BioSWR - Semantic Web services Registry for Bioinformatics

Article About the Authors Metrics Comments Related Content Abstract Introduction Functionality Implementation Discussion Acknowledgments Author Contributions References Reader Comments (0) Figures Abstract Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/​under the LGPL license.

Search Interfaces on the Web: Querying and Characterizing

Current-day web search engines (e.g., Google) do not crawl and index a significant portion of theWeb and, hence, web users relying on search engines only are unable to discover and access a large amount of information from the non-indexable part of the Web. Specifically, dynamic pages generated based on parameters provided by a user via web search forms (or search interfaces) are not indexed by search engines and cannot be found in searchers’ results. Such search interfaces provide web users with an online access to myriads of databases on the Web. In order to obtain some information from a web database of interest, a user issues his/her query by specifying query terms in a search form and receives the query results, a set of dynamic pages that embed required information from a database. At the same time, issuing a query via an arbitrary search interface is an extremely complex task for any kind of automatic agents including web crawlers, which, at least up to the present day, do not even attempt to pass through web forms on a large scale. In this thesis, our primary and key object of study is a huge portion of the Web (hereafter referred as the deep Web) hidden behind web search interfaces. We concentrate on three classes of problems around the deep Web: characterization of deep Web, finding and classifying deep web resources, and querying web databases. Characterizing deep Web: Though the term deep Web was coined in 2000, which is sufficiently long ago for any web-related concept/technology, we still do not know many important characteristics of the deep Web. Another matter of concern is that surveys of the deep Web existing so far are predominantly based on study of deep web sites in English. One can then expect that findings from these surveys may be biased, especially owing to a steady increase in non-English web content. In this way, surveying of national segments of the deep Web is of interest not only to national communities but to the whole web community as well. In this thesis, we propose two new methods for estimating the main parameters of deep Web. We use the suggested methods to estimate the scale of one specific national segment of the Web and report our findings. We also build and make publicly available a dataset describing more than 200 web databases from the national segment of the Web. Finding deep web resources: The deep Web has been growing at a very fast pace. It has been estimated that there are hundred thousands of deep web sites. Due to the huge volume of information in the deep Web, there has been a significant interest to approaches that allow users and computer applications to leverage this information. Most approaches assumed that search interfaces to web databases of interest are already discovered and known to query systems. However, such assumptions do not hold true mostly because of the large scale of the deep Web – indeed, for any given domain of interest there are too many web databases with relevant content. Thus, the ability to locate search interfaces to web databases becomes a key requirement for any application accessing the deep Web. In this thesis, we describe the architecture of the I-Crawler, a system for finding and classifying search interfaces. Specifically, the I-Crawler is intentionally designed to be used in deepWeb characterization studies and for constructing directories of deep web resources. Unlike almost all other approaches to the deep Web existing so far, the I-Crawler is able to recognize and analyze JavaScript-rich and non-HTML searchable forms. Querying web databases: Retrieving information by filling out web search forms is a typical task for a web user. This is all the more so as interfaces of conventional search engines are also web forms. At present, a user needs to manually provide input values to search interfaces and then extract required data from the pages with results. The manual filling out forms is not feasible and cumbersome in cases of complex queries but such kind of queries are essential for many web searches especially in the area of e-commerce. In this way, the automation of querying and retrieving data behind search interfaces is desirable and essential for such tasks as building domain-independent deep web crawlers and automated web agents, searching for domain-specific information (vertical search engines), and for extraction and integration of information from various deep web resources. We present a data model for representing search interfaces and discuss techniques for extracting field labels, client-side scripts and structured data from HTML pages. We also describe a representation of result pages and discuss how to extract and store results of form queries. Besides, we present a user-friendly and expressive form query language that allows one to retrieve information behind search interfaces and extract useful data from the result pages based on specified conditions. We implement a prototype system for querying web databases and describe its architecture and components design.

Aplicaciones digitales con software libre para City Branding de Valledupar

El uso de las TIC se ha masificado dentro del ámbito del turismo convirtiéndose en herramienta fundamental y un aliado para llegar a conquistar turistas para los diferentes destinos que se promocionan a través de aplicaciones moviles o de website.Cada vez más las entidades turísticas o las empresas recurren a las tecnologías de la información, en particular Internet, como medio para promocionar sus productos y servicios turísticos. Estas nuevas tecnologías han cambiado el concepto de vida de personas en cuanto a la consulta de precio y rapidez de información de los diferentes servicios turísticos.En Valledupar se debe: aprovechar la tendencia mundial al rescate de los valores auténticos, el medio ambiente y las comunidades indígenas a través de diferentes modalidades de turismo: Ecoturismo, etnoturismo, agroturismo, cultural, religioso, compras, aventura, salud, deportivo, ciudad capital. Se debe ampliar el conocimiento del territorio municipal y de los valores autóctonos. Mediante uso de software libre y de código abierto se pueden crear soluciones para fortalecer la promoción del sector turístico de la ciudad de Valledupar.

