RedeR Web : uma plataforma web para organização e análise de redes modulares

Orientador: Prof. Dr. Mauro Antonio Alves CastroCoorientador: Prof. Dr. Alessandro BrawemanDissertação (mestrado) - Universidade Federal do Paraná, Setor de Educação Profissional e Tecnológica, Programa de Pós-Graduação em Bioinformática. Defesa : Curitiba, 29/09/2017Inclui referências: p.60-64Resumo: A visualização de grafos ou redes tem como principal objetivo auxiliar o processo de análise e compreensão de conjuntos de dados complexos, proporcionando perspectivas diferenciadas da mesma informação, potencializando a apropriação do conhecimento pelo usuário. Tratando-se de sistemas biológicos, a visualização e análise de redes moleculares têm sido centrais para o entendimento desses sistemas. No entanto, ainda há uma grande lacuna tecnológica, pois a maioria dos softwares de visualização de redes existentes não tem tirado proveito da modularidade e hierarquia características de sistemas biológicos, principalmente quando essas sistemas possuem diversos níveis hierárquicos. A consequência disso é que muitas vezes a visualização da informação acaba sendo comprometida, dificultando a interpretação dos dados. Motivado pelos atributos do software RedeR (Castro et al., 2012), um pacote R/Bioconductor combinado com uma aplicação Java SE, apresentamos a versão RedeR Web, uma plataforma Web, intuitiva, responsiva que visa a simplificação da visualização de redes modulares. Neste estudo mostraremos como essa nova plataforma obtém proveito da modularidade e da hierarquia das redes biológicas, como otimizamos o tempo de renderização dos elementos, bem como apresentaremos um estudo de caso para demostrando como podemos usar esta ferramenta para visualizar a estrutura hierárquica de termos do GeneOntology. Palavras-chave: grafos, visualização, redes, sistemas biológicos, modularidade, hierarquia.Abstract: Visualization of graphs or networks has as main objective to assist the process of analysis and understanding of complex data sets, providing different perspectives of the same information, enhancing the appropriation of knowledge by the user. In the case of biological systems, the visualization and analysis of molecular networks have been central to the understanding of these systems. However, there is still a large technological gap, since most of the existing visualization software networks have not taken advantage of the modularity and hierarchy characteristics of biological systems, especially when these systems have several hierarchical levels. The consequence of this is that often the information visualization ends up being compromised, making hard to interpret the data. Motivated by the attributes of RedeR software (Castro et al., 2012), a R/Bioconductor package combined with a Java SE application, we show the RedeR Web version, an intuitive, responsive Web platform aimed at simplifying the visualization of modular networks. In this study we will show how this new platform takes advantage of the modularity and hierarchy of biological networks, how we optimize the rendering time of the elements, and we will present a case study to demonstrate how we can use this tool to visualize the hierarchical structure of terms in GeneOntology. Keywords: graphs, visualization, networks, biological systems, modularity, hierarchy

Omics analysis of chaetothyrialian black yeasts focusing on virulence and bioremediation genes

