Monthly Archives: September 2007

MySQL installation in Debian Etch

After I setup a web application server, I would like to use a database for storing my data. MySQL is a free open source software that I am familiar with. For flexibility, I choose to install the binary non-rpm tar.gz … Continue reading

Posted in database, Linux | 7 Comments

Emacs 21 and JDE (JDEE) Installation in Debian Etch

To install JDE or JDEE or Java IDE for Emacs, it is easier to do it through Synaptic package manager than to manually install the package by following instructions on the JDEE web site ( However, we need to add … Continue reading

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How to Create an Entrez Utilities Java Library for Embedding in Java Applications

Update: April 24, 2009. ===================== With this update, I am describing how I recreated the latest version of NCBI Entrez Utilities Web Service Java library (v2.0),  eutils.jar, using Apache Axis2. Currently, I am using Debian Lenny RC2 AMD64 on Sony … Continue reading

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Opera web browser: Slow browsing problem in Linux

The problem is that ipv6 is automatically turned on for some reasons during the installation such as in Ubuntu 7.04. Since Opera is still not working on ipv6 but it has to use ipv6 first and then ipv4, that’s why the browsing … Continue reading

Posted in Linux | 1 Comment

Setup Microsoft True Type Fonts in Debian Etch

Using Microsoft true type fonts seems to make Linux appearance more pleasant at least in my opinion. In this blog, I would like to explain ways to set up Microsoft true type fonts in Linux by copying fonts from Windows … Continue reading

Posted in Linux | 5 Comments

Using Piccolo XML parser for parsing MEDLINE biomedical documents in XML format

Although Jdom XML parser is easy to understand and implement, it is suitable to only small XML files. The reason is that Jdom XML parser stores the whole XML structure into computer memory. In order to deal with large XML … Continue reading

Posted in Java | 7 Comments

Literature reading: Knowledge discovery across documents through concept chain queries

Title: Knowledge discovery across documents through concept chain queries Authors: Wei Jin and Rohini K. Srihari Publisher: Sixth IEEE International Conference on Data Mining – Workshops (ICDMW’06), IEEE Computer Society, 2006. In this paper, the authors combine Srinivasan’s topic profile and … Continue reading

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