About xerial.org

This web site xerial.org is managed by Taro L. Saito.

English/Japanese

Taro L. Saito (leo)

Affiliation

Assistant Professor at Morishita Laboratory (Bioinformatics & Database Systems)

Department of Computational Biology, Graduate School of Frontier Sciences University of Tokyo

Address & Phone

5-1-5 Kashiwanoha, Kashiwa City Chiba Pref. 277-8562, JAPAN

Phone: +81-47-136-4065

Curriculum Vitae (CV)

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)

Publications

• see Publications
• My DBLP Entry

Research Interests

XML Database Management System (Xerial)

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

Database Implementation

• Transaction processing
• Query optimization
• Database Storage & Indexes

Biological Database Managenment

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

Programming

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/tomcat-server/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
  • Features: 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

Articles

• 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

Study Group Activities in Our Laboratory

• Since 2007. Learning Database Systems