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.

Caso de demonstração de uma framework para automatização do teste de APIs de aplicações SaaS

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines

The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef

Multiuser detection in a dynamic environment — Part II: Joint user identification and parameter estimation

The problem of jointly estimating the number, the identities, and the data of active users in a time-varying multiuser environment was examined in a companion paper (IEEE Trans. Information Theory, vol. 53, no. 9, September 2007), at whose core was the use of the theory of finite random sets on countable spaces. Here we extend that theory to encompass the more general problem of estimating unknown continuous parameters of the active-user signals. This problem is solved here by applying the theory of random finite sets constructed on hybrid spaces. We doso deriving Bayesian recursions that describe the evolution withtime of a posteriori densities of the unknown parameters and data.Unlike in the above cited paper, wherein one could evaluate theexact multiuser set posterior density, here the continuous-parameter Bayesian recursions do not admit closed-form expressions. To circumvent this difficulty, we develop numerical approximationsfor the receivers that are based on Sequential Monte Carlo (SMC)methods (“particle filtering”). Simulation results, referring to acode-divisin multiple-access (CDMA) system, are presented toillustrate the theory.

Biana: a software framework for compiling biological interactions and analyzing networks

Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.Results: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.Conclusions: BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

Iowa Pavement Asset Management Decision-Making Framework & Pavement Treatment Selection Tool for Local Agencies, TR-651, 2015

Most local agencies in Iowa currently make their pavement treatment decisions based on their limited experience due primarily to lack of a systematic decision-making framework and a decision-aid tool. The lack of objective condition assessment data of agency pavements also contributes to this problem. This study developed a systematic pavement treatment selection framework for local agencies to assist them in selecting the most appropriate treatment and to help justify their maintenance and rehabilitation decisions. The framework is based on an extensive literature review of the various pavement treatment techniques in terms of their technical applicability and limitations, meaningful practices of neighboring states, and the results of a survey of local agencies. The treatment selection framework involves three different steps: pavement condition assessment, selection of technically feasible treatments using decision trees, and selection of the most appropriate treatment considering the return-on-investment (ROI) and other non-economic factors. An Excel-based spreadsheet tool that automates the treatment selection framework was also developed, along with a standalone user guide for the tool. The Pavement Treatment Selection Tool (PTST) for Local Agencies allows users to enter the severity and extent levels of existing distresses and then, recommends a set of technically feasible treatments. The tool also evaluates the ROI of each feasible treatment and, if necessary, it can also evaluate the non-economic value of each treatment option to help determine the most appropriate treatment for the pavement. It is expected that the framework and tool will help local agencies improve their pavement asset management practices significantly and make better economic and defensible decisions on pavement treatment selection.

A Framework for Building Hypercubes Using MapReduce

The European Space Agency's Gaia mission will create the largest and most precise three dimensional chart of our galaxy (the Milky Way), by providing unprecedented position, parallax, proper motion, and radial velocity measurements for about one billion stars. The resulting catalogue will be made available to the scientific community and will be analyzed in many different ways, including the production of a variety of statistics. The latter will often entail the generation of multidimensional histograms and hypercubes as part of the precomputed statistics for each data release, or for scientific analysis involving either the final data products or the raw data coming from the satellite instruments. In this paper we present and analyze a generic framework that allows the hypercube generation to be easily done within a MapReduce infrastructure, providing all the advantages of the new Big Data analysis paradigmbut without dealing with any specific interface to the lower level distributed system implementation (Hadoop). Furthermore, we show how executing the framework for different data storage model configurations (i.e. row or column oriented) and compression techniques can considerably improve the response time of this type of workload for the currently available simulated data of the mission. In addition, we put forward the advantages and shortcomings of the deployment of the framework on a public cloud provider, benchmark against other popular solutions available (that are not always the best for such ad-hoc applications), and describe some user experiences with the framework, which was employed for a number of dedicated astronomical data analysis techniques workshops.