Desenvolupament de visor web per a consulta de guia urbana única dels municipis de Mallorca

Disseny i implementació d’aplicació web destinada a consulta d’informació urbana en els municipis de Mallorca. Localització de punts d’interès. Implementació pilot en el municipi de Santa Eugènia, Mallorca

Learning Preferences with Kernel-Based Methods

Learning of preference relations has recently received significant attention in machine learning community. It is closely related to the classification and regression analysis and can be reduced to these tasks. However, preference learning involves prediction of ordering of the data points rather than prediction of a single numerical value as in case of regression or a class label as in case of classification. Therefore, studying preference relations within a separate framework facilitates not only better theoretical understanding of the problem, but also motivates development of the efficient algorithms for the task. Preference learning has many applications in domains such as information retrieval, bioinformatics, natural language processing, etc. For example, algorithms that learn to rank are frequently used in search engines for ordering documents retrieved by the query. Preference learning methods have been also applied to collaborative filtering problems for predicting individual customer choices from the vast amount of user generated feedback. In this thesis we propose several algorithms for learning preference relations. These algorithms stem from well founded and robust class of regularized least-squares methods and have many attractive computational properties. In order to improve the performance of our methods, we introduce several non-linear kernel functions. Thus, contribution of this thesis is twofold: kernel functions for structured data that are used to take advantage of various non-vectorial data representations and the preference learning algorithms that are suitable for different tasks, namely efficient learning of preference relations, learning with large amount of training data, and semi-supervised preference learning. Proposed kernel-based algorithms and kernels are applied to the parse ranking task in natural language processing, document ranking in information retrieval, and remote homology detection in bioinformatics domain. Training of kernel-based ranking algorithms can be infeasible when the size of the training set is large. This problem is addressed by proposing a preference learning algorithm whose computation complexity scales linearly with the number of training data points. We also introduce sparse approximation of the algorithm that can be efficiently trained with large amount of data. For situations when small amount of labeled data but a large amount of unlabeled data is available, we propose a co-regularized preference learning algorithm. To conclude, the methods presented in this thesis address not only the problem of the efficient training of the algorithms but also fast regularization parameter selection, multiple output prediction, and cross-validation. Furthermore, proposed algorithms lead to notably better performance in many preference learning tasks considered.

A química newtoniana

The work of Newton exerted a profound influence on the development of science. In chemistry this newtonian influence was present in Query 31 of Newton's Optics. However, the incursion of Newton's thought into chemistry brought upon the chemists an epistemological question, that of the nature of their discipline. Would chemistry be a discipline in its own right, or simply a branch of physics? In this work we present the newtonian program for chemistry, as well as the reaction of traditional chemists to it. We conclude by proposing that Lavoisier carried through a synthesis between newtonian methodology and the singularity of traditional chemistry.

Talvivaaran Kaivososakeyhtiö Oyj:n yhteiskuntavastuuraportoinnin kehittäminen

Talvivaaran Kaivososakeyhtiö Oyj:n tavoitteena on julkaista yhtiön ensimmäinen yhteiskuntavastuuraportti vuonna 2011. Vastuuraportin tavoitteena on täyttää GRI (Global Reporting Initiative) -ohjeiston C-tason raportointivaatimukset. Diplomityö liittyy olennaisena osana Talvivaaran yhteiskuntavastuuraportoinnin kehittämiseen. Diplomityön tavoitteena oli määrittää Talvivaaran ensimmäiseen raporttiin soveltuvat GRI-ohjeiston mukaiset mittarit. Työssä tarkastellaan Talvivaaran vuosikertomusta 2009. Työssä selvitettiin kuinka raporttia tulisi täydentää, jotta se täyttäisi GRI:n perussisällön C-tason vaatimukset. Näiden lisäksi työssä tehtiin sidosryhmäkartoitus, jossa selvitettiin yhtiön näkemys sidosryhmien odotuksista. Tulevaan vastuuraporttiin suunniteltujen mittareiden valintaan vaikutti sidosryhmien kiinnostuksen lisäksi se, kuinka olennaisia mittarit ovat Talvivaaran toiminnan kannalta. Valittujen mittareiden osalta yhtiön tuleva vastuuraportti täyttää selvästi C-tason raportointivaatimukset. Työssä annetaan ehdotus jatkotoimenpiteistä, joilla viestintää voidaan edelleen kehittää.

