The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

Under what conditions? Therapist and client characteristics moderate the role of change talk in brief motivational intervention.

OBJECTIVE: Client change talk has been proposed as a mechanism of change in motivational interviewing (MI) by mediating the link between therapist MI-consistent behaviors (MICO) and client behavioral outcomes. We tested under what circumstances this mechanism was supported in the context of a clinical trial of brief MI for heavy drinking among nontreatment seeking young men. METHOD: We conducted psycholinguistic coding of 174 sessions using the MI Skill Code 2.1 and derived the frequency of MICO and the strength of change talk (CTS) averaged over the session. CTS was examined as a mediator of the relationship between MICO and a drinking composite score measured at 3-month follow-up, controlling for the composite measure at baseline. Finally, we tested therapist gender and MI experience as well as client readiness to change and alcohol problem severity as moderators of this mediation model. RESULTS: CTS significantly predicted outcome (higher strength related to less drinking), but MICO did not predict CTS. However, CTS mediated the relationship between MICO and drinking outcomes when therapists had more experience in MI and when clients had more severe alcohol problems (i.e., significant conditional indirect effects). CONCLUSIONS: The mechanism hypothesized by MI theory was operative in our brief MI with heavy drinking young men, but only under particular conditions. Our results suggest that attention should be paid to therapist selection, training, and/or supervision until they reach a certain level of competence, and that MI might not be appropriate for nontreatment seeking clients drinking at a lower level of risk. (PsycINFO Database Record

DAI-DEPUR: an integrated and distributed architecture for wastewater treatment plants supervision

The activated sludge process - the main biological technology usually applied towastewater treatment plants (WWTP) - directly depends on live beings (microorganisms), and therefore on unforeseen changes produced by them. It could be possible to get a good plant operation if the supervisory control system is able to react to the changes and deviations in the system and can take thenecessary actions to restore the system’s performance. These decisions are oftenbased both on physical, chemical, microbiological principles (suitable to bemodelled by conventional control algorithms) and on some knowledge (suitable to be modelled by knowledge-based systems). But one of the key problems in knowledge-based control systems design is the development of an architecture able to manage efficiently the different elements of the process (integrated architecture), to learn from previous cases (spec@c experimental knowledge) and to acquire the domain knowledge (general expert knowledge). These problems increase when the process belongs to an ill-structured domain and is composed of several complex operational units. Therefore, an integrated and distributed AIarchitecture seems to be a good choice. This paper proposes an integrated and distributed supervisory multi-level architecture for the supervision of WWTP, that overcomes some of the main troubles of classical control techniques and those of knowledge-based systems applied to real world systems

Context exchange between devices in mobile environment

Context awareness is emerging on mobile devices. Context awareness can be used to improve usability of a mobile device. Context awareness is particularly important on mobile devices due the limitations they have. At first in this work, a literature review on context awareness and mobile environment is made. For aiding context awareness there exist an implementation of a Context Framework for Symbian S60 devices. It provides a possibility for exchanging the contexts inside the device between the client applications of the local Context Framework. The main contribution of this thesis is to design and implement an enhancement to the S60 Context Framework for providing possibility to exchange context over device boundaries. Using the implemented Context Exchange System, the context exchange is neither depending on the type of the context nor the type of the client. In addition, the clients and the contexts can reside on any interconnected device. The usage of the system is independent of the programming language since in addition to using only Symbian C++ function interfaces it can also be utilized using XML scripts. The Meeting Sniffer application, which uses the Context Exchange System, was also developed in this work. Using this application, it is possible to recognize a meeting situation and suggest device profile change to a user.

Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences

Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (~800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.

Base de dades bursàtil basada en J2EE

El TFC s'ha basat en la creació d'una aplicació basada en tecnologia J2EE que permet obtenir informació bursàtil a través de la font d'informació de Yahoo Finances. La informació obtinguda a través d'aquesta font és de dos tipus: en forma de dades incloses en un arxiu descarregable o en forma de gràfica que el client pot veure directament a l'aplicació. Així doncs, l'aplicació permet mostrar gràfiques de preus d'accions bursàtils i també descarregar-ne arxius amb dades.

