|Version 85 (modified by leo, 5 years ago)|
Taro L. Saito (leo)
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
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)
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)
- Transaction processing
- Query optimization
- Database Storage & Indexes
Biological Database Managenment
- UTGB (University of Tokyo Genome Browser)
- SCMD (Saccharomyces Cerevisiae Morphological Database)
I have been developing several utilities, implemented mainly in C++ and Java:
- Xerial http://www.xerial.org
- 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.
- 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://maven.xerial.org/repository/site/xerial-core/apidocs/org/xerial/json/JSONPullParser.html
- Command-Line Argument Parser (OptionParser?)
- for Java 1.5 or higher
- contained in the XerialCore package
- API: http://maven.xerial.org/repository/site/xerial-core/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.
- which is integrated into UTGB framework.
- Maven ANTLR 3 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.
- 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
Study Group Activities in Our Laboratory
- Since 2007. Learning Database Systems