2,224 research outputs found

    EcoGIS – GIS tools for ecosystem approaches to fisheries management

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    Executive Summary: The EcoGIS project was launched in September 2004 to investigate how Geographic Information Systems (GIS), marine data, and custom analysis tools can better enable fisheries scientists and managers to adopt Ecosystem Approaches to Fisheries Management (EAFM). EcoGIS is a collaborative effort between NOAA’s National Ocean Service (NOS) and National Marine Fisheries Service (NMFS), and four regional Fishery Management Councils. The project has focused on four priority areas: Fishing Catch and Effort Analysis, Area Characterization, Bycatch Analysis, and Habitat Interactions. Of these four functional areas, the project team first focused on developing a working prototype for catch and effort analysis: the Fishery Mapper Tool. This ArcGIS extension creates time-and-area summarized maps of fishing catch and effort from logbook, observer, or fishery-independent survey data sets. Source data may come from Oracle, Microsoft Access, or other file formats. Feedback from beta-testers of the Fishery Mapper was used to debug the prototype, enhance performance, and add features. This report describes the four priority functional areas, the development of the Fishery Mapper tool, and several themes that emerged through the parallel evolution of the EcoGIS project, the concept and implementation of the broader field of Ecosystem Approaches to Management (EAM), data management practices, and other EAM toolsets. In addition, a set of six succinct recommendations are proposed on page 29. One major conclusion from this work is that there is no single “super-tool” to enable Ecosystem Approaches to Management; as such, tools should be developed for specific purposes with attention given to interoperability and automation. Future work should be coordinated with other GIS development projects in order to provide “value added” and minimize duplication of efforts. In addition to custom tools, the development of cross-cutting Regional Ecosystem Spatial Databases will enable access to quality data to support the analyses required by EAM. GIS tools will be useful in developing Integrated Ecosystem Assessments (IEAs) and providing pre- and post-processing capabilities for spatially-explicit ecosystem models. Continued funding will enable the EcoGIS project to develop GIS tools that are immediately applicable to today’s needs. These tools will enable simplified and efficient data query, the ability to visualize data over time, and ways to synthesize multidimensional data from diverse sources. These capabilities will provide new information for analyzing issues from an ecosystem perspective, which will ultimately result in better understanding of fisheries and better support for decision-making. (PDF file contains 45 pages.

    TLAD 2010 Proceedings:8th international workshop on teaching, learning and assesment of databases (TLAD)

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    This is the eighth in the series of highly successful international workshops on the Teaching, Learning and Assessment of Databases (TLAD 2010), which once again is held as a workshop of BNCOD 2010 - the 27th International Information Systems Conference. TLAD 2010 is held on the 28th June at the beautiful Dudhope Castle at the Abertay University, just before BNCOD, and hopes to be just as successful as its predecessors.The teaching of databases is central to all Computing Science, Software Engineering, Information Systems and Information Technology courses, and this year, the workshop aims to continue the tradition of bringing together both database teachers and researchers, in order to share good learning, teaching and assessment practice and experience, and further the growing community amongst database academics. As well as attracting academics from the UK community, the workshop has also been successful in attracting academics from the wider international community, through serving on the programme committee, and attending and presenting papers.This year, the workshop includes an invited talk given by Richard Cooper (of the University of Glasgow) who will present a discussion and some results from the Database Disciplinary Commons which was held in the UK over the academic year. Due to the healthy number of high quality submissions this year, the workshop will also present seven peer reviewed papers, and six refereed poster papers. Of the seven presented papers, three will be presented as full papers and four as short papers. These papers and posters cover a number of themes, including: approaches to teaching databases, e.g. group centered and problem based learning; use of novel case studies, e.g. forensics and XML data; techniques and approaches for improving teaching and student learning processes; assessment techniques, e.g. peer review; methods for improving students abilities to develop database queries and develop E-R diagrams; and e-learning platforms for supporting teaching and learning

    TLAD 2010 Proceedings:8th international workshop on teaching, learning and assesment of databases (TLAD)

