levels. It is expected that climate change phenomena will contribute to the intensification of coastal storms. In this context, an estimation of coastal flooding hazards is of paramount importance for the planning and management of coastal zones. Consequently, carrying out a series of storm scenarios and analyzing their impacts through numerical modeling is of prime interest to coastal decision-makers. Firstly, throughout this work, historical storm tracks and intensities are characterized for the northeastern region of United States coast, in terms of probability of occurrence. Secondly, several storm events with high potential of occurrence are generated using a specific tool of DelftDashboard interface for Delft3D software. Hydrodynamic models are then used to generate ensemble simulations to assess storms' effects on coastal water levels. For the United States’ northeastern coast, a highly refined regional domain is considered surrounding the area of The Battery, New York, situated in New York Harbor. Based on statistical data of numerical modeling results, a review of the impact of coastal storms to different locations within the study area is performed.

A UML-based approach for modeling industrial control applications

The main purpose of the poster is to present how the Unified Modeling Language (UML) can be used for diagnosing and optimizing real industrial production systems. By using a car radios production line as a case study, the poster shows the modeling process that can be followed during the analysis phase of complex control applications. In order to guarantee the continuity mapping of the models, the authors propose some guidelines to transform the use cases diagrams into a single object diagram, which is the main diagram for the next phases of the development.

Vascular disease modeling using induced pluripotent stem cells: Focus in Hutchinson-Gilford Progeria Syndrome

Transparency document related to this article can be found online at http://dx.doi.org/10.1016/j.bbrc.2015.10.014