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Arquitetura de computação em grade aplicada a saúde: um estudo de caso em bioinformática para oncologia.; Architecture of grid computing applied to health: a case study in bioinformatics for oncology.

Campos Junior, Moacir Alves de
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 29/10/2008 PT
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Atualmente o câncer e a terceira causa de óbitos em ambos os sexos e em todas as faixas de idade. O Ministério da Saúde relata que a alta complexidade da atenção ontológica demanda alto custo financeiro e alta tecnologia. Cada vez mais, as atividades de pesquisa, prevenção, diagnóstico e tratamento do câncer são realizadas sobre um domínio multidisciplinar envolvendo medicina, química, genética, bioinformática e engenharia. Estas atividades são responsáveis por gerar e manipular grandes quantidades de dados que são geograficamente distribuídos entre as unidades de tratamento deste país. Estes dados necessitam ser integrados e processados, a sua utilização é empregada para melhorar a gestão e viabilizar colaborações de pesquisa entre as instituições do setor. O processamento destas informações demandaria grande capacidade computacional. Particularmente, verificamos que a bioinformática manipula uma grande quantidade de dados, e tem cada vez mais contribuído para a pesquisa e no diagnóstico de várias doenças, principalmente do câncer. A proposta desta dissertação consiste na pesquisa e desenvolvimento de uma infra-estrutura computacional baseada na tecnologia de grades computacionais para atender as demandas de alto processamento computacional...

Análise da via de regulação gênica por ácido retinóico: uma abordagem por bioinformática e biologia estrutural; Analysis of retinoic acid pathway: an approach by bioinformatics and structural biology.

Sobreira, Tiago José Paschoal
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 11/12/2008 PT
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As vias de sinalização celular por meio de moléculas são um dos principais meios de controle funcional de um organismo. O entendimento das funções de moléculas sinalizadoras facilita a compreensão das vias metabólicas de um organismo, assim possibilitando uma melhor compreensão de vários eventos biológicos e também de várias doenças. A sinalização pelo ácido retinóico (AR), e seus derivados, é responsável pelo controle de várias funções, por exemplo: crescimento celular, diferenciação celular, formação da retina, desenvolvimento cardíaco e também relacionado a várias patologias como diabetes, obesidades, cânceres, e doenças cardiovasculares. A ação do ácido retinóico é controlada em dois níveis: no metabolismo de síntese/degradação e na sua utilização na sinalização para a expressão gênica. A maquinaria que controla o metabolismo inclui as enzimas de síntese do AR (aldeído desidrogenase ALDH) e as enzimas de degradação do AR (Cyp26), que controlam a distribuição espaço-temporal do AR durante a embriogênese. As ALDHs são enzimas NAD(P)+ dependentes, que oxidam uma ampla gama de aldeídos para os seus correspondentes ácidos carboxílicos, sendo ALDH1A2 a principal enzima na transformação de retinal em ácido retinóico. A maquinaria da sinalização celular por AR contém os receptores nucleares controlados por AR (RARs) que estão envolvidos com o controle da transcrição gênica. Os mecanismos de controle de expressão mais comuns são os que ocorrem na fase transcricional. Um desses mecanismos envolve proteínas que se ligam às regiões promotoras de transcrição...

Busca guiada de patentes de Bioinformática; Guided Search of Bioinformatics Patents

Dutra, Marcio Branquinho
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 17/10/2013 PT
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As patentes são licenças públicas temporárias outorgadas pelo Estado e que garantem aos inventores e concessionários a exploração econômica de suas invenções. Escritórios de marcas e patentes recomendam aos interessados na concessão que, antes do pedido formal de uma patente, efetuem buscas em diversas bases de dados utilizando sistemas clássicos de busca de patentes e outras ferramentas de busca específicas, com o objetivo de certificar que a criação a ser depositada ainda não foi publicada, seja na sua área de origem ou em outras áreas. Pesquisas demonstram que a utilização de informações de classificação nas buscas por patentes melhoram a eficiência dos resultados das consultas. A pesquisa associada ao trabalho aqui reportado tem como objetivo explorar artefatos linguísticos, técnicas de Recuperação de Informação e técnicas de Classificação Textual para guiar a busca por patentes de Bioinformática. O resultado dessa investigação é o Sistema de Busca Guiada de Patentes de Bioinformática (BPS), o qual utiliza um classificador automático para guiar as buscas por patentes de Bioinformática. A utilização do BPS é demonstrada em comparações com ferramentas de busca de patentes atuais para uma coleção específica de patentes de Bioinformática. No futuro...

