Tools for mixed-criticality partitioned systems: partitioning algorithm and extensibility support

The development of mixed-criticality virtualized multicore systems poses new challenges that are being subject of active research work. There is an additional complexity: it is now required to identify a set of partitions, and allocate applications to partitions. In this job, a number of issues have to be considered, such as the criticality level of the application, security and dependability requirements, operating system used by the application, time requirements granularity, specific hardware needs, etc. MultiPARTES [6] toolset relies on Model Driven Engineering (MDE) [12], which is a suitable approach in this setting. In this paper, it is described the support provided for automatic system partitioning generation and toolset extensibility.

Functional genomics tools to decipher the pathogenicity mechanisms of the necrotrophic fungus Plectosphaerella cucumerina in Arabidopsis thaliana

The analysis of the interaction between Arabidopsis thaliana and adapted (PcBMM) and nonadapted (Pc2127) isolates of the necrotrophic fungus Plectosphaerella cucumerina has contributed to the identification of molecular mechanisms controlling plant resistance to necrotrophs.To characterize the pathogenicity bases of the virulence of necrotrophic fungi in Arabidopsis, we developed P. cucumerina functional genomics tools using Agrobacterium tumefaciens-mediated transformation.We generated PcBMM-GFP and Pc2127-GFP transformants constitutively expressing the green fluorescence protein (GFP), and a collection of random T-DNA insertional PcBMM transformants. Confocal microscopy analyses of the initial stages of PcBMM-GFP infection revealed that this pathogen, like other necrotrophic fungi, does not form an appressorium or penetrate into plant cells, but causes successive degradation of leaf cell layers

The optimal allocation rule and the water market as the most effective tools of managing water shortage in an irrigation district

The conference program will cover all areas of environmental and resource economics, ranging from topics prevailing in the general debate, such as climate change, energy sources, water management and ecosystem services evaluation, to more specialized subjects such as biodiversity conservation or persistent organic pollutants. The congress will be held on the Faculty of Economics of the University of Girona, located in Montilivi, a city quarter situated just few minutes from the city center, conveniently connected by bus lines L8 and L11.

Testing of Android testing tools: development of a benchmark for the evaluation

With the ever growing trend of smart phones and tablets, Android is becoming more and more popular everyday. With more than one billion active users i to date, Android is the leading technology in smart phone arena. In addition to that, Android also runs on Android TV, Android smart watches and cars. Therefore, in recent years, Android applications have become one of the major development sectors in software industry. As of mid 2013, the number of published applications on Google Play had exceeded one million and the cumulative number of downloads was more than 50 billionii. A 2013 survey also revealed that 71% of the mobile application developers work on developing Android applicationsiii. Considering this size of Android applications, it is quite evident that people rely on these applications on a daily basis for the completion of simple tasks like keeping track of weather to rather complex tasks like managing one’s bank accounts. Hence, like every other kind of code, Android code also needs to be verified in order to work properly and achieve a certain confidence level. Because of the gigantic size of the number of applications, it becomes really hard to manually test Android applications specially when it has to be verified for various versions of the OS and also, various device configurations such as different screen sizes and different hardware availability. Hence, recently there has been a lot of work on developing different testing methods for Android applications in Computer Science fraternity. The model of Android attracts researchers because of its open source nature. It makes the whole research model more streamlined when the code for both, application and the platform are readily available to analyze. And hence, there has been a great deal of research in testing and static analysis of Android applications. A great deal of this research has been focused on the input test generation for Android applications. Hence, there are a several testing tools available now, which focus on automatic generation of test cases for Android applications. These tools differ with one another on the basis of their strategies and heuristics used for this generation of test cases. But there is still very little work done on the comparison of these testing tools and the strategies they use. Recently, some research work has been carried outiv in this regard that compared the performance of various available tools with respect to their respective code coverage, fault detection, ability to work on multiple platforms and their ease of use. It was done, by running these tools on a total of 60 real world Android applications. The results of this research showed that although effective, these strategies being used by the tools, also face limitations and hence, have room for improvement. The purpose of this thesis is to extend this research into a more specific and attribute-­‐ oriented way. Attributes refer to the tasks that can be completed using the Android platform. It can be anything ranging from a basic system call for receiving an SMS to more complex tasks like sending the user to another application from the current one. The idea is to develop a benchmark for Android testing tools, which is based on the performance related to these attributes. This will allow the comparison of these tools with respect to these attributes. For example, if there is an application that plays some audio file, will the testing tool be able to generate a test input that will warrant the execution of this audio file? Using multiple applications using different attributes, it can be visualized that which testing tool is more useful for which kinds of attributes. In this thesis, it was decided that 9 attributes covering the basic nature of tasks, will be targeted for the assessment of three testing tools. Later this can be done for much more attributes to compare even more testing tools. The aim of this work is to show that this approach is effective and can be used on a much larger scale. One of the flagship features of this work, which also differentiates it with the previous work, is that the applications used, are all specially made for this research. The reason for doing that is to analyze just that specific attribute in isolation, which the application is focused on, and not allow the tool to get bottlenecked by something trivial, which is not the main attribute under testing. This means 9 applications, each focused on one specific attribute. The main contributions of this thesis are: A summary of the three existing testing tools and their respective techniques for automatic test input generation of Android Applications. • A detailed study of the usage of these testing tools using the 9 applications specially designed and developed for this study. • The analysis of the obtained results of the study carried out. And a comparison of the performance of the selected tools.