Applications of graph transformation in tools for domain-specific modeling languages

The use of domain-specific languages (DSLs) has been proposed as an approach to cost-e ectively develop families of software systems in a restricted application domain. Domain-specific languages in combination with the accumulated knowledge and experience of previous implementations, can in turn be used to generate new applications with unique sets of requirements. For this reason, DSLs are considered to be an important approach for software reuse. However, the toolset supporting a particular domain-specific language is also domain-specific and is per definition not reusable. Therefore, creating and maintaining a DSL requires additional resources that could be even larger than the savings associated with using them. As a solution, di erent tool frameworks have been proposed to simplify and reduce the cost of developments of DSLs. Developers of tool support for DSLs need to instantiate, customize or configure the framework for a particular DSL. There are di erent approaches for this. An approach is to use an application programming interface (API) and to extend the basic framework using an imperative programming language. An example of a tools which is based on this approach is Eclipse GEF. Another approach is to configure the framework using declarative languages that are independent of the underlying framework implementation. We believe this second approach can bring important benefits as this brings focus to specifying what should the tool be like instead of writing a program specifying how the tool achieves this functionality. In this thesis we explore this second approach. We use graph transformation as the basic approach to customize a domain-specific modeling (DSM) tool framework. The contributions of this thesis includes a comparison of di erent approaches for defining, representing and interchanging software modeling languages and models and a tool architecture for an open domain-specific modeling framework that e ciently integrates several model transformation components and visual editors. We also present several specific algorithms and tool components for DSM framework. These include an approach for graph query based on region operators and the star operator and an approach for reconciling models and diagrams after executing model transformation programs. We exemplify our approach with two case studies MICAS and EFCO. In these studies we show how our experimental modeling tool framework has been used to define tool environments for domain-specific languages.

Konventionaalisen jätehuollon kehittäminen Loviisan voimalaitoksella

Tämän diplomityön tarkoituksena oli löytää kehityskohteita Fortumin Loviisan ydinvoimalaitoksen konventionaalisesta, eli tavanomaisesta, jätehuollosta. Tavoitteena oli löytää erityisesti keinoja kaatopaikkajätteen määrän vähentämiseksi sekä lajittelun tehostamiseksi. Myös jätelainsäädännön kokonaisuudistuksen vaikutukset jätehuollon toimintaan olivat työn kannalta keskeisessä roolissa. Työ tehtiin jätehuoltosuunnitelman rakennetta noudattaen. Jätehuoltosuunnitelma koostuu alkukartoituksesta sekä jätehuoltosuunnitelman laatimisesta ja toteutuksesta. Varsinaisina kehitystarpeiden kartoittamismenetelminä käytettiin viranomaisvaatimusten selvittämistä, toiminnan tarkastelua, jätehuoltokyselyä voimalaitoksen työntekijöille, benchmarkingia sekä valittujen hyötykäyttö- ja loppusijoitusmenetelmien kustannusvertailua. Tulokseksi saatiin, että jätteiden lajittelua voitaisiin tehostaa ennen kaikkea lisäämällä työntekijöiden koulutusta. Lajittelun helpottamiseksi ohjeistuksen tulee olla paremmin saatavilla sekä voimalaitoksen omalle henkilöstölle kuin urakoitsijoillekin. Ongelmajätehuollossa eniten ongelmia ilmeni ongelmajätepakkausten merkitsemisessä jätteiden syntypaikoilla. Tähän ratkaisuna ehdotettiin kokeiltavaksi jätteiden syntykohteisiin sijoitettavia jätekortteja, joista pakkaajat voisivat helposti tarkistaa tarvittavat merkinnät. Myös mustan jäteöljyn keräämistä olisi mahdollista parantaa, jotta suurempi osa siitä saataisiin hyödynnettyä materiaalina. Kaatopaikkajätteen määrän vähentämiseksi työssä ehdotettiin sekajätteen viemistä kaatopaikan sijaan poltettavaksi. Muutoksen seurauksena voimalaitoksen jätehuollon kustannukset saattavat lisääntyä, mutta ympäristön kannalta muutos tulisi olemaan positiivinen.