Development a distributed simulation environment on a cluster of workstations

Simulation has traditionally been used for analyzing the behavior of complex real world problems. Even though only some features of the problems are considered, simulation time tends to become quite high even for common simulation problems. Parallel and distributed simulation is a viable technique for accelerating the simulations. The success of parallel simulation depends heavily on the combination of the simulation application, algorithm and message population in the simulation is sufficient, no additional delay is caused by this environment. In this thesis a conservative, parallel simulation algorithm is applied to the simulation of a cellular network application in a distributed workstation environment. This thesis presents a distributed simulation environment, Diworse, which is based on the use of networked workstations. The distributed environment is considered especially hard for conservative simulation algorithms due to the high cost of communication. In this thesis, however, the distributed environment is shown to be a viable alternative if the amount of communication is kept reasonable. Novel ideas of multiple message simulation and channel reduction enable efficient use of this environment for the simulation of a cellular network application. The distribution of the simulation is based on a modification of the well known Chandy-Misra deadlock avoidance algorithm with null messages. The basic Chandy Misra algorithm is modified by using the null message cancellation and multiple message simulation techniques. The modifications reduce the amount of null messages and the time required for their execution, thus reducing the simulation time required. The null message cancellation technique reduces the processing time of null messages as the arriving null message cancels other non processed null messages. The multiple message simulation forms groups of messages as it simulates several messages before it releases the new created messages. If the message population in the simulation is suffiecient, no additional delay is caused by this operation A new technique for considering the simulation application is also presented. The performance is improved by establishing a neighborhood for the simulation elements. The neighborhood concept is based on a channel reduction technique, where the properties of the application exclusively determine which connections are necessary when a certain accuracy for simulation results is required. Distributed simulation is also analyzed in order to find out the effect of the different elements in the implemented simulation environment. This analysis is performed by using critical path analysis. Critical path analysis allows determination of a lower bound for the simulation time. In this thesis critical times are computed for sequential and parallel traces. The analysis based on sequential traces reveals the parallel properties of the application whereas the analysis based on parallel traces reveals the properties of the environment and the distribution.

The permanence of the client under uncertain estimations

Marketing has studied the permanence of a client within an enterprise because it is a key element in the study of the value (economic) of the client (CLV). The research that they have developed is based in deterministic or random models, which allowed estimating the permanence of the client, and the CLV. However, when it is not possible to apply these schemes for not having the panel data that this model requires, the period of time of a client with the enterprise is uncertain data. We consider that the value of the current work is to have an alternative way to estimate the period of time with subjective information proper of the theory of uncertainty.

How are riparian plants distributed along the riverbank topographic gradient in Mediterranean rivers? Application to minimally altered river stretches in Southern Spain.

Species structure and composition in Mediterranean riparian forests are determined by hydrological features, longitudinal zonation, and riverbank topography. This study assesses the distribution of four native riparian plants along the riverbank topographic gradient in three river stretches in southern Spain, with special emphasis on the occupation of adult and young feet of each species. The studied stretches suffered minimal human disturbances, displayed semi-arid conditions, and had wide riparian areas to allow the development of the target species: black alder (Alnus glutinosa), salvia leaf willow (Salix salviifolia), narrow-leafed ash (Fraxinus angustifolia), and oleander (Nerium oleander). Thalweg height was used to define the riverbank topographic gradient. The results showed a preferential zone for black alder and salvia leaf willow in the range of 0-150 cm from the channel thalweg, with adult alders and willows being more common between 51 and 150 cm and young alders being more common under 50 cm. Conversely, narrow-leafed ash and oleander were much more frequent, and showed greater development, in the ranges of 151-200 cm and 201-250 cm, respectively, whereas the young feet of both species covered the entire topographic range. Adult feet of the four species were spatially segregated along the riverbank topographic gradient, indicating their differential ability to cope with water stress from the non-tolerant alders and willows to more tolerant narrow-leafed ash trees and oleanders. Young feet, however, showed a strategy more closely linked to the initial availability of colonisation sites within riparian areas to the dispersion strategy of each species and to the distribution of adult feet. In Mediterranean areas, where riparian management has traditionally faced great challenges, the incorporation of species preferences along riverbank gradients could improve the performance of restoration projects.

Integrating distributed generation and Smart Grids into single-family house

This study examines Smart Grids and distributed generation, which is connected to a single-family house. The distributed generation comprises small wind power plant and solar panels. The study is done from the consumer point of view and it is divided into two parts. The first part presents the theoretical part and the second part presents the research part. The theoretical part consists of the definition of distributed generation, wind power, solar energy and Smart Grids. The study examines what the Smart Grids will enable. New technology concerning Smart Grids is also examined. The research part introduces wind and sun conditions from two countries. The countries are Finland and Germany. According to the wind and sun conditions of these two countries, the annual electricity production from wind power plant and solar panels will be calculated. The costs of generating electricity from wind and solar energy are calculated from the results of annual electricity productions. The study will also deal with feed-in tariffs, which are supporting systems for renewable energy resources. It is examined in the study, if it is cost-effective for the consumers to use the produced electricity by themselves or sell it to the grid. Finally, figures for both countries are formed. The figures include the calculated cost of generating electricity from wind power plant and solar panels, retail and wholesale prices and feed-in tariffs. In Finland, it is not cost-effective to sell the produced electricity to the grid, before there are support systems. In Germany, it is cost-effective to sell the produced electricity from solar panels to the grid because of feed-in tariffs. On the other hand, in Germany it is cost-effective to produce electricity from wind to own use because the retail price is higher than the produced electricity from wind.

