Disseminació, integració i visualització de dades biològiques

La recent revolució en les tècniques de generació de dades genòmiques ha portat a una situació de creixement exponencial de la quantitat de dades generades i fa més necessari que mai el treball en la optimització de la gestió i maneig d'aquesta informació. En aquest treball s'han atacat tres vessants del problema: la disseminació de la informació, la integració de dades de diverses fonts i finalment la seva visualització. Basant-nos en el Sistema d'Anotacions Distribuides, DAS, hem creat un aplicatiu per a la creació automatitzada de noves fonts de dades en format estandaritzat i accessible programàticament a partir de fitxers de dades simples. Aquest progrtamari, easyDAS, està en funcionament a l'Institut Europeu de Bioinformàtica. Aquest sistema facilita i encoratja la compartició i disseminació de dades genòmiques en formats usables. jsDAS és una llibreria client de DAS que permet incorporar dades DAS en qualsevol aplicatiu web de manera senzilla i ràpida. Aprofitant els avantatges que ofereix DAS és capaç d'integrar dades de múltiples fonts de manera coherent i robusta. GenExp és el prototip de navegador genòmic basat en web altament interactiu i que facilita l'exploració dels genomes en temps real. És capaç d'integrar dades de quansevol font DAS i crear-ne una representació en client usant els últims avenços en tecnologies web.

Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

GENCODE: producing a reference annotation for ENCODE

Background: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manualannotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.Results: The GENCODE gene features are divided into eight different categories of which onlythe first two (known and novel coding sequence) are confidently predicted to be protein-codinggenes. 5’ rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentallyverify the initial annotation. Of the 420 coding loci tested, 229 RACE products have beensequenced. They supported 5’ extensions of 30 loci and new splice variants in 50 loci. In addition,46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15putative transcripts. We assessed the comprehensiveness of the GENCODE annotation byattempting to validate all the predicted exon boundaries outside the GENCODE annotation. Outof 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only twoof them in intergenic regions.Conclusions: In total, 487 loci, of which 434 are coding, have been annotated as part of theGENCODE reference set available from the UCSC browser. Comparison of GENCODEannotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained withinthe two sets, which is a reflection of the high number of alternative splice forms with uniqueexons annotated. Over 50% of coding loci have been experimentally verified by 5’ RACE forEGASP and the GENCODE collaboration is continuing to refine its annotation of 1% humangenome with the aid of experimental validation.

Use of mobile devices to answer online surveys: implications for research.

BACKGROUND: There is a growing use of mobile devices to access the Internet. We examined whether participants who used a mobile device to access a brief online survey were quicker to respond to the survey but also, less likely to complete it than participants using a traditional web browser. FINDINGS: Using data from a recently completed online intervention trial, we found that participants using mobile devices were quicker to access the survey but less likely to complete it compared to participants using a traditional web browser. More concerning, mobile device users were also less likely to respond to a request to complete a six week follow-up survey compared to those using traditional web browsers. CONCLUSIONS: With roughly a third of participants using mobile devices to answer an online survey in this study, the impact of mobile device usage on survey completion rates is a concern. TRIAL REGISTRATION: ClinicalTrials.gov: NCT01521078.

Sistema de Informação Geográfica na Internet para apoio à gestão de Infra-estruturas, baseado em ferramentas Open Source