Orientadora: Profª Drª. Vania A. VicenteTese (doutorado) - Universidade Federal do Paraná, Setor de Tecnologia, Programa de Pós-Graduação em Engenharia de Bioprocessos e Biotecnologia. Defesa : Curitiba, 21/12/2020Inclui referências: p.136-163Resumo: As primeiras aparições do termo "levedura negra" ocorreram entre as décadas de 1890 e 1920, usado provisoriamente para descrever fungos polimórficos que não formam esporos ou possuem poder fermentativo, mas foram incluídos entre os fungos secretores de pigmento que ocorrem no leite, ar, sangue de insetos. De 1895 ate fevereiro de 2020, envolvendo 92 países, 2.065 instituições e 9.622 autores, a revisão bibliométrica (Capitulo 1) revela que a partir da década de 1970 as publicações aumentaram exponencialmente. Os conceitos agrupados demonstram uma alta relação com o aprimoramento das técnicas moleculares e ciências ômicas por meio da bioinformática. As leveduras negras são definidas como fungos melanizados, encontrados em diferentes nichos e habitats, com ecologia variada e muitas vezes encontradas em ambientes altamente tóxicos e assim, um grupo representativo pertence a ordem Chaetothyriales. Esta ordem e muito diversa, incluindo muitos agentes oportunistas de doenças em humanos e vertebrados de sangue frio. Por outro lado, algumas espécies tem sido descritas com capacidade de degradar compostos aromáticos e xenobióticos voláteis em aplicações de biorremediação como Cladophialophora exuberans (Capitulo 2). No total, fornecemos 12 sequenciamentos de genomas e montagens de dois gêneros bem conhecidos, Cladophialophora (1), Exophiala (11). A comparação dos dados do genoma foi realizada entre E. dermatitidis e E. spinifera, produtoras de capsulas, revelando que existiam perfis de virulência nessas duas leveduras negras, incluindo genes que estão possivelmente ligados a invasão cerebral, compartilhados com a espécie neurotrópica Rhinocladiella mackenziei. A ausência de perfis associados a virulência apoia a hipótese de que as leveduras negras são oportunistas, e não patógenos primários (Capitulo 3). Também foram avaliados os fatores de virulência, aptidão e as principais diferenças genéticas e de expressão genica na arvore de Exophiala spp. por meio da tecnologia de RNAseq. Um total de 48 genes únicos diferencialmente expressos foram e exclusivamente encontrados para a linhagem clinica, incluindo genes de vários genes processos metabólicos e regulação transcricional, e os genes regulados positivamente estão principalmente envolvidos no transporte transmembrana, processos biossintéticos e metabólico (Capitulo 4). Este estudo forneceu novos insights a respeito da virulência intrínseca das espécies dentro da ordem Chaetothyriales e indicando variabilidade intraespecífica e genes chave associados as interações patógeno hospedeiro. A identificação dos mecanismos de patogenicidade e das estratégias adaptativas aos tecidos de hospedeiros especialmente em imunocompetentes, podem auxiliar na elucidação do potencial destes agentes para as aplicações em processos de biorremediação.Abstract: The first appearances of the term "black yeast" occurred in the between the 1890s and 1920s used provisionally to describe polymorphous fungi which do not form spores and do not possess fermentative power but have been included among the pigment-secreting fungi occurring in milk, air, the blood of insects. Until February of 2020, involving 92 countries, 2065 institutions and 9622 authors. The bibliometric review (Chapter 1) reveals that after 1970s publications increased exponentially. The clustered concepts demonstrate a high relationship with the improvement of molecular techniques and omics sciences through bioinformatics. Nowadays, the black yeasts are defined as melanized fungi, found in different habitats and having different ecologies, often in polluted environments and a representative group belongs to the Chaetothyriales order. This order is much diverse, including many opportunistic agents of diseases in humans and cold-blooded vertebrates. On the other hand, some species has been described with capability to degrate aromatic compounds and xenobiotic volatiles in bioremediation applications as Cladophialophora exuberans (Chapter 2). In total, it was provided 12 genomes sequencing and assemblies of some well-known genera as following Cladophialophora (1) and Exophiala (11). Comparison of genome data were performed between the capsule-producing E. dermatitidis and E. spinifera revealing that virulence profiles existed in these two black yeasts, including genes that are possibly linked with brain invasion, shared with the neurotropic species Rhinocladiella mackenziei. The absence of consistent virulence-associated profiles supports the hypothesis that black yeasts are opportunists rather than primary pathogens (Chapter 3). It was also evaluated the virulence factors, fitness, and the major genetic and gene expression differences along the tree Exophiala spp. through of RNAseq technology. There were 48 unique genes differentially expressed exclusively to the clinical strain, including genes from various metabolic processes and transcriptional regulation, and the up-regulated genes are mainly involved in transmembrane transport, biosynthetic and metabolic processes (Chapter 4). This study provided new insights into the intrinsic virulence of species within the Chaetothyriales order indicating intraspecific variability and key genes associated with interactions between host and pathogen. The identification of pathogenic mechanisms and adaptive strategies to host tissues, especially in immunocompetent ones, can help in elucidating the potential of these agents and so, discriminate strains for bioremediation applications