A Framework for Building Hypercubes Using MapReduce

The European Space Agency's Gaia mission will create the largest and most precise three dimensional chart of our galaxy (the Milky Way), by providing unprecedented position, parallax, proper motion, and radial velocity measurements for about one billion stars. The resulting catalogue will be made available to the scientific community and will be analyzed in many different ways, including the production of a variety of statistics. The latter will often entail the generation of multidimensional histograms and hypercubes as part of the precomputed statistics for each data release, or for scientific analysis involving either the final data products or the raw data coming from the satellite instruments. In this paper we present and analyze a generic framework that allows the hypercube generation to be easily done within a MapReduce infrastructure, providing all the advantages of the new Big Data analysis paradigmbut without dealing with any specific interface to the lower level distributed system implementation (Hadoop). Furthermore, we show how executing the framework for different data storage model configurations (i.e. row or column oriented) and compression techniques can considerably improve the response time of this type of workload for the currently available simulated data of the mission. In addition, we put forward the advantages and shortcomings of the deployment of the framework on a public cloud provider, benchmark against other popular solutions available (that are not always the best for such ad-hoc applications), and describe some user experiences with the framework, which was employed for a number of dedicated astronomical data analysis techniques workshops.

Messaging Application Engine for Symbian Platform

Tämä diplomityö kuvaa viestintä sovelluksen ytimen kehitystyön Symbian-alustalle. Koko sovelluksen vaatimuksena oli vastaamattomiin puheluihin vastaaminen ennalta määritellyillä tekstiviesteillä käyttäjän määrittelemien sääntöjen mukaisesti. Ei-toiminnallisia vaatimuksia olivat resurssien käytön vähentäminen ja uudelleenkäytön mahdollistaminen. Täten tämän työn tavoitteena oli kehittää ydin, joka kapseloi sovelluksen sellaisen toiminnallisuuden, joka on käyttöliittymästä riippumatonta ja uudelleenkäytettävää. Kehitystyössä ohjasi Unified Process, joka on iteroiva, käyttötapauksien ohjaama ja arkkitehtuurikeskeinen ohjelmistoprosessi. Se kannusti käyttämään myös muita teollisuudenalan vakiintuneita menetelmiä, kuten suunnittelumalleja ja visuaalista mallintamista käyttäen Unified Modelling Languagea. Suunnittelumalleja käytettiin kehitystyön aikana ja ohjelmisto mallinnettiin visuaalisesti suunnittelun edistämiseksi ja selkiyttämiseksi. Alustan palveluita käytettiin hyväksi kehitysajan ja resurssien käytön minimoimiseksi. Ytimen päätehtäviksi määrättiin viestien lähettäminen sekä sääntöjen talletus ja tarkistaminen. Sovelluksen eri alueet, eli sovelluspalvelin ja käyttöliittymää, pystyivät käyttämään ydintä ja sillä ei ollut riippuvuuksia käyttöliittymätasolle. Täten resurssien käyttö väheni ja uudelleenkäytettävyys lisääntyi. Viestien lähettäminen toteutettiin Symbian-alustan menetelmin. Sääntöjen tallettamiseen tehtiin tallennuskehys, joka eristää sääntöjen sisäisen ja ulkoisen muodon. Tässä tapauksessa ulkoiseksi tallennustavaksi valittiin relaatiotietokanta. Sääntöjen tarkastaminen toteutettiin tavanomaisella olioiden yhteistoiminnalla. Päätavoite saavutettiin. tämä ja muut hyviksi arvioidut lopputulokset, kuten uudelleenkäytettävyys ja vähentynyt resurssien käyttö, arveltiin juontuvan suunnittelumallien ja Unified Processin käytöstä. Kyseiset menetelmät osoittivat mukautuvansa pieniinkin projekteihin. Menetelmien todettiin myös tukevan ja kannustavan kehitystyön aikaista oppimista, mikä oli välttämätöntä tässä tapauksessa.

Characterizing the vulnerability of frequent emergency department users by applying a conceptual framework: a controlled, cross-sectional study.