    Get PDF
    This is the eighth in the series of highly successful international workshops on the Teaching, Learning and Assessment of Databases (TLAD 2010), which once again is held as a workshop of BNCOD 2010 - the 27th International Information Systems Conference. TLAD 2010 is held on the 28th June at the beautiful Dudhope Castle at the Abertay University, just before BNCOD, and hopes to be just as successful as its predecessors.The teaching of databases is central to all Computing Science, Software Engineering, Information Systems and Information Technology courses, and this year, the workshop aims to continue the tradition of bringing together both database teachers and researchers, in order to share good learning, teaching and assessment practice and experience, and further the growing community amongst database academics. As well as attracting academics from the UK community, the workshop has also been successful in attracting academics from the wider international community, through serving on the programme committee, and attending and presenting papers.This year, the workshop includes an invited talk given by Richard Cooper (of the University of Glasgow) who will present a discussion and some results from the Database Disciplinary Commons which was held in the UK over the academic year. Due to the healthy number of high quality submissions this year, the workshop will also present seven peer reviewed papers, and six refereed poster papers. Of the seven presented papers, three will be presented as full papers and four as short papers. These papers and posters cover a number of themes, including: approaches to teaching databases, e.g. group centered and problem based learning; use of novel case studies, e.g. forensics and XML data; techniques and approaches for improving teaching and student learning processes; assessment techniques, e.g. peer review; methods for improving students abilities to develop database queries and develop E-R diagrams; and e-learning platforms for supporting teaching and learning

    Molecular Similarity and Xenobiotic Metabolism

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    MetaPrint2D, a new software tool implementing a data-mining approach for predicting sites of xenobiotic metabolism has been developed. The algorithm is based on a statistical analysis of the occurrences of atom centred circular fingerprints in both substrates and metabolites. This approach has undergone extensive evaluation and been shown to be of comparable accuracy to current best-in-class tools, but is able to make much faster predictions, for the first time enabling chemists to explore the effects of structural modifications on a compound’s metabolism in a highly responsive and interactive manner.MetaPrint2D is able to assign a confidence score to the predictions it generates, based on the availability of relevant data and the degree to which a compound is modelled by the algorithm.In the course of the evaluation of MetaPrint2D a novel metric for assessing the performance of site of metabolism predictions has been introduced. This overcomes the bias introduced by molecule size and the number of sites of metabolism inherent to the most commonly reported metrics used to evaluate site of metabolism predictions.This data mining approach to site of metabolism prediction has been augmented by a set of reaction type definitions to produce MetaPrint2D-React, enabling prediction of the types of transformations a compound is likely to undergo and the metabolites that are formed. This approach has been evaluated against both historical data and metabolic schemes reported in a number of recently published studies. Results suggest that the ability of this method to predict metabolic transformations is highly dependent on the relevance of the training set data to the query compounds.MetaPrint2D has been released as an open source software library, and both MetaPrint2D and MetaPrint2D-React are available for chemists to use through the Unilever Centre for Molecular Science Informatics website.----Boehringer-Ingelhie

    Web-based interface for environmental niche modelling

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    Marine species are subject to anthropogenic impacts, such as noise pollution, marine litter, and direct impact collisions. While there are efforts in the marine community and crowd-sourcing to report the occurrence of marine species, not enough projects explore the prediction of where such animals may be. This dissertation analyzes the state of the art in species distribution model ing (SDM) systems, capable of reporting and predicting marine biodiversity. The proposal implements the algorithms for predicting species through publicly avail able repositories of data, provides means to ease the upload and management of occurrence points as well as methods for prediction analysis. A web-based user interface is proposed using Ecological Niche Modelling (ENM) as an automated alerting mechanism towards ecological awareness. Performed user studies evaluate marine biodiversity concerns from fisherman and whale-watching sea-vessels, assessing attitudes, threats, values, and motiva tion of both samples. Further, biologists and experts on ENMs will evaluate the workflow and interface, reviewing the proposal’s potential to enable ecologists to create solutions for their custom problems using simple protocols without the need for any third-party entities and extensive knowledge in programming.Espécies marinhas estão sujeitas a impactos antropogênicos, tais como poluição sonora, lixo marinho, e colisões com tráfego marinho. Apesar de existirem al guns esforços da comunidade marinha e crowdsourcing relativamente ao registo de ocorrências de biodiversidade marinha, não existem projeto suficientes que exploram as previsões de onde estas espécies poderão estar. Esta dissertação analisa o estado da arte em sistemas de modelação de dis tribuição de espécies, capazes de relatar e prever biodiversidade marinha. A pro posta implementa os algoritmos para prever espécies por meio de repositórios consolidados de dados disponíveis online, fornece meios para facilitar o carrega mento e gestão de pontos de ocorrência, bem como métodos para análise das previsões. Uma interface web de utilizador é proposta utilizando Ecological Niche Modeling como um mecanismo de alerta automatizado para incrementar a con sciência ecológica. Os estudos do sistema irão avaliar as preocupações relativas a biodiversi dade marinha de embarcações de pesca e navios de observação de baleias. Desta forma é possível determinar atitudes, ameaças, valores e motivação de ambas as amostras para com a biodiversidade marinha. Além disso, biólogos e espe cialistas nesta tipologia de sistemas, avaliarão o fluxo de trabalho e a inter face desenvolvida, avaliando o potencial do sistema, permitindo aos ecologistas criar soluções personalizados através de protocolos simples, sem a necessidade de quaisquer entidades terceirizadas e conhecimento em programação