SIGA - sistema de gestão acadêmica para a pós-graduação da UFPR

Acompanha CD-ROMOrientador: Paulo Vitor dos Santos ZeferinoMonografia (graduação) - Universidade Federal do Paraná, Setor de Educação Profissional e Tecnológica, Curso de Tecnologia em Análise e Desenvolvimento de Sistemas

SIGA - sistema de gestão acadêmica para a pós-graduação da UFPR

Acompanha CD-ROMOrientador: Paulo Vitor dos Santos ZeferinoMonografia (graduação) - Universidade Federal do Paraná, Setor de Educação Profissional e Tecnológica, Curso de Tecnologia em Análise e Desenvolvimento de Sistemas

The origin of human pathogenicity and biological interactions in Chaetothyriales

Fungi in the order Chaetothyriales are renowned for their ability to cause human infections. Nevertheless, they are not regarded as primary pathogens, but rather as opportunists with a natural habitat in the environment. Extremotolerance is a major trend in the order, but quite diferent from black yeasts in Capnodiales which focus on endurance, an important additional parameter is advancing toxin management. In the ancestral ecology of rock colonization, the association with metabolite-producing lichens is signifcant. Ant-association, dealing with pheromones and repellents, is another mainstay in the order. The phylogenetically derived family, Herpotrichiellaceae, shows dual ecology in monoaromatic hydrocarbon assimilation and the ability to cause disease in humans and cold-blooded vertebrates. In this study, data on ecology, phylogeny, and genomics were collected and analyzed in order to support this hypothesis on the evolutionary route of the species of Chaetothyriales. Comparing the ribosomal tree with that of enzymes involved in toluene degradation, a signifcant expansion of cytochromes is observed and the toluene catabolism is found to be complete in some of the Herpotrichiellaceae. This might enhance human systemic infection. However, since most species have to be traumatically inoculated in order to cause disease, their invasive potential is categorized as opportunism. Only in chromoblastomycosis, true pathogenicity might be surmised. The criterion would be the possible escape of agents of vertebrate disease from the host, enabling dispersal of adapted genotypes to subsequent generations.info:eu-repo/semantics/publishedVersio

Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019

Background: In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. Methods: GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death Ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw values of the posterior distribution. Findings: Global health has steadily improved over the past 30 years as measured by age-standardised DALY rates. After taking into account population growth and ageing, the absolute number of DALYs has remained stable. Since 2010, the pace of decline in global age-standardised DALY rates has accelerated in age groups younger than 50 years compared with the 1990–2010 time period, with the greatest annualised rate of decline occurring in the 0–9-year age group. Six infectious diseases were among the top ten causes of DALYs in children younger than 10 years in 2019: lower respiratory infections (ranked second), diarrhoeal diseases (third), malaria (fifth), meningitis (sixth), whooping cough (ninth), and sexually transmitted infections (which, in this age group, is fully accounted for by congenital syphilis; ranked tenth). In adolescents aged 10–24 years, three injury causes were among the top causes of DALYs: road injuries (ranked first), self-harm (third), and interpersonal violence (fifth). Five of the causes that were in the top ten for ages 10–24 years were also in the top ten in the 25–49-year age group: road injuries (ranked first), HIV/AIDS (second), low back pain (fourth), headache disorders (fifth), and depressive disorders (sixth). In 2019, ischaemic heart disease and stroke were the top-ranked causes of DALYs in both the 50–74-year and 75-years-and-older age groups. Since 1990, there has been a marked shift towards a greater proportion of burden due to YLDs from non-communicable diseases and injuries. In 2019, there were 11 countries where non-communicable disease and injury YLDs constituted more than half of all disease burden. Decreases in age-standardised DALY rates have accelerated over the past decade in countries at the lower end of the SDI range, while improvements have started to stagnate or even reverse in countries with higher SDI. Interpretation: As disability becomes an increasingly large component of disease burden and a larger component of health expenditure, greater research and developm nt investment is needed to identify new, more effective intervention strategies. With a rapidly ageing global population, the demands on health services to deal with disabling outcomes, which increase with age, will require policy makers to anticipate these changes. The mix of universal and more geographically specific influences on health reinforces the need for regular reporting on population health in detail and by underlying cause to help decision makers to identify success stories of disease control to emulate, as well as opportunities to improve. Funding: Bill & Melinda Gates Foundation. © 2020 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 licens

