Shinpei Hayashi

ATTED-II provides coexpressed gene networks for Arabidopsis

ATTED-II (http://atted.jp) is a database of gene coexpression in Arabidopsis that can be used to design a wide variety of experiments, including the prioritization of genes for functional identification or for studies of regulatory relationships. Here, we report updates of ATTED-II that focus especially on functionalities for constructing gene networks with regard to the following points: (i) introducing a new measure of gene coexpression to retrieve functionally related genes more accurately, (ii) implementing clickable maps for all gene networks for step-by-step navigation, (iii) applying Google Maps API to create a single map for a large network, (iv) including information about protein–protein interactions, (v) identifying conserved patterns of coexpression and (vi) showing and connecting KEGG pathway information to identify functional modules. With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis.

ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis

Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction database (ATTED-II) that provides co-regulated gene relationships based on co-expressed genes deduced from microarray data and the predicted cis elements. ATTED-II () includes the following features: (i) lists and networks of co-expressed genes calculated from 58 publicly available experimental series, which are composed of 1388 GeneChip data in A.thaliana; (ii) prediction of cis-regulatory elements in the 200 bp region upstream of the transcription start site to predict co-regulated genes amongst the co-expressed genes; and (iii) visual representation of expression patterns for individual genes. ATTED-II can thus help researchers to clarify the function and regulation of particular genes and gene networks.

COXPRESdb: a database of coexpressed gene networks in mammals

A database of coexpressed gene sets can provide valuable information for a wide variety of experimental designs, such as targeting of genes for functional identification, gene regulation and/or protein–protein interactions. Coexpressed gene databases derived from publicly available GeneChip data are widely used in Arabidopsis research, but platforms that examine coexpression for higher mammals are rather limited. Therefore, we have constructed a new database, COXPRESdb (coexpressed gene database) (http://coxpresdb.hgc.jp), for coexpressed gene lists and networks in human and mouse. Coexpression data could be calculated for 19 777 and 21 036 genes in human and mouse, respectively, by using the GeneChip data in NCBI GEO. COXPRESdb enables analysis of the four types of coexpression networks: (i) highly coexpressed genes for every gene, (ii) genes with the same GO annotation, (iii) genes expressed in the same tissue and (iv) user-defined gene sets. When the networks became too big for the static picture on the web in GO networks or in tissue networks, we used Google Maps API to visualize them interactively. COXPRESdb also provides a view to compare the human and mouse coexpression patterns to estimate the conservation between the two species.

Refactoring edit history of source code

This paper proposes a concept for refactoring an edit history of source code and a technique for its automation. The aim of our history refactoring is to improve the clarity and usefulness of the history without changing its overall effect. We have defined primitive history refactorings including their preconditions and procedures, and large refactorings composed of these primitives. Moreover, we have implemented a supporting tool that automates the application of history refactorings in the middle of a source code editing process. Our tool enables developers to pursue some useful applications using history refactorings such as task level commit from an entangled edit history and selective undo of past edit operations.

A Tool for Attributed Goal-Oriented Requirements Analysis

his paper presents an integrated supporting tool for Attributed Goal-Oriented Requirements Analysis (AGORA), which is an extended version of goal-oriented analysis. Our tool assists seamlessly requirements analysts and stakeholders in their activities throughout AGORA steps including constructing goal graphs with group work, prioritizing goals, and version control of goal graphs.

Sentence-to-Code Traceability Recovery with Domain Ontologies

We propose an ontology-based technique for recovering trace ability links between a natural language sentence specifying features of a software product and the source code of the product. Some software products have been released without detailed documentation. To automatically detect code fragments associated with sentences describing a feature, the relations between source code structures and problem domains are important. We model the knowledge of the problem domains as domain ontologies having concepts of the domains and their relations. Using semantic relations on the ontologies in addition to method invocation relations and the similarity between an identifier on the code and words in the sentences, we locate the code fragments corresponding to the given sentences. Additionally, our prioritization mechanism which orders the located results of code fragments based on the ontologies enables users to select and analyze the results effectively. To show effectiveness of our approach in terms of accuracy, a case study was carried out with our proof-of-concept tool and summarized.

Recovering traceability links between a simple natural language sentence and source code using domain ontologies

This paper proposes an ontology-based technique for recovering traceability links between a natural language sentence specifying features of a software product and the source code of the product. Some software products have been released without detailed documentation. To automatically detect code fragments associated with the functional descriptions written in the form of simple sentences, the relationships between source code structures and problem domains are important. In our approach, we model the knowledge of the problem domains as domain ontologies. By using semantic relationships of the ontologies in addition to method invocation relationships and the similarity between an identifier on the code and words in the sentences, we can detect code fragments corresponding to the sentences. A case study within a domain of painting software shows that we obtained results of higher quality than without ontologies.

Design Pattern Detection by Using Meta Patterns

One of the approaches to improve program understanding is to extract what kinds of design pattern are used in existing object-oriented software. This paper proposes a technique for efficiently and accurately detecting occurrences of design patterns included in source codes. We use both static and dynamic analyses to achieve the detection with high accuracy. Moreover, to reduce computation and maintenance costs, detection conditions are hierarchically specified based on Prees meta patterns as common structures of design patterns. The usage of Prolog to represent the detection conditions enables us to easily add and modify them. Finally, we have implemented an automated tool as an Eclipse plug-in and conducted experiments with Java programs. The experimental results show the effectiveness of our approach.

Sintering behaviour of diopside, CaMgSi2O6, from various powder preparation methods

Des poudres de diopside ont ete preparees par calcination, fusion et trempe ou par procede sol-gel. On etudie leur distribution granulometrique, les phases cristallines formees lors de la cuisson, la microstructure et la composition chimique des grains cristallins et des joints de grain

Recording finer-grained software evolution with IDE: an annotation-based approach

This paper proposes a formalized technique for generating finer-grained source code deltas according to a developers editing intentions. Using the technique, the developer classifies edit operations of source code by annotating the time series of the edit history with the switching information of their editing intentions. Based on the classification, the history is sorted and converted automatically to appropriate source code deltas to be committed separately to a version repository. This paper also presents algorithms for automating the generation process and a prototyping tool to implement them.