Metodologias de bioinformatica para detecção e estudo de sequencias repetitivas em loci genicos de transcritos quimericos; Bioinformatics methodologies for detection and study of repetitive sequences in gene loci of chimeric transcripts

Roberto Hirochi Herai
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 23/02/2010 PT
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A grande quantidade de dados biológicos gerados recentemente permitiu verificar que os genomas são repletos de seqüências repetitivas (SR), como microsatélites e elementos genéticos móveis, altamente improváveis de ocorrer estatisticamente se os genomas fossem gerados a partir de uma distribuição aleatória de nucleotídeos. Tal comprovação motivou a classificação de tais seqüências e também a construção de diversas ferramentas de bioinformática, além de mecanismos de armazenamento baseados em sistemas de gerenciamento de bancos de dados (SGBD) para permitir localizá-las e armazená-las para posterior estudo. Entretanto, foi com a comprovação biológica da importância das SR, como no mecanismo de interferência por RNAi (SR reversa complementar), que as SR despertaram maior interesse por parte da comunidade científica. Atualmente, já há fortes evidências que associam as SR com fenômenos biológicos bastante interessantes, como o processamento de RNA por cis-splicing e a formação de transcritos quiméricos, freqüentes em organismos inferiores e muito raro em organismos superiores. Tais tipos de transcritos podem ser gerados a partir de trans-splicing ou, como conjecturamos nesse trabalho, pela transposição de elementos genéticos móveis (como por exemplo transposons ou retrotransposons). Em virtude disso...

Re-mapping the molecular features of the human immunodeficiency virus type 1 and human T-cell lymphotropic virus type 1 Brazilian sequences using a bioinformatics unit established in Salvador, Bahia, Brazil, to give support to the viral epidemiology studies

Queiroz,Artur Trancoso Lopo de; Mota-Miranda,Aline Cristina Andrade; Oliveira,Tulio de; Moreau,Domingos Ramon; Urpia,Caroline de Carvalho; Carvalho,Chandra Mara; Galvão-Castro,Bernardo; Alcantara,Luiz Carlos Junior
Fonte: Instituto Oswaldo Cruz, Ministério da Saúde Publicador: Instituto Oswaldo Cruz, Ministério da Saúde
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/03/2007 EN
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The analysis of genetic data for human immunodeficiency virus type 1 (HIV-1) and human T-cell lymphotropic virus type 1 (HTLV-1) is essential to improve treatment and public health strategies as well as to select strains for vaccine programs. However, the analysis of large quantities of genetic data requires collaborative efforts in bioinformatics, computer biology, molecular biology, evolution, and medical science. The objective of this study was to review and improve the molecular epidemiology of HIV-1 and HTLV-1 viruses isolated in Brazil using bioinformatic tools available in the Laboratório Avançado de Sáude Pública (Lasp) bioinformatics unit. The analysis of HIV-1 isolates confirmed a heterogeneous distribution of the viral genotypes circulating in the country. The Brazilian HIV-1 epidemic is characterized by the presence of multiple subtypes (B, F1, C) and B/F1 recombinant virus while, on the other hand, most of the HTLV-1 sequences were classified as Transcontinental subgroup of the Cosmopolitan subtype. Despite the high variation among HIV-1 subtypes, protein glycosylation and phosphorylation domains were conserved in the pol, gag, and env genes of the Brazilian HIV-1 strains suggesting constraints in the HIV-1 evolution process. As expected...