Global age-sex-specific fertility, mortality, healthy life expectancy (HALE), and population estimates in 204 countries and territories, 1950-2019 : a comprehensive demographic analysis for the Global Burden of Disease Study 2019

Background: Accurate and up-to-date assessment of demographic metrics is crucial for understanding a wide range of social, economic, and public health issues that affect populations worldwide. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 produced updated and comprehensive demographic assessments of the key indicators of fertility, mortality, migration, and population for 204 countries and territories and selected subnational locations from 1950 to 2019. Methods: 8078 country-years of vital registration and sample registration data, 938 surveys, 349 censuses, and 238 other sources were identified and used to estimate age-specific fertility. Spatiotemporal Gaussian process regression (ST-GPR) was used to generate age-specific fertility rates for 5-year age groups between ages 15 and 49 years. With extensions to age groups 10–14 and 50–54 years, the total fertility rate (TFR) was then aggregated using the estimated age-specific fertility between ages 10 and 54 years. 7417 sources were used for under-5 mortality estimation and 7355 for adult mortality. ST-GPR was used to synthesise data sources after correction for known biases. Adult mortality was measured as the probability of death between ages 15 and 60 years based on vital registration, sample registration, and sibling histories, and was also estimated using ST-GPR. HIV-free life tables were then estimated using estimates of under-5 and adult mortality rates using a relational model life table system created for GBD, which closely tracks observed age-specific mortality rates from complete vital registration when available. Independent estimates of HIV-specific mortality generated by an epidemiological analysis of HIV prevalence surveys and antenatal clinic serosurveillance and other sources were incorporated into the estimates in countries with large epidemics. Annual and single-year age estimates of net migration and population for each country and territory were generated using a Bayesian hierarchical cohort component model that analysed estimated age-specific fertility and mortality rates along with 1250 censuses and 747 population registry years. We classified location-years into seven categories on the basis of the natural rate of increase in population (calculated by subtracting the crude death rate from the crude birth rate) and the net migration rate. We computed healthy life expectancy (HALE) using years lived with disability (YLDs) per capita, life tables, and standard demographic methods. Uncertainty was propagated throughout the demographic estimation process, including fertility, mortality, and population, with 1000 draw-level estimates produced for each metric. Findings: The global TFR decreased from 2·72 (95% uncertainty interval [UI] 2·66–2·79) in 2000 to 2·31 (2·17–2·46) in 2019. Global annual livebirths increased from 134·5 million (131·5–137·8) in 2000 to a peak of 139·6 million (133·0–146·9) in 2016. Global livebirths then declined to 135·3 million (127·2–144·1) in 2019. Of the 204 countries and territories included in this study, in 2019, 102 had a TFR lower than 2·1, which is considered a good approximation of replacement-level fertility. All countries in sub-Saharan Africa had TFRs above replacement level in 2019 and accounted for 27·1% (95% UI 26·4–27·8) of global livebirths. Global life expectancy at birth increased from 67·2 years (95% UI 66·8–67·6) in 2000 to 73·5 years (72·8–74·3) in 2019. The total number of deaths increased from 50·7 million (49·5–51·9) in 2000 to 56·5 million (53·7–59·2) in 2019. Under-5 deaths declined from 9·6 million (9·1–10·3) in 2000 to 5·0 million (4·3–6·0) in 2019. Global population increased by 25·7%, from 6·2 billion (6·0–6·3) in 2000 to 7·7 billion (7·5–8·0) in 2019. In 2019, 34 countries had negative natural rates of increase; in 17 of these, the population declined because immigration was not sufficient to counteract the negative rate of decline. Globally, HALE increased from 58·6 years (56·1–60·8) in 2000 to 63·5 years (60·8–66·1) in 2019. HALE increased in 202 of 204 countries and territories between 2000 and 2019

Omics analysis of chaetothyrialian black yeasts focusing on virulence and bioremediation genes

