English/Japanese

Assistant Professor at Morishita Laboratory (Bioinformatics & Database Systems)
Department of Computational Biology, Graduate School of Frontier Sciences.
University of Tokyo

5-1-5 Kashiwanoha, Kashiwa City
Chiba Pref. 277-8562, JAPAN
+81-47-136-4065

March 2002 : Bachelor of Science (Department of Information Science, Faculty of Science, University of Tokyo, Japan)
March 2004 : Master of Information Science and Technology (Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, Japan)
April 2005 - March 2007 : Research fellow of the Japan Society for the Promotion of Science (JSPS)
March 2007 : Ph. D. (Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, Japan)
April 2007 - (current) : Assistant Professor (Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Japan)

• see Publications
• My DBLP Entry

• Relational-Style XML Query
• XML Query Optimization
• Update-tolerant XML Indexing
• Transaction management for XML (lock protocols, concurrency control)

• Transaction processing
• Query optimization
• Database Storage & Indexes

• UTGB (University of Tokyo Genome Browser)
• SCMD (Saccharomyces Cerevisiae Morphological Database)
• etc...

I have been developing several utilities, implemented mainly in C++ and Java:

• Xerial http://www.xerial.org
• XML Database Management System (C++/Java development in progress)
• Xerial (C++), XerialJ (Java)
• XerialJ includes XerialCore , XerialStorage packages.
• For now, Xerial C++ is not an open-source project until the problem #108 is resolved.
• (Obsolete) Setup information: wiki:devel/Setup
• SQLite JDBC
• Java Database Connection (JDBC) Driver for SQLite
• SQLite is a ready-to-use relational-database engine that can be run on a single file (or multiple files), which does not require any installation process.
• BeanUtil
• Java Object and Tree-Structured Data (XML, JSON, Map, ANTLR Parse Tree, etc.) Binding Toolkit
• Contained in XerialCore package.
• I use this BeanUtil to read XML/JSON/ANTLR Parse tree data into my Java programs. With this BeanUtil library, it becomes fun to handle tree-structured data, since there is no need to write complex SAX/DOM style programs.
• BeanUtil library is also utilized in UTGB (University of Tokyo Genome Browser) Framework, which is a web-based database development framework that enables the Biology researchers, who are usually not familiar with programming, to launch a new web-site for instantly serving Biological databases.
• JSON Pull Parser
• Pull-Style JSON Data Reader for Java
• contained in the XerialCore package
• API: http://www.xerial.org/maven/repository/site/xerial-project/apidocs/org/xerial/json/JSONPullParser.html
• Command-Line Argument Parser (OptionParser )
• for Java 1.5 or higher
• contained in the XerialCore package
• API: http://www.xerial.org/maven/repository/site/xerial-project/apidocs/org/xerial/util/cui/OptionParser.html
• UTGB (The University of Tokyo Genome Browser Framework)
• UTGB is a bundle of Java libraries for developing web-based database servers. This includes portable Tomcat server, SQLite database engine (or connection to other DBMSs through JDBC), AJAX-style graphical user interface for data browsing, which is implemented using Google Web Toolkit (GWT).
• Portable Tomcat Web Server
• With this program, you can start up the Tomcat Web Application Server from your Java programs. No daemon process.
• http://www.xerial.org/maven/repository/site/xerial-project/apidocs/index.html
• which is integrated into UTGB framework.
• Maven ANTLR 3 Plugin
• http://www.xerial.org/maven/repository/artifact/org/xerial/maven/maven-antlr-plugin/
• A maven plugin for generating Java lexer/parser codes from ANTLR grammar files in your source folder.

• Xerial Aqua Lecture Management System
• Student Data Management, Report Submission through the Web, Edit Scores, etc.
• http://www.xerial.org/svn/project/ruby/trunk/lecture
• written using Ruby on Rails

• How to use Subversion , the version control system.
• How to develop web applications in Java
• This article covers Servlet, Tomcat, Google Web Toolkit (GWT), etc.
• MPI Programming

• Since 2007. Learning Database Systems