We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.
A first course on programming remains a core initial component of any CS undergraduate programme. Our position is that CS students need to be taught aspects of design and problem-solving in parallel with programming. We have adopted a top-down approach in our initial programming courses, emphasising the need for design, using an appropriate notation, before coding begins. Since we are interested in developing skills in object orientation the main abstractions we are concerned with are those for types and objects. Our type design notation, adapted from that for algorithm design, emphasises type interface design without reference to details of implementation (e.g. in C++). It avoids having to show, and explain at the design stage, the 'concrete representation' of a type -its 'attributes' (private member variables).We are also interested in imperative languages, so we also need to capture concepts concerned with algorithms and control-flow. Using diagrammatic representations in this context is not new and despite the fact that disparaging remarks are often used about such techniques, the general concept is of value. Nevertheless, we recognise the need to get away from the 'goto' mentality of flowcharts.Our approach has been, at the very least, a qualified success. We remain convinced of its value as evidenced by those students who recognise the value of design at the outset (especially those who arrive with no baggage from previous programming experience) and carry on in this way throughout their undergraduate careers.
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