Papyrus, EATOP, and MetaEdit+: a comparison between the EAST-ADL modeling tools

Several Architecture Description Languages (ADLs) are emerging as models to describe and represent system architectures. Among others, EAST-ADL language is highlighted. It represents an abstraction of embedded software systems for automobiles. Given the need to implement the EAST-ADL language, there are many modeling tools to perform this task. The scope of this thesis is a detailed comparison of three EAST-ADL editors: Papyrus, EATOP and MetaEdit +, providing a conceptual framework, describing the comparison criteria, and finally exemplifying thanks to the Brake-By-Wire use case which has been provided, and whose development is not the subject of this project. The motivation for developing this project is to provide comparison guide between these three modeling tools to facilitate developers choice when deciding the tool in which develop their work. RESUMEN. Diversos Lenguajes de Descripción de Arquitecturas (ADLs) están surgiendo como modelos para describir y representar arquitecturas de sistemas. Entre ellos es destacado el lenguaje EAST-ADL, que representa una abstracción de los sistemas de software embebido para automóviles. Ante la necesidad de implementar el lenguaje EAST-ADL, han surgido diversas herramientas de modelado que llevan a cabo esta tarea. El alcance de este proyecto consiste en una comparación detallada de tres editores EAST-ADL: Papyrus, EATOP y MetaEdit+, proporcionando un marco conceptual, describiendo los criterios de comparación y finalmente ejemplificando con el caso de uso Brake-By-Wire que nos ha sido proporcionado, y cuyo desarrollo no es sujeto de este proyecto. La motivación para desarrollar este proyecto parte de proporcionar al usuario una guía comparativa de estas tres herramientas de modelado para facilitar su elección a la hora de desarrollar su trabajo.

Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data

Upon the completion of the Saccharomyces cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) Nature, 387, 5], several creative and ambitious projects have been initiated to explore the functions of gene products or gene expression on a genome-wide scale. To help researchers take advantage of these projects, the Saccharomyces Genome Database (SGD) has created two new tools, Function Junction and Expression Connection. Together, the tools form a central resource for querying multiple large-scale analysis projects for data about individual genes. Function Junction provides information from diverse projects that shed light on the role a gene product plays in the cell, while Expression Connection delivers information produced by the ever-increasing number of microarray projects. WWW access to SGD is available at genome-www.stanford.edu/Saccharomyces/.

A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm

The database reported here is derived using the Combinatorial Extension (CE) algorithm which compares pairs of protein polypeptide chains and provides a list of structurally similar proteins along with their structure alignments. Using CE, structure–structure alignments can provide insights into biological function. When a protein of known function is shown to be structurally similar to a protein of unknown function, a relationship might be inferred; a relationship not necessarily detectable from sequence comparison alone. Establishing structure–structure relationships in this way is of great importance as we enter an era of structural genomics where there is a likelihood of an increasing number of structures with unknown functions being determined. Thus the CE database is an example of a useful tool in the annotation of protein structures of unknown function. Comparisons can be performed on the complete PDB or on a structurally representative subset of proteins. The source protein(s) can be from the PDB (updated monthly) or uploaded by the user. CE provides sequence alignments resulting from structural alignments and Cartesian coordinates for the aligned structures, which may be analyzed using the supplied Compare3D Java applet, or downloaded for further local analysis. Searches can be run from the CE web site, http://cl.sdsc.edu/ce.html, or the database and software downloaded from the site for local use.

PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data

The Plasmodium falciparum Genome Database (http://PlasmoDB.org) integrates sequence information, automated analyses and annotation data emerging from the P.falciparum genome sequencing consortium. To date, raw sequence coverage is available for >90% of the genome, and two chromosomes have been finished and annotated. Data in PlasmoDB are organized by chromosome (1–14), and can be accessed using a variety of tools for graphical and text-based browsing or downloaded in various file formats. The GUS (Genomics Unified Schema) implementation of PlasmoDB provides a multi-species genomic relational database, incorporating data from human and mouse, as well as P.falciparum. The relational schema uses a highly structured format to accommodate diverse data sets related to genomic sequence and gene expression. Tools have been designed to facilitate complex biological queries, including many that are specific to Plasmodium parasites and malaria as a disease. Additional projects seek to integrate genomic information with the rich data sets now becoming available for RNA transcription, protein expression, metabolic pathways, genetic and physical mapping, antigenic and population diversity, and phylogenetic relationships with other apicomplexan parasites. The overall goal of PlasmoDB is to facilitate Internet- and CD-ROM-based access to both finished and unfinished sequence information by the global malaria research community.

Creating local bibliographic databases: new tools for evidence-based health care*

The Internet has created new opportunities for librarians to present literature search results to clinicians. In order to take full advantage of these opportunities, libraries need to create locally maintained bibliographic databases. A simple method of creating a local bibliographic database and publishing it on the Web is described. The method uses off-the-shelf software and requires minimal programming. A hedge search strategy for outcome studies of clinical process interventions is created, and Ovid is used to search MEDLINE. The search results are saved and imported into EndNote libraries. The citations are modified, exported to a Microsoft Access database, and published on the Web. Clinicians can use a Web browser to search the database. The bibliographic database contains 13,803 MEDLINE citations of outcome studies. Most searches take between four and ten seconds and retrieve between ten and 100 citations. The entire cost of the software is under $900. Locally maintained bibliographic databases can be created easily and inexpensively. They significantly extend the evidence-based health care services that libraries can offer to clinicians.

Transposon tools for recombinant DNA manipulation: characterization of transcriptional regulators from yeast, Xenopus, and mouse.

Transposon Tn1000 has been adapted to deliver novel DNA sequences for manipulating recombinant DNA. The transposition procedure for these "tagged" Tn1000s is simple and applicable to most plasmids in current use. For yeast molecular biology, tagged Tn1000s introduce a variety of yeast selective markers and replication origins into plasmids and cosmids. In addition, the beta-globin minimal promoter and lacZ gene of Tn(beta)lac serve as a mobile reporter of eukaryotic enhancer activity. In this paper, Tn(beta)lac was used to localize a mouse HoxB-complex enhancer in transgenic mice. Other tagged transposons create Gal4 DNA-binding-domain fusions, in either Escherichia coli or yeast plasmids, for use in one- and two-hybrid tests of transcriptional activation and protein-protein interaction, respectively. With such fusions, the Saccharomyces cerevisiae Swi6 G1/S-phase transcription factor and the Xenopus laevis Pintallavis developmental regulator are shown to activate transcription. Furthermore, the same transposon insertions also facilitated mapping of the Swi6 and Pintallavis domains responsible for transcriptional activation. Thus, as well as introducing novel sequences, tagged transposons share the numerous other applications of transposition such as producing insertional mutations, creating deletion series, or serving as mobile primer sites for DNA sequencing.

Interisland and interarchipelago transfer of stone tools in prehistoric Polynesia.

Tracing interisland and interarchipelago movements of people and artifacts in prehistoric Polynesia has posed a challenge to archaeologists due to the lack of pottery and obsidian, two materials most readily used in studies of prehistoric trade or exchange. Here we report the application of nondestructive energy-dispersive x-ray fluorescence (EDXRF) analysis to the sourcing of Polynesian artifacts made from basalt, one of the most ubiquitous materials in Polynesian archaeological sites. We have compared excavated and surface-collected basalt adzes and adze flakes from two sites in Samoa (site AS-13-1) and the Cook Islands (site MAN-44), with source basalts from known prehistoric quarries in these archipelagoes. In both cases, we are able to demonstrate the importing of basalt adzes from Tutuila Island, a distance of 100 km to Ofu Island, and of 1600 km to Mangaia Island. These findings are of considerable significance for Polynesian prehistory, as they demonstrate the movement of objects not only between islands in the same group (where communities were culturally and linguistically related) but also between distant island groups. Further applications of EDXRF analysis should greatly aid archaeologists in their efforts to reconstruct ancient trade and exchange networks, not only in Polynesia but also in other regions where basalt was a major material for artifact production.