BACKGROUND: Frequent emergency department (ED) users meet several of the criteria of vulnerability, but this needs to be further examined taking into consideration all vulnerability's different dimensions. This study aimed to characterize frequent ED users and to define risk factors of frequent ED use within a universal health care coverage system, applying a conceptual framework of vulnerability. METHODS: A controlled, cross-sectional study comparing frequent ED users to a control group of non-frequent users was conducted at the Lausanne University Hospital, Switzerland. Frequent users were defined as patients with five or more visits to the ED in the previous 12 months. The two groups were compared using validated scales for each one of the five dimensions of an innovative conceptual framework: socio-demographic characteristics; somatic, mental, and risk-behavior indicators; and use of health care services. Independent t-tests, Wilcoxon rank-sum tests, Pearson's Chi-squared test and Fisher's exact test were used for the comparison. To examine the -related to vulnerability- risk factors for being a frequent ED user, univariate and multivariate logistic regression models were used. RESULTS: We compared 226 frequent users and 173 controls. Frequent users had more vulnerabilities in all five dimensions of the conceptual framework. They were younger, and more often immigrants from low/middle-income countries or unemployed, had more somatic and psychiatric comorbidities, were more often tobacco users, and had more primary care physician (PCP) visits. The most significant frequent ED use risk factors were a history of more than three hospital admissions in the previous 12 months (adj OR:23.2, 95%CI = 9.1-59.2), the absence of a PCP (adj OR:8.4, 95%CI = 2.1-32.7), living less than 5 km from an ED (adj OR:4.4, 95%CI = 2.1-9.0), and household income lower than USD 2,800/month (adj OR:4.3, 95%CI = 2.0-9.2). CONCLUSIONS: Frequent ED users within a universal health coverage system form a highly vulnerable population, when taking into account all five dimensions of a conceptual framework of vulnerability. The predictive factors identified could be useful in the early detection of future frequent users, in order to address their specific needs and decrease vulnerability, a key priority for health care policy makers. Application of the conceptual framework in future research is warranted.

Improving and User Interface to E-Procurement Software Used in Asset Accounting and Investigating Effects to Efficiency

This diploma thesis has been done to international organization which takes care from the accounting actions of two major companies. In this organization are used three different purchasing tools which are used when new asset master data is wanted to input to SAP R/3- system. The aim of this thesis is to find out how much changing the user interface of one of these three e-procurement programs will affect to overall efficiency in asset accounting. As an addition will be introduced project framework which can be used in future projects and which help to avoid certain steps in the development process. At the moment data needs to be inputted manually with many useless mouse clicks and data needs to be searched from many various resources which slow down the process. Other organization has better tools at the moment than the myOrders system which is under investigation Research was started by exploring the main improvement areas. After this possible defects were traced. Suggested improvements were thought by exploring literature which has been written from usability design and research. Meanwhile also directional calculations from the benefits of the project were done alongside with the analysis of the possible risks and threats. After this NSN IT approved the changes which they thought was acceptable. The next step was to program them into tool and test them before releasing to production environment. The calculations were made also from implemented improvements and compared them to planned ones From whole project was made a framework which can be utilized also to other similar projects. The complete calculation was not possible because of time schedule of the project. Important observation in the project was that efficiency is not improved not only by changing the GUI but also improving processes without any programming. Feedback from end user should be also listened more in development process. End-user is after all the one who knows the best how the program should look like.

Disconnect.Me. User Engagement and Facebook

In the beginning of its 10th year of existence Facebook has engaged and connected 1.2 billion monthly active users. This article-based dissertation Disconnect.Me – User Engagement and Facebook approaches this engagement from the opposite direction: disconnection. The research articles focus on social media specific phenomena including leaving Facebook, tactical media works such as Web 2.0 SuicideMachine, memorializing dead Facebook users and Facebook trolling. The media theoretical framework for this study is built around affect theory, software studies, biopolitics as well as different critical studies of new media. The argument is that disconnection is a necessary condition of social media connectivity and exploring social media through disconnection – as an empirical phenomenon, future potential and theoretical notion – helps us to understand how users are engaged with social media, its uses and subsequent business models. The results of the study indicate that engagement is a relation that precedes user participation, a notion often used to conceptualize social media. Furthermore, this engagement turns the focus from users’ actions towards the platform and how the platform actively controls users and their behavior. Facebook aims to engage new users and maintain the old ones by renewing its platform and user interface. User engagement with the platform is thus social but also technical and affective. When engaged, the user is positioned to algorithmic connectivity where machinc processes mine user data. This data is but sold also used to affect and engage other users. In the heart of this study is the notion that our networked engagements matter and disconnection can bring us to the current limits of network culture.

Invenio v2.0: A Pythonic Framework for Large-Scale Digital Libraries

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Invenio v2.0: A Pythonic Framework for Large-Scale Digital Libraries

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014