Publicação
Development and implementation of bioinformatics tools for the reconstruction of GiSMos
| Resumo: | The reconstruction of Genomic-Scale Metabolic Model (GiSMo)s is an increasingly growing methodology, which allows to develop models that can be used to perform in silico predictions on the phenotypical response of an organism to environmental changes and genetic modifications. These predictions allow focusing in vivo experiments on methodologies that will, theoretically, present better results, thus reducing the high costs on time and money spent in laboratorial experiments. GiSMos are a mathematical representation of the organism’s genome, in the form of metabolic networks. As complex as these can be, because of the large number of compounds involved in many different reactions and pathways, the treatment of all such data is not easily manually performed. Several bioinformatics software were developed with the aims of improving this procedure, by automating many operations in the reconstruction process. Metabolic Models Reconstruction Using Genome-Scale Information (merlin) is one of such tools, following a philosophy that thrives on providing an intuitive and powerful graphical environment, to annotate data on key metabolic components and building a complete genome-scale model. While already encompassing a wide range of tools, it is still a work in development. Upon analyzing its functioning, several improvement opportunities were identified, mainly in existing operations. Moreover, missing important features for the reconstruction of GiSMos were as well identified. This work details the results of this analysis and the improvements performed to enrich merlin’s toolbox. |
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| Autores principais: | Dias, António Carlos Fortuna Ribeiro |
| Assunto: | Merlin Genome-Scale Metabolic Models Software Development |
| Ano: | 2017 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| Resumo: | The reconstruction of Genomic-Scale Metabolic Model (GiSMo)s is an increasingly growing methodology, which allows to develop models that can be used to perform in silico predictions on the phenotypical response of an organism to environmental changes and genetic modifications. These predictions allow focusing in vivo experiments on methodologies that will, theoretically, present better results, thus reducing the high costs on time and money spent in laboratorial experiments. GiSMos are a mathematical representation of the organism’s genome, in the form of metabolic networks. As complex as these can be, because of the large number of compounds involved in many different reactions and pathways, the treatment of all such data is not easily manually performed. Several bioinformatics software were developed with the aims of improving this procedure, by automating many operations in the reconstruction process. Metabolic Models Reconstruction Using Genome-Scale Information (merlin) is one of such tools, following a philosophy that thrives on providing an intuitive and powerful graphical environment, to annotate data on key metabolic components and building a complete genome-scale model. While already encompassing a wide range of tools, it is still a work in development. Upon analyzing its functioning, several improvement opportunities were identified, mainly in existing operations. Moreover, missing important features for the reconstruction of GiSMos were as well identified. This work details the results of this analysis and the improvements performed to enrich merlin’s toolbox. |
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