A gestão de infra-estruturas é um processo de coordenação, avaliação sistemática e manutenção efectiva das infra-estruturas relacionadas com os serviços básicos. A gestão eficaz de infra-estruturas exige que a disposição dos equipamentos no meio urbano seja conhecida, bem como sua relação com o uso do solo. Sendo a gestão de infra-estruturas uma questão de natureza espacial, é natural pensar na utilização de um Sistema de Informação Geográfica como ferramenta com potencial de grande utilidade, pois permite a georreferenciação de dados espaciais e sua interligação com atributos alfanuméricos, para além da realização de análises complexas e a possibilidade de simular diversos cenários de modo a propiciar uma tomada de decisão eficaz. O elevado custo das licenças e a especificidade de utilização a nível técnico, tornam-se obstáculos na criação e manutenção de dados geográficos. Contudo os recentes desenvolvimentos em tecnologias da Internet têm contribuído para o acesso, publicação, exploração e distribuição da Informação Geográfica. A utilização de SIG distribuídos na Internet (WebGIS), nomeadamente na vertente livre, pode ser uma solução adequada visto que coloca funcionalidades de SIG ao alcance de utilizadores, através de um simples browser, sem necessidade de investimentos em relação a software ou mesmo em formação técnica especializada. Assim, com este projecto pretende-se a criação de um sistema de Informação geográfico na Internet, utilizando softwares livres, que disponibiliza toda a informação geográfica e alfanumérica das infra-estruturas construídas e sob a responsabilidade do Ministério das Infra-estruturas e Economia Marítima, permitindo a visualização e a realização de pesquisas e operações de análise.

Sistemas de Informação WEB para gestão de stock

Este projecto consiste no desenvolvimento de um Sistema de Informação Web para Gestão de Stock e que funciona também em um ambiente sem internet. O mesmo faz a entrada de stock, venda, devolução de clientes, lança os produtos deteriorados, no fim de cada dia faz o fecho de caixa, resumo de vendas, resumo das entradas de stock, resumo dos produtos deteriorados, resumo de fecho de caixa, inventário, registo de funcionário, registo de fornecedor, registo de artigo, backup periodicamente e disponibilizando ao gerente informações rápidas sobre seu stock e estatísticas de vendas. Com o sistema em funcionamento pretende-se garantir transações rápidas e eficientes entre funcionários, clientes e o gerente. È muito importante dizer que o sistema tem um funcionamento muito simples e foi implementado a pensar nas micro e pequenas empresas, visto que é um sector que se encontra em pleno desenvolvimento em Cabo Verde e que nos dias de hoje é obrigatório ter um software de gestão para que o Ministério das Finanças possa ter maior controlo sobre os resultados das empresas. Para o desenvolvimento do sistema (Simple Gest), utilizei um servidor web (Apache), servidor de base de dados (MySQL), interpretadores para linguagem de script PHP fornecidos através da ferramenta XAMPP (servidor independente de plataforma), a linguagem de programação PHP para fazer a conecção entre o sistema e a base de dados, HTML para criar e apresentar as páginas na web, CSS para dar estilo as páginas através de um browser e UML para a modelação dos dados. Na análise do sistema foram identificados os requisitos funcionais e os requisitos não funcionais, foram desenvolvidos os casos de usos necessários, os diagramas de casos de uso, diagramas de sequência e o modelo entidade-relacionamento para demonstrar o fluxo de dados.

Desenvolupament d'una aplicació per a la creació de pressupostos on-line

En aquests moments, el mercat no es troba en una bona situació, per aquest motiu les empreses han de buscar noves maneres de créixer, expandir-se i noves formes d’interactuar amb els clients. La idea original d’aquest projecte sorgeix de la necessitat de disposar d’una manera diferent de promocionar-se i oferir nous serveis a través d’internet mitjançant una pàgina web. Degut a la situació actual, el preu és un aspecte molt important i influent a l’hora de realitzar una obra. Per aquest motiu es va pensar que seria molt interessant que el client pogués demanar de forma fàcil i ràpida un pressupost, i a l’instant tingués un preu orientatiu del que li pot costar la obra. D’aquesta manera l’interessat s’estalvia i agilitza molts passos previs abans de començar una obra. Després d’analitzar quina era la millor manera de portar a terme el projecte informàtic, s’ha determinat que la pàgina web es desenvoluparà utilitzant els llenguatges HTML i PHP combinant-lo amb el framework CodeIgniter. El disseny de la web es realitzarà mitjançant fulles d’estil CSS conjuntament amb el framework BootStrap. Per realitzar l’aplicació web que realitza els pressupostos s’utilitzarà AJAX i jQuery perquè d’aquesta manera el procés sigui dinàmic. L’entorn de desenvolupament escollit és el NetBeans i per provar el projecte s’utilitza el XAMPP. Un usuari només necessitarà un navegador i connexió a internet per fer servir totes les funcions de la web. Podrà realitzar pressupostos, concertar visites, contactar i per suposat veure tota la part informativa de la pàgina.