Opportunities at the Intersection of Bioinformatics and Health Informatics: A Case Study

Miller, Perry L.
Fonte: American Medical Informatics Association Publicador: American Medical Informatics Association
Tipo: Artigo de Revista Científica
Publicado em //2000 EN
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This paper provides a “viewpoint discussion” based on a presentation made to the 2000 Symposium of the American College of Medical Informatics. It discusses potential opportunities for researchers in health informatics to become involved in the rapidly growing field of bioinformatics, using the activities of the Yale Center for Medical Informatics as a case study. One set of opportunities occurs where bioinformatics research itself intersects with the clinical world. Examples include the correlations between individual genetic variation with clinical risk factors, disease presentation, and differential response to treatment; and the implications of including genetic test results in the patient record, which raises clinical decision support issues as well as legal and ethical issues. A second set of opportunities occurs where bioinformatics research can benefit from the technologic expertise and approaches that informaticians have used extensively in the clinical arena. Examples include database organization and knowledge representation, data mining, and modeling and simulation. Microarray technology is discussed as a specific potential area for collaboration. Related questions concern how best to establish collaborations with bioscientists so that the interests and needs of both sets of researchers can be met in a synergistic fashion...

The Interactions Between Clinical Informatics and Bioinformatics: A Case Study

Altman, Russ B.
Fonte: American Medical Informatics Association Publicador: American Medical Informatics Association
Tipo: Artigo de Revista Científica
Publicado em //2000 EN
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For the past decade, Stanford Medical Informatics has combined clinical informatics and bioinformatics research and training in an explicit way. The interest in applying informatics techniques to both clinical problems and problems in basic science can be traced to the Dendral project in the 1960s. Having bioinformatics and clinical informatics in the same academic unit is still somewhat unusual and can lead to clashes of clinical and basic science cultures. Nevertheless, the benefits of this organization have recently become clear, as the landscape of academic medicine in the next decades has begun to emerge. The author provides examples of technology transfer between clinical informatics and bioinformatics that illustrate how they complement each other.

A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons

Hamilton, Russell S.; Hartswood, Eve; Vendra, Georgia; Jones, Cheryl; Van De Bor, Veronique; Finnegan, David; Davis, Ilan
Fonte: Cold Spring Harbor Laboratory Press Publicador: Cold Spring Harbor Laboratory Press
Tipo: Artigo de Revista Científica
Publicado em /02/2009 EN
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mRNA localization is a widespread mode of delivering proteins to their site of function. The embryonic axes in Drosophila are determined in the oocyte, through Dynein-dependent transport of gurken/TGF-α mRNA, containing a small localization signal that assigns its destination. A signal with a similar secondary structure, but lacking significant sequence similarity, is present in the I factor retrotransposon mRNA, also transported by Dynein. It is currently unclear whether other mRNAs exist that are localized to the same site using similar signals. Moreover, searches for other genes containing similar elements have not been possible due to a lack of suitable bioinformatics methods for searches of secondary structure elements and the difficulty of experimentally testing all the possible candidates. We have developed a bioinformatics approach for searching across the genome for small RNA elements that are similar to the secondary structures of particular localization signals. We have uncovered 48 candidates, of which we were able to test 22 for their localization potential using injection assays for Dynein mediated RNA localization. We found that G2 and Jockey transposons each contain a gurken/I factor-like RNA stem–loop required for Dynein-dependent localization to the anterior and dorso–anterior corner of the oocyte. We conclude that I factor...

Development of an Undergraduate Bioinformatics Degree Program at a Liberal Arts College

Bagga, Paramjeet S.
Fonte: YJBM Publicador: YJBM
Tipo: Artigo de Revista Científica
Publicado em 25/09/2012 EN
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The highly interdisciplinary field of bioinformatics has emerged as a powerful modern science. There has been a great demand for undergraduate- and graduate-level trained bioinformaticists in the industry as well in the academia. In order to address the needs for trained bioinformaticists, its curriculum must be offered at the undergraduate level, especially at four-year colleges, where a majority of the United States gets its education. There are many challenges in developing an undergraduate-level bioinformatics program that needs to be carefully designed as a well-integrated and cohesive interdisciplinary curriculum that prepares the students for a wide variety of career options. This article describes the challenges of establishing a highly interdisciplinary undergraduate major, the development of an undergraduate bioinformatics degree program at Ramapo College of New Jersey, and lessons learned in the last 10 years during its management.