Effectiveness of Pilotage

The objective of the pilotage effectiveness study was to come up with a process descrip-tion of the pilotage procedure, to design performance indicators based on this process description, to be used by Finnpilot, and to work out a preliminary plan for the imple-mentation of the indicators within the Finnpilot organisation. The theoretical aspects of pilotage as well as the guidelines and standards used were determined through a literature review. Based on the literature review, a process flow model with the following phases was created: the planning of pilotage, the start of pilo-tage, the act of pilotage, the end of pilotage and the closing of pilotage. The model based on the literature review was tested through interviews and observation of pilotage. At the same time an e-mail survey directed at foreign pilotage organisations, which included a questionnaire concerning their standards and management systems, operations procedures, measurement tools and their attitude to the passage planning, was conducted. The main issues in the observations and interviews were the passage plan and the bridge team co-operation. The phases of the pilotage process model emerged in both the pilotage activities and the interviews whereas bridge team co-operation was relatively marginal. Most of the pilotage organisations, who responded to the query, also use some standard-based management system. All organisations who answered the survey use some sort of a pilotage process model. According to the query, the main measuring tools for pilotage are statistical information concerning pilotage and the organisations, the customer feedback surveys, and financial results. Attitudes to-wards passage planning were mostly positive among the organisations. A workshop with pilotage experts was arranged where the process model constructed on the basis of the literature review was tuned to match practical pilotage. In the workshop it was determined that certain phases and the corresponding tasks, through which pilo-tage can be described as a process, were identifiable in all pilotage. The result of the workshop was a complemented process model, which separates incoming and outgoing traffic, as well as the fairway pilotage and harbour pilotage from each other. Addition-ally indicators divided according to the data gathering method were defined. Data con-cerning safety and traffic flow is gathered in the form of customer feedback. The pilot's own perceptions of the pilotage process are gathered through self-assessment. The measurement data which is connected to the phases of the pilotage process is generated e.g. by gathering statistics of the success of the pilot dispatches, the accuracy of the pi-lotage and the incidents that occurred during the pilotage, near misses, deviations and accidents. The measurement data is collected via the PilotWeb at the closing of the pilo-tage. A separate project and a project group with pilots also participating will be established for the deployment of the performance indicators. The phases of the project are: the definition phase, the implementation phase and the deployment phase. The purpose of the definition phase is to prepare questions for ship commanders concerning the cus-tomer feedback questionnaire and also to work out the self-assessment queries and the queries concerning the process indicators.

Paperitehtaan arkittamon kokonaistehokkuuden nostaminen kunnossapitoa kehittämällä

Tämän diplomityön tavoitteena oli tutkia, miten UPM:n Kymin tehtaan A4- arkittamon kunnossapitotoimintaa pystyttäisiin kehittämään niin, että tuotantolaitoksen kokonaistehokkuutta saataisiin kasvatettua. Työssä on pohdittu keinoja nykyisen, pääasiallisesti korjaavan kunnossapitotoiminnan muuttamiseksi suunnitelmalliseksi eri teorialähtökohtien pohjalta. Keskeinen teoria, johon työn tulokset pohjautuvat, on kokonaisvaltainen tuottava kunnossapito (TPM). Kirjallisuuslähteisiin tukeutuvaa tutkimusta täydensivät useat haastattelut, A4-valmistajille suunnattu laitteiden kuntokartoituskysely ja tuotannon- ja toiminnanohjausjärjestelmistä kerätty mittausaineisto. Työn merkittävimmät tulokset osoittavat, että A4-arkittamon kunnossapitotoimintaa tulisi suunnata nykyistä enemmän käyttökunnossapitolähtöiseksi. Käyttökunnossapito perustuu tuotannon operaattoreiden osallistumiseen kunnossapitotoimiin varsinaisen kunnossapitohenkilöstön ohella. Tuotantooperaattoreilla on työnsä vuoksi parhaat mahdollisuudet käyttämiensä laitteiden kunnonvalvontaan ja näin ollen mahdollisten vikaantumisten ennakointiin jo varhaisessa vaiheessa. Ennakoimalla pystyttäisiin parantamaan kunnossapidon suunnitelmallisuutta, minkä ansiosta laitteiden käytettävyys ja sitä kautta tuotantolaitoksen kokonaistehokkuus olisivat nykyistä korkeampia.

Building a Research Data Registry for the UK

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

Tag Cloud of Search Queries for Repository System

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

pp-Blast: a "pseudo-parallel" Blast

We have developed a software called pp-Blast that uses the publicly available Blast package and PVM (parallel virtual machine) to partition a multi-sequence query across a set of nodes with replicated or shared databases. Benchmark tests show that pp-Blast running in a cluster of 14 PCs outperformed conventional Blast running in large servers. In addition, using pp-Blast and the cluster we were able to map all human cDNAs onto the draft of the human genome in less than 6 days. We propose here that the cost/benefit ratio of pp-Blast makes it appropriate for large-scale sequence analysis. The source code and configuration files for pp-Blast are available at http://www.ludwig.org.br/biocomp/tools/pp-blast.