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.

Subtelomeric deletion of chromosome 10p15.3: clinical findings and molecular cytogenetic characterization.

We describe 19 unrelated individuals with submicroscopic deletions involving 10p15.3 characterized by chromosomal microarray (CMA). Interestingly, to our knowledge, only two individuals with isolated, submicroscopic 10p15.3 deletion have been reported to date; however, only limited clinical information is available for these probands and the deleted region has not been molecularly mapped. Comprehensive clinical history was obtained for 12 of the 19 individuals described in this study. Common features among these 12 individuals include: cognitive/behavioral/developmental differences (11/11), speech delay/language disorder (10/10), motor delay (10/10), craniofacial dysmorphism (9/12), hypotonia (7/11), brain anomalies (4/6) and seizures (3/7). Parental studies were performed for nine of the 19 individuals; the 10p15.3 deletion was de novo in seven of the probands, not maternally inherited in one proband and inherited from an apparently affected mother in one proband. Molecular mapping of the 19 individuals reported in this study has identified two genes, ZMYND11 (OMIM 608668) and DIP2C (OMIM 611380; UCSC Genome Browser), mapping within 10p15.3 which are most commonly deleted. Although no single gene has been identified which is deleted in all 19 individuals studied, the deleted region in all but one individual includes ZMYND11 and the deleted region in all but one other individual includes DIP2C. There is not a clearly identifiable phenotypic difference between these two individuals and the size of the deleted region does not generally predict clinical features. Little is currently known about these genes complicating a direct genotype/phenotype correlation at this time. These data however, suggest that ZMYND11 and/or DIP2C haploinsufficiency contributes to the clinical features associated with 10p15 deletions in probands described in this study.

Desarrollo de una aplicación para móviles basada en la tecnología de realidad aumentada

En este TFC se pretende implementar en un dispositivo móvil Android la funcionalidad de una aplicación de AR (Augmented Reality, "realidad aumentada") basada en Wikitude World Browser de Mobilizy para encontrar las paradas de autobús que más se ajustan a las necesidades del usuario.

DnaSP v5: A software for comprehensive analysis of DNA polymorphism data

DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.

GENCODE: producing a reference annotation for ENCODE.

BACKGROUND: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. RESULTS: The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. CONCLUSION: In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.

Ympäristötietämyksen hallintasovelluksen kehittäminen

Uudistunut ympäristölainsäädäntö vaatii energiantuotantolaitoksilta yhä enemmän järjestelmällistä ympäristötiedon hallintaa. LCP- ja jätteenpolttoasetuksen velvoitteet ovat asettaneet uusia vaatimuksia päästöjen valvontaan ja siihen käytettävien mittausjärjestelmien laadunvarmennukseen sekä päästötietojen raportointiin. Uudistukset ovat lisänneet huomattavasti laitoksilla ympäristötiedon käsittelyyn kuluvaa aikaa. Laitosten toimintaehdot määritellään ympäristöviranomaisen myöntämässä ympäristöluvassa, joka on tärkein yksittäinen laitoksen toimintaa ohjaava tekijä. Tämän lisäksi monet toimijat haluavat parantaa ympäristöasioiden tasoaan vapaaehtoisilla ympäristöjärjestelmillä. Tässä diplomityössä kuvataan energiantuotantolaitosten ympäristöasioiden tallentamiseen ja hallintaan kehitetty selainpohjainen Metso Automationin DNAecoDiary'sovellus. Työ on rajattu koskemaan Suomessa toimivia LCP- ja/tai jätteenpolttoasetuksen alaisia laitoksia. Sovelluksen avulla voidaan varmistaa energiantuotantolaitosten poikkeamien, häiriöilmoitusten, päästömittalaitteisiin liittyvien tapahtumien ja muun ympäristöasioiden valvontaan liittyvän informaation tehokas hallinta. Sovellukseen tallennetaan ympäristötapahtumiin liittyvät perustiedot sekä etenkin käyttäjien tapahtumiin liittyvä kokemustietämys. Valvontakirjaukseen voidaan liittää tapahtuman perustietojen lisäksi myös tiedostoja ja kuvia. Sovellusta ja sillä kerättyä tietoa voidaan hyödyntää laitoksella käsilläolevien ongelmien ratkaisuun, ympäristötapahtumien todentamiseen sekä ympäristöraporttien laadintaan. Kehitystyön tueksi järjestettiin asiakastarvekartoitus, jonka perusteella ideoitiin sovelluksen ominaisuuksia. Tässä työssä on esitetty ympäristötiedon hallinan perusteet, selvitetty DNAecoDiaryn toimintaperiaatteet ja annettu esimerkkejä sen hyödyntämisestä. Sovelluksen lopullinen sisältö määritellään kunkin asiakkaan ympäristöluvan ja oma-valvonnan tarpeiden mukaisesti. Sovellus toimii itsenäisesti tai osana laajempaa Metso Automationin päästöjenhallinta- ja raportointisovelluskokonaisuutta.