Point sampling with uniformly distributed lines

In this paper we address the problem of extracting representative point samples from polygonal models. The goal of such a sampling algorithm is to find points that are evenly distributed. We propose star-discrepancy as a measure for sampling quality and propose new sampling methods based on global line distributions. We investigate several line generation algorithms including an efficient hardware-based sampling method. Our method contributes to the area of point-based graphics by extracting points that are more evenly distributed than by sampling with current algorithms

Kuormitustestausvälineen valinta Microsoft Office SharePoint Server 2007 – toteutuksessa

Kuormitustestaus on osa web-sovellusten kehitystä ja käyttöönottoa. Sillä varmistetaan sovellusten toimivuus ennalta määrätyn kuorman alla. Microsoft Office SharePoint Server 2007 (MOSS) on palvelintuote nykyaikaisten web-sovellusten luontiin ja ylläpitoon. Työssä vertaillaan kahta eri uormitustestaustyökalua: SilkPerformer 2008 ja Visual Studio Team System 2008 Test Edition ja valitaan MOSS – web-sovelluksille paremmin sopiva työkalu. Työssä vertaillaan työkaluja niiden ominaisuuksien perusteella sekä suorittamalla kuormitustestausta testausta varten luodulle MOSS – web-sovellukselle. Vaikuttavien tekijöiden perusteella työkaluja arvioidaan ja tämän perusteella saadaan tulos vertailulle. Työn tuloksena Visual Studio Team System 2008 Test Edition sopii paremmin MOSS – web-sovelluksen kuormitustestausvälineeksi. Vertailussa kuitenkin havaittiin, että työkalut ovat melko tasavertaisia, ja käytännön tilanteesta riippuu, kumpi sopii paremmin. Tämä työ auttaa valinnan teossa.

Sistema per gestionar les incidències d'un servei d'informàtica amb una arquitectura J2EE distribuïda en tres nivells

Tant en la meva etapa d’estudiant com en la meva curta vida laboral, he participat en el desenvolupament de varies aplicacions de gestió, tant d’escriptori com web, que majoritàriament sempre estaven dividides en tres capes però en dos nivells: la base de dades i l’aplicació, que contenia tant la lògica de negoci com la vista. Des de fa temps he tingut la curiositat i la necessitat d’intentar desenvolupar una aplicació de gestió que estigui distribuïda en tres o més nivells, separant el model de dades i la lògica de negoci de la vista. Crec que el treball de fi de carrera és idoni per desenvolupar-la. L’aplicació a desenvolupar anirà destinada a la gestió d’un servei d’informàtica, que s’encarrega de resoldre les incidències, inventariar i realitzar el manteniment preventiu dels equips informàtics d’una o de varies empreses. Es crearà una aplicació que contindrà el model de dades i la lògica de negoci. També es crearan dues aplicacions clients: una aplicació d’escriptori que donarà accés a totes i cadascuna de les funcionalitats del sistema i una aplicació web que oferirà un accés lleuger i des de qualsevol ubicació a les funcionalitats d’explotació del sistema. Per últim, també es crearà una altre aplicació web que s’encarregarà de generar els llistats sol•licitats per les dues aplicacions clients. D’aquesta manera també es centralitzarà la gestió dels llistats de les aplicacions del sistema. Per desenvolupar el sistema, s’utilitzarà la plataforma J2EE de Java, i es comptarà amb l’ajuda de marcs de treball com, per exemple, Oracle ADF o JasperReports. Com a conclusió general, puc assegurar que si es distribueixen les tres capes d’un sistema en tres nivells s’obtenen beneficis en l’administració, en el manteniment, en l’escalabilitat, en la flexibilitat i en la reutilització de les aplicacions. El principal inconvenient és el possible augment de lentitud en les aplicacions clients.

Virtualització de servidors. Avantatges. Implantació en una PIME real

En la societat d’avui dia, les empreses depenen en gran part dels seus recursos informàtics. La seva capacitat de supervivència i innovació en el mercat actual, on la competitivitat és cada dia més forta, passa per una infraestructura informàtica que els permeti, no només desplegar i implantar ordinadors i servidors de manera ràpida i eficient sinó que també les protegeixi contra parades del sistema informàtic, problemes amb servidors, caigudes o desastres físics de hardware. Per evitar aquests problemes informàtics susceptibles de poder parar el funcionament d’una empresa es va començar a treballar en el camp de la virtualització informàtica amb l’objectiu de poder trobar solucions a aquests problemes a la vegada que s’aprofitaven els recursos de hardware existents d’una manera més òptim a i eficient, reduint així també el cost de la infraestructura informàtica. L’objectiu principal d’aquest treball és veure en primer pla la conversió d’una empresa real amb una infraestructura informàtica del tipus un servidor físic -una funció cap a una infraestructura virtual del tipus un servidor físic -varis servidors virtual -vàries funcions. Analitzarem l’estat actual de l’empresa, servidors i funcions, adquirirem el hardware necessari i farem la conversió de tots els seus servidors cap a una nova infraestructura virtual. Faig especial atenció a les explicacions de perquè utilitzo una opció i no un altre i també procuro sempre donar vàries opcions. Igualment remarco en quadres verds observacions a tenir en compte complementàries al que estic explicant en aquell moment, i en quadres vermells temes en els que s’ha de posar especial atenció en el moment en que es fan. Finalment, un cop feta la conversió, veurem els molts avantatges que ens ha reportat aquesta tecnologia a nivell de fiabilitat, estabilitat, capacitat de tolerància a errades, capacitat de ràpid desplegament de noves màquines, capacitat de recuperació del sistema i aprofitament de recursos físics