Thriving in Multidisciplinary Research: Advice for New Bioinformatics Students

Auerbach, Raymond K.
Fonte: YJBM Publicador: YJBM
Tipo: Artigo de Revista Científica
Publicado em 25/09/2012 EN
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The sciences have seen a large increase in demand for students in bioinformatics and multidisciplinary fields in general. Many new educational programs have been created to satisfy this demand, but navigating these programs requires a non-traditional outlook and emphasizes working in teams of individuals with distinct yet complementary skill sets. Written from the perspective of a current bioinformatics student, this article seeks to offer advice to prospective and current students in bioinformatics regarding what to expect in their educational program, how multidisciplinary fields differ from more traditional paths, and decisions that they will face on the road to becoming successful, productive bioinformaticists.

Composable languages for bioinformatics: the NYoSh experiment

Simi, Manuele; Campagne, Fabien
Fonte: PeerJ Inc. Publicador: PeerJ Inc.
Tipo: Artigo de Revista Científica
Publicado em 02/01/2014 EN
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Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts...

CNBi: the new Brazilian National Consortium for Bioinformatics.

HERAI, R. H.; VIDAL, R. O.; CARAZZOLLE, M. F.; COSTA, G. G. L.; FALCAO, P. R. K.; YAMAGISHI, M. E. B.; FRANCHINI, K. G.; PEREIRA, G. G. A.
Fonte: In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.], 2010. Publicador: In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.], 2010.
Tipo: Resumo em anais de congresso (ALICE) Formato: p. 110.
EN
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PRESENTATION: The National Consortium for Bioinformatics (CNBi) is a multidisciplinary center dedicated to research, development, management and technical support on questions arising from bioinformatics. It was created by a joint effort between three laboratories from São Paulo state in Brazil: the Genomic and Expression Laboratory (UNICAMP), Applied Bioinformatics Laboratory (EMBRAPA/CNPTIA) and National Laboratory of Biosciences (LNBio), and is organized as a distributed center inside the mentioned laboratories. MISSION: As a national center for bioinformatics, CNBi?s mission is the generation of new biotechnological information and advanced methods of computer-based information processing. Moreover it intends to act in the ?eld of genomics, proteomics (including protein structure and mass cryptography) and systems biology. In this way, CNBi brings together scientists from many knowledge areas, including computer science, molecular biology, genetics, mathematics, and physics, all of whom sharing a common interest. STRUCTURE: CNBi provides an advanced structure with powerful machines. Actually, there are several high-performance computational systems capable to analyze and simulate massive sets of data, very large storage devices to house major data collections...

Embrapa Bioinformatics Multi-Users Laboratory - LMB.

KUSER-FALCÃO, P. R.; YAMAGISHI, M. E. B.; GIACHETTO, P. F.; SILVA, F. R.; LOBO, F. P.; CINTRA, L. C.; ZERLOTINI, A.; HIGA, R.; VIEIRA, F.
Fonte: In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 8., 2012, Campinas. Abstract book... Ribeirão Preto: AB3C, 2012. Publicador: In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 8., 2012, Campinas. Abstract book... Ribeirão Preto: AB3C, 2012.
Tipo: Resumo em anais de congresso (ALICE) Formato: Não paginado.
EN
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The Bioinformatics Multi-Users Laboratory of Embrapa provides an array of shared research resources and infra-structure to the Embrapa community and research collaborators The primary mission of the LMB is to address the increasing need of Embrapa investigators for support and solutions in Bioinformatics in a collaborative environment. To fulfill this mission, the LMB collaborates on research projects that require expertise in genome assembly, meta-genomics analysis to unravel candidate genes, molecular markers, differential gene expression, and structural bioinformatics, and assists in the implementation of computational solutions .; 2012; X-MEETING 2012.

