Swiss EMBnet node web server.

EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a 'node', a group responsible for the maintenance of local services for their users (e.g. education, training, software, database distribution, technical support, helpdesk). Among these services a web portal with links and access to locally developed and maintained software is essential and different for each node. Our web portal targets biomedical scientists in Switzerland and elsewhere, offering them access to a collection of important sequence analysis tools mirrored from other sites or developed locally. We describe here the Swiss EMBnet node web site (http://www.ch.embnet.org), which presents a number of original services not available anywhere else.

The Gene Ontology in 2010: extensions and refinements.

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.

El suport familiar en la malaltia mental: influència del suport familiar en el control de la malaltia en una persona que pateix un transtorn mental server

Aquest treball té com a objectiu principal conèixer si hi ha millora en el control de la malaltia d’una persona que pateix un trastorn mental sever quan disposa d’un suport adequat de la família. Els objectius específics marcats són, avaluar la càrrega familiar que suposa tenir la responsabilitat de cuidar un familiar amb malaltia mental, conèixer les actituds dels familiars de persones que pateixen una malaltia mental, involucrar a la família dins de la teràpia del familiar amb malaltia mental severa, i aconseguir un grau de cooperació i comunicació favorable de la família al pacient. Es tracta d’un estudi d’investigació quantitatiu, transversal i de tipus analític, el qual la mostra de la població estudiada estarà composta de 100 pacients entre 20 i 30 anys amb diagnòstic de trastorn mental sever segons el DSM-IV, atesos durant l’últim any en el Centre de Salut Mental d’Adults de Vic i els seus cuidadors principals o persones més properes. Es realitzarà recollida de dades a través de la revisió de les històries clíniques, informació facilitada pel terapeuta que tracta al pacient i entrevistes als familiars cuidadors o persona més propera i als mateixos pacients. Aquesta entrevista la faran professionals entrenats i competents. Amb tot això s’establirà una correlació entre les variables d’estrès, suport als familiars i el desenvolupament dels rols, i s’agruparan les variables de manera que quedin estructurades en subgrups.

Gene Ontology Function prediction in Mollicutes using Protein-Protein Association Networks

Abstract Background: Many complex systems can be represented and analysed as networks. The recent availability of large-scale datasets, has made it possible to elucidate some of the organisational principles and rules that govern their function, robustness and evolution. However, one of the main limitations in using protein-protein interactions for function prediction is the availability of interaction data, especially for Mollicutes. If we could harness predicted interactions, such as those from a Protein-Protein Association Networks (PPAN), combining several protein-protein network function-inference methods with semantic similarity calculations, the use of protein-protein interactions for functional inference in this species would become more potentially useful. Results: In this work we show that using PPAN data combined with other approximations, such as functional module detection, orthology exploitation methods and Gene Ontology (GO)-based information measures helps to predict protein function in Mycoplasma genitalium. Conclusions: To our knowledge, the proposed method is the first that combines functional module detection among species, exploiting an orthology procedure and using information theory-based GO semantic similarity in PPAN of the Mycoplasma species. The results of an evaluation show a higher recall than previously reported methods that focused on only one organism network.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

Personalized touristic routes implementing semantic web on GIS

Nowadays, when a user is planning a touristic route is very difficult to find out which are the best places to visit. The user has to choose considering his/her preferences due to the great quantity of information it is possible to find in the web and taking into account it is necessary to do a selection, within small time because there is a limited time to do a trip. In Itiner@ project, we aim to implement Semantic Web technology combined with Geographic Information Systems in order to offer personalized touristic routes around a region based on user preferences and time situation. Using ontologies it is possible to link, structure, share data and obtain the result more suitable for user's preferences and actual situation with less time and more precisely than without ontologies. To achieve these objectives we propose a web page combining a GIS server and a touristic ontology. As a step further, we also study how to extend this technology on mobile devices due to the raising interest and technological progress of these devices and location-based services, which allows the user to have all the route information on the hand when he/she does a touristic trip. We design a little application in order to apply the combination of GIS and Semantic Web in a mobile device.

First level ontology - case study

The file contains the ontology created and instantiated according to a case study as well as a little explanation of the framework in which it is included.

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

GRW as an ontology of dispositions

The paper argues that the formulation of quantum mechanics proposed by Ghirardi, Rimini and Weber (GRW) is a serious candidate for being a fundamental physical theory and explores its ontological commitments from this perspective. In particular, we propose to conceive of spatial superpositions of non-massless microsystems as dispositions or powers, more precisely propensities, to generate spontaneous localizations. We set out five reasons for this view, namely that (1) it provides for a clear sense in which quantum systems in entangled states possess properties even in the absence of definite values; (2) it vindicates objective, single-case probabilities; (3) it yields a clear transition from quantum to classical properties; (4) it enables to draw a clear distinction between purely mathematical and physical structures, and (5) it grounds the arrow of time in the time-irreversible manifestation of the propensities to localize.

Embedded Monitoring Server

This study investigates, designs, and implements an inexpensive application that allows local and remote monitoring of a home. The application consists of an array of sensors for monitoring different conditions in a home environment and also for accessing the devices that might be connected to the system. Only a few sensors are initially involved in this study and information about the temperature level, forced entry detection, smoke and water leakage detection can be obtained at any time from any location with an Internet connection. The application software (coded in C language) runs on an embedded system which is basically a wireless Linksys router running on a GNU/Linux based firmware for embedded systems. Interaction between the sensors and the application software is achieved through an implemented sensor interfacing circuit. The communication with the sensor interfacing unit is done through the serial port, and accessibility of the connected sensors is achieved through a telnet client. The sensors can be accessed from local and remote locations with the sensors giving reliable information. The resulting application shows that it is possible to use the router for other applications other than what it is intended for.