Orientadora: Profª Drª. Vania A. VicenteTese (doutorado) - Universidade Federal do Paraná, Setor de Tecnologia, Programa de Pós-Graduação em Engenharia de Bioprocessos e Biotecnologia. Defesa : Curitiba, 21/12/2020Inclui referências: p.136-163Resumo: As primeiras aparições do termo "levedura negra" ocorreram entre as décadas de 1890 e 1920, usado provisoriamente para descrever fungos polimórficos que não formam esporos ou possuem poder fermentativo, mas foram incluídos entre os fungos secretores de pigmento que ocorrem no leite, ar, sangue de insetos. De 1895 ate fevereiro de 2020, envolvendo 92 países, 2.065 instituições e 9.622 autores, a revisão bibliométrica (Capitulo 1) revela que a partir da década de 1970 as publicações aumentaram exponencialmente. Os conceitos agrupados demonstram uma alta relação com o aprimoramento das técnicas moleculares e ciências ômicas por meio da bioinformática. As leveduras negras são definidas como fungos melanizados, encontrados em diferentes nichos e habitats, com ecologia variada e muitas vezes encontradas em ambientes altamente tóxicos e assim, um grupo representativo pertence a ordem Chaetothyriales. Esta ordem e muito diversa, incluindo muitos agentes oportunistas de doenças em humanos e vertebrados de sangue frio. Por outro lado, algumas espécies tem sido descritas com capacidade de degradar compostos aromáticos e xenobióticos voláteis em aplicações de biorremediação como Cladophialophora exuberans (Capitulo 2). No total, fornecemos 12 sequenciamentos de genomas e montagens de dois gêneros bem conhecidos, Cladophialophora (1), Exophiala (11). A comparação dos dados do genoma foi realizada entre E. dermatitidis e E. spinifera, produtoras de capsulas, revelando que existiam perfis de virulência nessas duas leveduras negras, incluindo genes que estão possivelmente ligados a invasão cerebral, compartilhados com a espécie neurotrópica Rhinocladiella mackenziei. A ausência de perfis associados a virulência apoia a hipótese de que as leveduras negras são oportunistas, e não patógenos primários (Capitulo 3). Também foram avaliados os fatores de virulência, aptidão e as principais diferenças genéticas e de expressão genica na arvore de Exophiala spp. por meio da tecnologia de RNAseq. Um total de 48 genes únicos diferencialmente expressos foram e exclusivamente encontrados para a linhagem clinica, incluindo genes de vários genes processos metabólicos e regulação transcricional, e os genes regulados positivamente estão principalmente envolvidos no transporte transmembrana, processos biossintéticos e metabólico (Capitulo 4). Este estudo forneceu novos insights a respeito da virulência intrínseca das espécies dentro da ordem Chaetothyriales e indicando variabilidade intraespecífica e genes chave associados as interações patógeno hospedeiro. A identificação dos mecanismos de patogenicidade e das estratégias adaptativas aos tecidos de hospedeiros especialmente em imunocompetentes, podem auxiliar na elucidação do potencial destes agentes para as aplicações em processos de biorremediação.Abstract: The first appearances of the term "black yeast" occurred in the between the 1890s and 1920s used provisionally to describe polymorphous fungi which do not form spores and do not possess fermentative power but have been included among the pigment-secreting fungi occurring in milk, air, the blood of insects. Until February of 2020, involving 92 countries, 2065 institutions and 9622 authors. The bibliometric review (Chapter 1) reveals that after 1970s publications increased exponentially. The clustered concepts demonstrate a high relationship with the improvement of molecular techniques and omics sciences through bioinformatics. Nowadays, the black yeasts are defined as melanized fungi, found in different habitats and having different ecologies, often in polluted environments and a representative group belongs to the Chaetothyriales order. This order is much diverse, including many opportunistic agents of diseases in humans and cold-blooded vertebrates. On the other hand, some species has been described with capability to degrate aromatic compounds and xenobiotic volatiles in bioremediation applications as Cladophialophora exuberans (Chapter 2). In total, it was provided 12 genomes sequencing and assemblies of some well-known genera as following Cladophialophora (1) and Exophiala (11). Comparison of genome data were performed between the capsule-producing E. dermatitidis and E. spinifera revealing that virulence profiles existed in these two black yeasts, including genes that are possibly linked with brain invasion, shared with the neurotropic species Rhinocladiella mackenziei. The absence of consistent virulence-associated profiles supports the hypothesis that black yeasts are opportunists rather than primary pathogens (Chapter 3). It was also evaluated the virulence factors, fitness, and the major genetic and gene expression differences along the tree Exophiala spp. through of RNAseq technology. There were 48 unique genes differentially expressed exclusively to the clinical strain, including genes from various metabolic processes and transcriptional regulation, and the up-regulated genes are mainly involved in transmembrane transport, biosynthetic and metabolic processes (Chapter 4). This study provided new insights into the intrinsic virulence of species within the Chaetothyriales order indicating intraspecific variability and key genes associated with interactions between host and pathogen. The identification of pathogenic mechanisms and adaptive strategies to host tissues, especially in immunocompetent ones, can help in elucidating the potential of these agents and so, discriminate strains for bioremediation applications

