Efficient Reconstruction of Metabolic Pathways by Bidirectional Chemical Search

One of the main challenges in systems biology is the establishment of the metabolome: a catalogue of the metabolites and biochemical reactions present in a specific organism. Current knowledge of biochemical pathways as stored in public databases such as KEGG, is based on carefully curated genomic evidence for the presence of specific metabolites and enzymes that activate particular biochemical reactions. In this paper, we present an efficient method to build a substantial portion of the artificial chemistry defined by the metabolites and biochemical reactions in a given metabolic pathway, which is based on bidirectional chemical search. Computational results on the pathways stored in KEGG reveal novel biochemical pathways

Transformations on hypergraph families

We present a new general theory of function-based hypergraph transformations on finite families of finite hypergraphs. A function-based hypergraph transformation formalises the action of structurally modifying hypergraphs from a family in a consistent manner. The mathematical form of the transformations facilitates their analysis and incorporation into larger mathematical structures, and concurs with the function-based nature of modelling in the physical world. Since quotients of hypergraphs afford their simplification and comparison, we also discuss the notion of a quotient hypergraph transformation induced by an equivalence relation on the vertex set of a hypergraph family. Finally, we demonstrate function-based hypergraph transformations with two fundamental classes of examples involving the addition or deletion of hyperedges or hypergraphs

Especificación, análisis y generación de entornos para lenguajes visuales de dominio específico

Tesis doctoral inédita. Universidad Autónoma de Madrid, Escuela Politécnica Superior, diciembre de 200