We are currently in the process of integrating the metabolic, genetic and product-interaction net... more We are currently in the process of integrating the metabolic, genetic and product-interaction networks of Escherichia coli, with a view to creating a whole cell model [1]. In an effort to assess the physiological accuracy of our current model, we undertook extensive analysis of the metabolic component of the model, which consists of over 850 enzymes. Conversion of this network into a stoichiometric matrix allowed interpretation through the use of graph theory and its associated algorithms. Our strategy, and subsequent results, differed from that previously described [3]. Advantageously, our strategy allows consideration of either metabolites or enzymes as nodes and ameliorates the need to introduce temporary complexes. Various analyses were performed to describe the topology and other properties of the metabolic network. The ‘small-world’ characteristic described as being inherent in metabolic systems was investigated by determining node interconnectivity . To determine the metaboli...
The creation of cell models from annotated genome information, as well as additional data from ot... more The creation of cell models from annotated genome information, as well as additional data from other databases, requires both a format and medium for its distribution. Standards are described for the representation of the data in the form of Document Type Definitions (DTDs) for XML files. Separate DTDs are detailed for genetic, metabolic and gene product- interaction networks, which can
We are currently in the process of integrating the metabolic, genetic and product-interaction net... more We are currently in the process of integrating the metabolic, genetic and product-interaction networks of Escherichia coli, with a view to creating a whole cell model [1]. In an effort to assess the physiological accuracy of our current model, we undertook extensive analysis of the metabolic component of the model, which consists of over 850 enzymes. Conversion of this network into a stoichiometric matrix allowed interpretation through the use of graph theory and its associated algorithms. Our strategy, and subsequent results, differed from that previously described [3]. Advantageously, our strategy allows consideration of either metabolites or enzymes as nodes and ameliorates the need to introduce temporary complexes. Various analyses were performed to describe the topology and other properties of the metabolic network. The ‘small-world’ characteristic described as being inherent in metabolic systems was investigated by determining node interconnectivity . To determine the metaboli...
The creation of cell models from annotated genome information, as well as additional data from ot... more The creation of cell models from annotated genome information, as well as additional data from other databases, requires both a format and medium for its distribution. Standards are described for the representation of the data in the form of Document Type Definitions (DTDs) for XML files. Separate DTDs are detailed for genetic, metabolic and gene product- interaction networks, which can
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Papers by Hugh Spence