RedeR Web : uma plataforma web para organização e análise de redes modulares

Orientador: Prof. Dr. Mauro Antonio Alves CastroCoorientador: Prof. Dr. Alessandro BrawemanDissertação (mestrado) - Universidade Federal do Paraná, Setor de Educação Profissional e Tecnológica, Programa de Pós-Graduação em Bioinformática. Defesa : Curitiba, 29/09/2017Inclui referências: p.60-64Resumo: A visualização de grafos ou redes tem como principal objetivo auxiliar o processo de análise e compreensão de conjuntos de dados complexos, proporcionando perspectivas diferenciadas da mesma informação, potencializando a apropriação do conhecimento pelo usuário. Tratando-se de sistemas biológicos, a visualização e análise de redes moleculares têm sido centrais para o entendimento desses sistemas. No entanto, ainda há uma grande lacuna tecnológica, pois a maioria dos softwares de visualização de redes existentes não tem tirado proveito da modularidade e hierarquia características de sistemas biológicos, principalmente quando essas sistemas possuem diversos níveis hierárquicos. A consequência disso é que muitas vezes a visualização da informação acaba sendo comprometida, dificultando a interpretação dos dados. Motivado pelos atributos do software RedeR (Castro et al., 2012), um pacote R/Bioconductor combinado com uma aplicação Java SE, apresentamos a versão RedeR Web, uma plataforma Web, intuitiva, responsiva que visa a simplificação da visualização de redes modulares. Neste estudo mostraremos como essa nova plataforma obtém proveito da modularidade e da hierarquia das redes biológicas, como otimizamos o tempo de renderização dos elementos, bem como apresentaremos um estudo de caso para demostrando como podemos usar esta ferramenta para visualizar a estrutura hierárquica de termos do GeneOntology. Palavras-chave: grafos, visualização, redes, sistemas biológicos, modularidade, hierarquia.Abstract: Visualization of graphs or networks has as main objective to assist the process of analysis and understanding of complex data sets, providing different perspectives of the same information, enhancing the appropriation of knowledge by the user. In the case of biological systems, the visualization and analysis of molecular networks have been central to the understanding of these systems. However, there is still a large technological gap, since most of the existing visualization software networks have not taken advantage of the modularity and hierarchy characteristics of biological systems, especially when these systems have several hierarchical levels. The consequence of this is that often the information visualization ends up being compromised, making hard to interpret the data. Motivated by the attributes of RedeR software (Castro et al., 2012), a R/Bioconductor package combined with a Java SE application, we show the RedeR Web version, an intuitive, responsive Web platform aimed at simplifying the visualization of modular networks. In this study we will show how this new platform takes advantage of the modularity and hierarchy of biological networks, how we optimize the rendering time of the elements, and we will present a case study to demonstrate how we can use this tool to visualize the hierarchical structure of terms in GeneOntology. Keywords: graphs, visualization, networks, biological systems, modularity, hierarchy

SIGA - sistema de gestão acadêmica para a pós-graduação da UFPR

Acompanha CD-ROMOrientador: Paulo Vitor dos Santos ZeferinoMonografia (graduação) - Universidade Federal do Paraná, Setor de Educação Profissional e Tecnológica, Curso de Tecnologia em Análise e Desenvolvimento de Sistemas