1. About xerial.org
  2. Taro L. Saito, PhD (leo)
    1. Affiliation
    2. Address & Phone
    3. Curriculum Vitae (CV)
    4. Publications
    5. Research Interests
      1. XML Database Management System (Xerial)
      2. Database Implementation
      3. Biological Database Managenment
    6. Programming
    7. Lecture Notes
    8. Articles
    9. Blogs
    10. Study Group Activities in Our Laboratory

About xerial.org

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

English/Japanese

Taro L. Saito, PhD (leo)

http://www.xerial.org/leo-email.png

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: +81-471-36-3985

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

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:

  • 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.
  • UTGB Toolkit (The University of Tokyo Genome Browser Toolkit)
    • 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).
  • 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.

Lecture Notes

Articles

Blogs

Study Group Activities in Our Laboratory

Attachments