Kiinteistön sähköisen huoltokirjan kehittäminen

Ympäristöministeriö edellyttää kaikilta vuoden 2000 jälkeen valmistuneilta tai peruskorjatuilta asuinkiinteistöiltä huoltokirjaa. Huoltokirja on kiinteistön ylläpitoon liittyvä asiakirjakokonaisuus, johon kootaan kaikki tarvittavat tiedot kiinteistöstä ja sen hoidosta. Tämän diplomityön tavoitteena oli toteuttaa sähköinen huoltokirjajärjestelmä asuinkiinteistöille. Järjestelmän haluttiin palvelevan isännöitsijöiden ja huoltoyhtiöiden lisäksi myös kiinteistön omistajia, asukkaita, rakennuttajia ja kiinteistön välittäjiä. Tästä syystä järjestelmästä haluttiin Internet-selaimella käytettävä verkkopalvelu. Diplomityöhön kuului järjestelmän suunnittelu, toteutus ja testaus. Työn lopputuloksena syntynyt Pihapiiri.com järjestelmä otettiin käyttöön syksyllä 2002. Projektin aikanahavaittiin, että huoltokirjoja koskevat määrittelyt ja standardit olivat vasta kehitteillä. e-EHYT-hanke (elinkaarihallinnan yhteiset ydintie dot sähköisissä huoltokirjoissa) on merkittävä edistysaskel huoltokirjajärjestelmien sisällön ja tiedonsiirron standardoinnissa. Uusissa tuotekehityshankkeissa ja nykyisten huoltokirjajärjestelmien jatkokehityshankkeissa on olennaista huomioida e-EHYT-määritysten sekä yhteistyöverkoston merkitys. Käyttäjät ovat kritisoineet markkinoilla olevia tuotteita liian tarkoiksi. Liian teknisiä ja raskaita ratkaisuja tulee välttää varsinkin silloin kun tuotetta suunnitellaan asunto-osakeyhtiöille ja pientalo-omistajille.

Promoting good practices for handling nanomaterials : an international wiki project

As production and use of nanomaterials in commercial products grow it is imperative to ensure these materials are used safely with minimal unwanted impacts on human health or the environment. Foremost among the populations of potential concern are workers who handle nanomaterials in a variety of occupational settings, including university laboratories, industrial manufacturing plants and other institutions. Knowledge about prudent practices for handling nanomaterials is being developed by many groups around the world but may be communicated in a way that is difficult for practitioners to access or use. The GoodNanoGuide is a collaborative, open-access project aimed at creating an international forum for the development and discussion of prudent practices that can be used by researchers, workers and their representatives, occupational safety professionals, governmental officials and even the public. The GoodNanoGuide is easily accessed by anyone with access to a web browser and aims to become a living repository of good practices for the nanotechnology enterprise. Interested individuals are invited to learn more about the GoodNanoGuide at http://goodnanoguide.org.