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Early work on proteins identified the existence of helices and extended sheets in protein secondary structures, a high-level classification which remains popular today. Using the Snob program for information-theoretic Minimum Message Length (MML) classification, we are able to take the protein dihedral angles as determined by X-ray crystallography, and(More)
EDGAR (Extraction of Drugs, Genes and Relations) is a natural language processing system that extracts information about drugs and genes relevant to cancer from the biomedical literature. This automatically extracted information has remarkable potential to facilitate computational analysis in the molecular biology of cancer, and the technology is(More)
The trend toward high-throughput techniques in molecular biology and the explosion of online scientific data threaten to overwhelm the ability of researchers to take full advantage of available information. This problem is particularly severe in the rapidly expanding area of gene expression experiments, for example, those carried out with cDNA microarrays(More)
This paper describes a unified framework for visualizing the preparations for, and results of, hundreds of machine learning experiments. These experiments were designed to improve the accuracy of enzyme functional predictions from sequence, and in many cases were successful. Our system provides graphical user interfaces for defining and exploring training(More)
We developed a tool for visualizing data related to protein function, based on the nomenclature defined by the International Enzyme Commission. The method represents the 1327 specific reaction types and three additional levels of abstract classifications in the nomenclature as an interactive graph. Each node and link in the graph can have associated with it(More)
This paper outlines work in progress towards using information structure maps as a graphical means of informing the reader of his/her position in a hypertext array, and of the rhetorical intent of any given utterance. The graphical navigation aids described here support the non-native writer's (NNW) use of model technical text, and provide an inroad for(More)
In constructivist second language (L2) learning environments 1 , particularly in relatively teacher-remote situations such as those involving Learning Management Systems (LMS), task performance freedom can be an obstacle to the achievement of specific educational objectives. This paper presents an example of task narrowing achieved by Cmap 2 interface(More)
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