Web-Based Science Gateways for Structural Bioinformatics; Webbasierte Science Gateways für Strukturbioinformatik

Gesing, Sandra
Fonte: Universität Tübingen Publicador: Universität Tübingen
Tipo: Dissertation; info:eu-repo/semantics/doctoralThesis
EN
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Structural bioinformatics applies computational methods to analyse and model three-dimensional molecular structures. These methods address data-intensive and compute-intensive problems, which demand high-performance computing (HPC) to allow data analysis in an acceptable time. Thus, structural bioinformatic applications are ideal candidates for grid and cloud computing infrastructures, so-called DCIs (Distributed Computing Infrastructures). DCIs provide access to HPC facilities and services across organisational boundaries. However, the usability of DCIs is limited and the use of the complex methods in structural bioinformatics requires a lot of experience. In addition, users mainly process and analyse data not only via single jobs but via workflows. An approach to offer easy and intuitive access to applications on DCIs are science gateways. In general, a science gateway provides a single point of entry to a set of tools and data of a specific application domain while hiding the complex underlying infrastructure. Web-based science gateways are additionally characterised by only requiring a computer connected to the Internet and an installed web browser on the users' side. Developers of such gateways support the users with pre-configured user interfaces targeted for a specific application domain. The overall goal for creating science gateways is to increase the usability of applications. This work is focused on workflow-enabled grid portals that are specific web-based science gateways supporting the management of workflows on DCIs. Four major aspects in the context of workflow-enabled grid portals are addressed in this work: security in portals with underlying DCIs...

Emerging biotechnologies: bioinformatics services applied to agriculture.

BAMBINI, M. D.; GIACHETTO, P. F.; FALCAO, P. R. K.; OLIVEIRA, F. S. de
Fonte: In: CONGRESSO LATINO-IBEROAMERICANO DE GESTÃO DA TECNOLOGIA, 16., 2015, Porto Alegre. Inovação para além da tecnologia: anais. Porto Alegre: Universidade Federal do Rio Grande do Sul, 2015. Publicador: In: CONGRESSO LATINO-IBEROAMERICANO DE GESTÃO DA TECNOLOGIA, 16., 2015, Porto Alegre. Inovação para além da tecnologia: anais. Porto Alegre: Universidade Federal do Rio Grande do Sul, 2015.
Tipo: Artigo em anais de congresso (ALICE) Formato: Não paginado.
EN
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Abstract - Bioinformatics is an emergent biotechnological field of study marked by interdisciplinarity and complexity. It involves the application and development of computational tools to biological data in order to process, generate, and disseminate biological knowledge. Bioinformatics is characterized by an intense generation of data and information (configured as a context of big data and e-science), associated with the need for computational resources with high processing and storage capacities and highly qualified and interdisciplinary staff, often found only in academia. The objective of this paper is to describe the organizational model and collaborative innovation activities of the Bioinformatics Multi-user Laboratory (LMB, in the acronym in Portuguese). The LMB is a facility located at the Brazilian Agricultural Research Corporation (Embrapa), the main Brazilian agricultural research public institute, formed by 46 Research and Service Centers distributed throughout Brazil and by several laboratories and business offices abroad, in America, Africa, Asia and Europe. Its mission involves to contribute to the advance of the frontier of knowledge in bioinformatics by: incorporating new technologies and enabling efficient solutions to the demands related to this field; providing access to high performance computing infrastructure and developing human skills. Considering the importance of biotechnology in the context of agricultural research...

Chemistry in Bioinformatics

Murray-Rust, Peter; Mitchell, John B O; Rzepa, Henry S
Fonte: Universidade de Cambridge Publicador: Universidade de Cambridge
Tipo: Pré-impressão Formato: 27824 bytes; application/pdf
EN
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A preprint of an invited submission to BioMedCentral Bioinformatics. This short manuscript is an overview or the current problems and opportunities in publishing chemical information. Full details of technology are given in the sibling manuscript http://www.dspace.cam.ac.uk/handle/1810/34579 The manuscript is the authors' preprint although it has been automatically transformed into this archived PDF by the submission system. The authors are not responsible for the formatting; Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is Openly available and freely re?usable, most chemical information is closed and cannot be re?distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) Free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.

