Diseño de una herramienta para la asistencia en el ensamblaje sintético de la bacteria E. Coli en la producción de biocombustibles.
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Due to the impact of environmental pollution, it is valuable to produce high quality biofuels and to leverage organic waste that normally would have no use. Through Synthetic Biology, the science of designing and building new biological systems, it is possible to improve existing organisms to process waste that is not traditionally used for biofuels production, such as butter milk. Metabolic pathways are a set of chemical reactions catalyzed by enzymes that carry out essential functions within cells. Through the redesign of these pathways, it is possible to create connections that allow for the implementation of new functions that normally are not present in nature. From a computational point of view, metabolic pathways, which can be found in data sources as the Encyclopedia of Genes and Genomes (KEGG), can be converted to basic data structures, such as graphs. These transformations enable the application of well known algorithms, which allows for the optimization of the analyses required to achieve the assembly of new organisms. The present work aims to design a tool that allows for the transformation of metabolic pathways and the development of path finding algorithms that establish relevant links between compounds that are essential to the production of biofuels. As a result, a catalog of biobricks will be created from the analysis of a subset of paths. This will allow for the synthetic assembly of the E. Coli bacteria. The assembly's structure and functions will be characterized according to the pieces used. Finally, new constructions will be visualized with the goal of demonstrating and supporting the analysis processes, thus, assisting people that work in the field of Synthetic Biology.
Proyecto de Graduación (Maestría en Computación con énfasis en Ciencias de la Computación) Instituto Tecnológico de Costa Rica, Escuela de Ingeniería en Computación, 2014.