    SECURING THE DATA STORAGE AND PROCESSING IN CLOUD COMPUTING ENVIRONMENT

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    Organizations increasingly utilize cloud computing architectures to reduce costs and en- ergy consumption both in the data warehouse and on mobile devices by better utilizing the computing resources available. However, the security and privacy issues with publicly available cloud computing infrastructures have not been studied to a sufficient depth for or- ganizations and individuals to be fully informed of the risks; neither are private nor public clouds prepared to properly secure their connections as middle-men between mobile de- vices which use encryption and external data providers which neglect to encrypt their data. Furthermore, cloud computing providers are not well informed of the risks associated with policy and techniques they could implement to mitigate those risks. In this dissertation, we present a new layered understanding of public cloud comput- ing. On the high level, we concentrate on the overall architecture and how information is processed and transmitted. The key idea is to secure information from outside attack and monitoring. We use techniques such as separating virtual machine roles, re-spawning virtual machines in high succession, and cryptography-based access control to achieve a high-level assurance of public cloud computing security and privacy. On the low level, we explore security and privacy issues on the memory management level. We present a mechanism for the prevention of automatic virtual machine memory guessing attacks

    Power in numbers : in silico analysis of multigene families in Arabidopsis thaliana

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    A Unified Metamodel for Assessing and Predicting Software Evolvability Quality

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    Software quality is a key assessment factor for organizations to determine the ability of software ecosystems to meet the constantly changing requirements. Many quality models exist that capture and assess the changing factors affecting the quality of a software product. Common to these models is that they, contrary to the software ecosystems they are assessing, are not evolvable or reusable. The thesis first defines what constitutes a unified, evolvable, and reusable quality metamodel. We then introduce SE-EQUAM, a novel, ontological, quality assessment metamodel that was designed from the ground up to support quality unification, reuse, and evolvability. We then validate the reus-ability of our metamodel through instantiating a domain specific quality assessment model called OntEQAM that assesses evolvability as a non-functional software quality based on product and com-munity dimensions. A fuzzy logic based assessment process that addresses uncertainties around score boundaries supports the evolvability quality assessment. The presented assessment process also uses the unified representation of the input knowledge artifacts, the metamodel, and the model to provide a fuzzy assessment score. Finally, we further interpret and predict the evolvability as-sessment scores using a novel, cross-disciplinary approach that re-applies financial technical analy-sis, which are indicators, and patterns typically used for price analysis and the forecasting of stocks in financial markets. We performed several case studies to illustrate and evaluate the applicability of our proposed evolvability score prediction approach