Increasing Access To Bioinformatics Resources: Increase Community Curation by Increasing Your Community

Jennifer M. Williams
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
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The amount of biological data has risen exponentially over the last decade. Along with this rise, the number and types of bioinformatics resources has risen such that the sheer number of bioinformatics resources is overwhelming. For these resources to attain their full potential, they must be efficiently and extensively utilized. But in such a plethora of resources, how does a researcher new to a field find the resources that will meet their needs. Once a resource is found, how does the researcher quickly learn to utilize that resource fully? There are resource lists such as those provided by the journal Nucleic Acid Research (NAR), BioMed Central and the Univ. of Pittsburgh Health Sciences Library, and most resources include their own documentation. But lists and site documentation don’t always cast a wide enough net to catch all users. For a resource to truly maximize their user community, it often takes multiple different outreach approaches. OpenHelix specializes in providing customized outreach services to bioinformatics resources, including those featured on this poster. Based on the conclusions from our Phase I SBIR grant, which tested the efficiency of several methods for training researchers on the use of genomic resources...

Metacuration Standards and Minimum Information about a Bioinformatics Investigation

Tin Wee Tan; Asif M. Khan; Shen Jean Lim; Yong Li Hu; Mark de Silva; Kuan Siong Lim
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
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Many bioinformatics databases published in journals are here this year and gone the next. There is generally (i) no requirement, mandatory or otherwise, by reviewers, editors or publishers for full disclosure of how databases are built and how they are maintained; (ii) no standardized requirement for data in public access databases to be kept as backup for release and access when a project ends, when funds expire and website terminates; (iii) the case of proprietary resources, there is no requirement for data to be kept in escrow for release under stated conditions such as when a published database disappears due to company closure. Consequently, much of the biological databases published in the past twenty years are easily lost, even though the publications describing or referencing these databases and webservices remain. Given the volume of publications today, even though it is practically possible for reviewers to re-create databases as described in a manuscript, there is usually insufficient disclosure and raw data for this to be done, even if there is sufficient time and resources available to perform this. Consequently, verification and validation is assumed, and claims of the paper accepted as true and correct at face value. A solution to this growing problem is to experiment with some kind of minimum standards of reporting such as the Minimum Information About a Bioinformatics Investigation (MIABi) and standardized requirements of data deposition and escrow for enabling persistence and reproducibility. With easy availability of cloud computing...

Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS).

Jonas Almeida; Helena Deus; Wolfgang Maass
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
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Use of semantic web abstractions, in particular of domain neural Knowledge Organization Systems (KOS), to manage distributed, cloud based, integrative bioinformatics infrastructure. This presentation derives from recent publication: Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID 20646315]. These PowerPoint slides were presented at Semantic Web Applications and Tools for Life Sciences December 10th, 2010, Berlin, Germany (http://www.swat4ls.org/2010/progr.php), keynote 9-10 am.

The Importance of Modularity in Bioinformatics Tools

Martina Kutmon; Martijn P. van Iersel; Thomas Kelder; Chris T. Evelo
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
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In the last decade the amount of Bioinformatics tools has increased enormously. There are tools to store, analyse, visualize, edit or generate biological data and there are still more in development. Still, the demand for increased functionality in a single piece of software must be balanced by the need for modularity to keep the software maintainable. In complex systems, the conflicting demands of features and maintainability are often solved by plug-in systems. For example Cytoscape, an open source platform for Complex-Network Analysis and Visualization, is using a plug-in system to allow the extension of the application without changing the core. This not only allows the integration of new functionality without a new release but offers the possibility for other developers to contribute plug-ins which are needed in their research. Most tools have their own, individual plug-in system to meet the needs of the application. These are often very simple and easy to use. However, the increasing complexity of plug-ins demands more functionality of the plug-in system. We want to reuse components in different contexts, we want to have simple plug-in interfaces and we want to allow communication and dependencies between plug-ins. Many tools implemented in Java are facing these problems and there seems to be a common solution: the integration of an established modularity framework...