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Architecture of basic building blocks in protein and domain structural interaction networks
, 2005
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An applicative randomaccess stack
 Information Processing Letters
, 1983
"... Kqwords: Applicative programming, linked list, number system. randomaccess stack 1. Introduction 2. The skewbinary number system Applicative (functional) programming has long been advocated on theoretical grounds as the formal properties of such programs are simple and elegant. Recently, there has ..."
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Kqwords: Applicative programming, linked list, number system. randomaccess stack 1. Introduction 2. The skewbinary number system Applicative (functional) programming has long been advocated on theoretical grounds as the formal properties of such programs are simple and elegant. Recently, there has been a trend to bring
DESIGN STRUCTURE AND ITERATIVE RELEASE OF SCIENTIFIC SOFTWARE
"... I dedicate this thesis to my wife and parents. iii One of the main objectives of software development in scientific computing is efficiency. Being focused on highly specialized application domain, important software quality metrics, e.g., usability, extensibility,etc may not be amongst the list of ..."
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I dedicate this thesis to my wife and parents. iii One of the main objectives of software development in scientific computing is efficiency. Being focused on highly specialized application domain, important software quality metrics, e.g., usability, extensibility,etc may not be amongst the list of primary objectives. In this research, we have studied the design structures and iterative releases of scientific research software using Design Structure Matrix(DSM). We implemented a DSM partitioning algorithm using sparse matrix data structure Compressed Row Storage(CRS), and its timing was better than those obtained from the most widely used C++ library boost. Secondly, we computed several architectural complexity metrics, compared releases and total release costs of a number of open source scientific research software. One of the important finding is the absence of circular dependencies in studied software which attributes to the strong emphasis on computational performance of the code. Iterative release analysis indicates that there might be a correspondence between “clustering coefficient ” and “release
BIOINFORMATICS Architecture of Basic Building Blocks in Protein and Domain Structural Interaction Networks
"... Motivation: The structural interaction of proteins and their domains in networks is one of the most basic molecular mechanisms for biological cells. Topological analysis of such networks can provide an understanding of and solutions for predicting properties of proteins and their evolution in terms ..."
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Motivation: The structural interaction of proteins and their domains in networks is one of the most basic molecular mechanisms for biological cells. Topological analysis of such networks can provide an understanding of and solutions for predicting properties of proteins and their evolution in terms of domains. A single paradigm for the analysis of interactions at different layers, such as domain and protein layers, is needed. Results: Applying a colored vertex graph model, we integrated two basic interaction layers under a unified model: (1) structural domains, and (2) their protein/complex networks. We identified four basic and distinct elements in the model that explains protein interactions at the domain level. We searched for motifs in the networks to detect their topological characteristics using a pruning strategy and a hash table for rapid detection. We obtained the following results: First, compared with a random distribution, a substantial part of the protein interactions could be explained by domainlevel structural interaction information. Second, there were distinct kinds of protein interaction patterns classified by specific and distinguishable numbers of domains. The intermolecular domain interaction was the most dominant protein interaction pattern. Third, despite the coverage of the protein interaction information differing among species, the similarity of their networks indicated shared architectures of protein interaction network in living organisms. Remarkably, there were only a few basic architectures in the model (fewer than ten for a fournode network topology), and we propose that most biological combinations of domains into proteins and complexes can be explained by a small number of key topological motifs.
An Efficient Algorithm for the Reliability of Consecutivekn Networks
"... A consecutivekn network is a generalization of the wellknown consecutivekoutofn system, and has many practical applications. This network consists of n + 2 nodes (node 0, the source, nodes 1, 2, …, n, and node n + 1, the target) and directed links from node i to node j (0 ≤ i < j ≤ n + 1, ..."
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A consecutivekn network is a generalization of the wellknown consecutivekoutofn system, and has many practical applications. This network consists of n + 2 nodes (node 0, the source, nodes 1, 2, …, n, and node n + 1, the target) and directed links from node i to node j (0 ≤ i < j ≤ n + 1, j − i ≤ k). Because all nodes except the source and target, and all links are fallible, the network works if and only if there exists a working path from the source to the target. For the k = 2 case, based on identical node reliabilities and some assumptions on link reliabilities, Chen, Hwang and Li (1993) gave a recursive algorithm for the reliability of the consecutive2n network. In this paper we give a closed form equation for the reliability of the general consecutivekn network by means of a novel Markov chain method. Based on the equation, we propose an algorithm which is more efficient than other published ones for the reliability of the consecutivekn network.
Behaviour of the Related Algorithms
, 1982
"... Representation techniques for relational languages and the worst case asymptotical time complexity behaviour of the related algorithms. Futaci, Suha. ..."
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Representation techniques for relational languages and the worst case asymptotical time complexity behaviour of the related algorithms. Futaci, Suha.