Highly Available Enterprise-level Application Server Architecture

Korkeasaatavuus on olennainen osa nykyaikaisissa, integroiduissa yritysjärjestelmissä. Yritysten kansainvälistyessä tiedon on oltava saatavissa ympärivuorokautisesti, mikä asettaa yhä kovempia vaatimuksia järjestelmän yksittäisten osien saatavuudelle. Kasvava tietojärjestelmäintegraatio puolestaan tekee järjestelmän solmukohdista kriittisiä liiketoiminnan kannalta. Tässä työssä perehdytään hajautettujen järjestelmien ominaisuuksiin ja niiden asettamiin haasteisiin. Esiteltyjä teknologioita ovat muun muassa väliohjelmistot, klusterit ja kuormantasaus. Yrityssovellusten pohjana käytetty Java 2 Enterprise Edition (J2EE) -teknologia käsitellään olennaisilta osiltaan. Työssä käytetään sovelluspalvelinalustana BEA WebLogic Server -ohjelmistoa, jonka ominaisuudet käydään läpi hajautuksen kannalta. Työn käytännön osuudessa toteutetaan kahdelle erilaiselle olemassa olevalle yrityssovellukselle korkean saatavuuden sovelluspalvelinympäristö, joissa sovellusten asettamat rajoitukset on otettu huomioon.

Transparent and secure remote network storage system using an untrusted server

Työssä kehitettin läpinäkyvä Internet Small Computer Systems Interface-verkkolevyä (iSCSI) käyttävä varmistusjärjestelmä. Verkkolevyn sisältö suojattiin asiakaspään salauskerroksella (dm-crypt). Järjestely mahdollisti sen, että verkkolevylle tallennetut varmuuskopiot pysyivät luottamuksellisina, vaikka levypalvelinta tarjoava taho oli joko epäluotettava tai suorastaan vihamielinen. Järjestelmän hyötykäyttöä varten kehitettiin helppokäyttöinen prototyyppisovellus. Järjestelmän riskit ja haavoittuvuudet käytiin läpi ja analysoitiin. Järjestelmälle tehtiin myös karkea kryptoanalyysi sen teknistenominaisuuksien pohjalta. Suorituskykymittaukset tehtiin sekä salatulle että salaamattomalle iSCSI-liikenteelle. Näistä todettiin, että salauksen vaikutus suorituskykyyn oli häviävän pieni jopa 100 megabittiä sekunnissa siirtävillä verkkonopeuksilla. Lisäksi pohdittiin teknologian muita sovelluskohteita ja tulevia tutkimusalueita.

The business model ontology a proposition in a design science approach

The goal of this dissertation is to find and provide the basis for a managerial tool that allows a firm to easily express its business logic. The methodological basis for this work is design science, where the researcher builds an artifact to solve a specific problem. In this case the aim is to provide an ontology that makes it possible to explicit a firm's business model. In other words, the proposed artifact helps a firm to formally describe its value proposition, its customers, the relationship with them, the necessary intra- and inter-firm infrastructure and its profit model. Such an ontology is relevant because until now there is no model that expresses a company's global business logic from a pure business point of view. Previous models essentially take an organizational or process perspective or cover only parts of a firm's business logic. The four main pillars of the ontology, which are inspired by management science and enterprise- and processmodeling, are product, customer interface, infrastructure and finance. The ontology is validated by case studies, a panel of experts and managers. The dissertation also provides a software prototype to capture a company's business model in an information system. The last part of the thesis consists of a demonstration of the value of the ontology in business strategy and Information Systems (IS) alignment. Structure of this thesis: The dissertation is structured in nine parts: Chapter 1 presents the motivations of this research, the research methodology with which the goals shall be achieved and why this dissertation present a contribution to research. Chapter 2 investigates the origins, the term and the concept of business models. It defines what is meant by business models in this dissertation and how they are situated in the context of the firm. In addition this chapter outlines the possible uses of the business model concept. Chapter 3 gives an overview of the research done in the field of business models and enterprise ontologies. Chapter 4 introduces the major contribution of this dissertation: the business model ontology. In this part of the thesis the elements, attributes and relationships of the ontology are explained and described in detail. Chapter 5 presents a case study of the Montreux Jazz Festival which's business model was captured by applying the structure and concepts of the ontology. In fact, it gives an impression of how a business model description based on the ontology looks like. Chapter 6 shows an instantiation of the ontology into a prototype tool: the Business Model Modelling Language BM2L. This is an XML-based description language that allows to capture and describe the business model of a firm and has a large potential for further applications. Chapter 7 is about the evaluation of the business model ontology. The evaluation builds on literature review, a set of interviews with practitioners and case studies. Chapter 8 gives an outlook on possible future research and applications of the business model ontology. The main areas of interest are alignment of business and information technology IT/information systems IS and business model comparison. Finally, chapter 9 presents some conclusions.

Content value chains modelling using a copyright ontology

Existing digital rights management (DRM) systems, initiatives like Creative Commons or research works as some digital rights ontologies provide limited support for content value chains modelling and management. This is becoming a critical issue as content markets start to profit from the possibilities of digital networks and the World Wide Web. The objective is to support the whole copyrighted content value chain across enterprise or business niches boundaries. Our proposal provides a framework that accommodates copyright law and a rich creation model in order to cope with all the creation life cycle stages. The dynamic aspects of value chains are modelled using a hybrid approach that combines ontology-based and rule-based mechanisms. The ontology implementation is based on Web Ontology Language and Description Logic (OWL-DL) reasoners, are directly used for license checking. On the other hand, for more complex aspects of the dynamics of content value chains, rule languages are the choice.