    Computational analysis of human genomic variants and lncRNAs from sequence data

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    The high-throughput sequencing technologies have been developed and applied to the human genome studies for nearly 20 years. These technologies have provided numerous research applications and have significantly expanded our knowledge about the human genome. In this thesis, computational methods that utilize sequence data to study human genomic variants and transcripts were evaluated and developed. Indel represents insertion and deletion, which are two types of common genomic variants that are widespread in the human genome. Detecting indels from human genomes is the crucial step for diagnosing indel related genomic disorders and may potentially identify novel indel makers for studying certain diseases. Compared with previous techniques, the high-throughput sequencing technologies, especially the next- generation sequencing (NGS) technology, enable to detect indels accurately and efficiently in wide ranges of genome. In the first part of the thesis, tools with indel calling abilities are evaluated with an assortment of indels and different NGS settings. The results show that the selection of tools and NGS settings impact on indel detection significantly, which provide suggestions for tool selection and future developments. In bioinformatics analysis, an indel’s position can be marked inconsistently on the reference genome, which may result in an indel having different but equivalent representations and cause troubles for downstream. This problem is related to the complex sequence context of the indels, for example, short tandem repeats (STRs), where the same short stretch of nucleotides is amplified. In the second part of the thesis, a novel computational tool VarSCAT was described, which has various functions for annotating the sequence context of variants, including ambiguous positions, STRs, and other sequence context features. Analysis of several high- confidence human variant sets with VarSCAT reveals that a large number of genomic variants, especially indels, have sequence features associated with STRs. In the human genome, not all genes and their transcripts are translated into proteins. Long non-coding ribonucleic acid (lncRNA) is a typical example. Sequence recognition built with machine learning models have improved significantly in recent years. In the last part of the thesis, several machine learning-based lncRNA prediction tools were evaluated on their predictions for coding potentiality of transcripts. The results suggest that tools based on deep learning identify lncRNAs best. Ihmisen genomivarianttien ja lncRNA:iden laskennallinen analyysi sekvenssiaineistosta Korkean suorituskyvyn sekvensointiteknologioita on kehitetty ja sovellettu ihmisen genomitutkimuksiin lähes 20 vuoden ajan. Nämä teknologiat ovat mahdollistaneet ihmisen genomin laaja-alaisen tutkimisen ja lisänneet merkittävästi tietoamme siitä. Tässä väitöstyössä arvioitiin ja kehitettiin sekvenssiaineistoa hyödyntäviä laskennallisia menetelmiä ihmisen genomivarianttien sekä transkriptien tutkimiseen. Indeli on yhteisnimitys lisäys- eli insertio-varianteille ja häviämä- eli deleetio-varianteille, joita esiintyy koko genomin alueella. Indelien tunnistaminen on ratkaisevaa geneettisten poikkeavuuksien diagnosoinnissa ja eri sairauksiin liittyvien uusien indeli-markkereiden löytämisessä. Aiempiin teknologioihin verrattuna korkean suorituskyvyn sekvensointiteknologiat, erityisesti seuraavan sukupolven sekvensointi (NGS) mahdollistavat indelien havaitsemisen tarkemmin ja tehokkaammin laajemmilta genomialueilta. Väitöstyön ensimmäisessä osassa indelien kutsumiseen tarkoitettuja laskentatyökaluja arvioitiin käyttäen laajaa valikoimaa indeleitä ja erilaisia NGS-asetuksia. Tulokset osoittivat, että työkalujen valinta ja NGS-asetukset vaikuttivat indelien tunnistukseen merkittävästi ja siten ne voivat ohjata työkalujen valinnassa ja kehitystyössä. Bioinformatiivisessa analyysissä saman indelin sijainti voidaan merkitä eri kohtiin referenssigenomia, joka voi aiheuttaa ongelmia loppupään analyysiin, kuten indeli-kutsujen arviointiin. Tämä ongelma liittyy sekvenssikontekstiin, koska variantit voivat sijoittua lyhyille perättäisille tandem-toistojaksoille (STR), jossa sama lyhyt nukleotidijakso on monistunut. Väitöstyön toisessa osassa kehitettiin laskentatyökalu VarSCAT, jossa on eri toimintoja, mm. monitulkintaisten sijaintitietojen, vierekkäisten alueiden ja STR-alueiden tarkasteluun. Luotettaviksi arvioitujen ihmisen varianttiaineistojen analyysi VarSCAT-työkalulla paljasti, että monien geneettisten varianttien ja erityisesti indelien ominaisuudet liittyvät STR-alueisiin. Kaikkia ihmisen geenejä ja niiden geenituotteita, kuten esimerkiksi ei-koodaavia RNA:ta (lncRNA) ei käännetä proteiiniksi. Koneoppimismenetelmissä ja sekvenssitunnistuksessa on tapahtunut huomattavaa parannusta viime vuosina. Väitöstyön viimeisessä osassa arvioitiin useiden koneoppimiseen perustuvien lncRNA-ennustustyökalujen ennusteita. Tulokset viittaavat siihen, että syväoppimiseen perustuvat työkalut tunnistavat lncRNA:t parhaiten
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