Monthly Archives: September 2007

MySQL installation in Debian Etch

Posted on September 28, 2007 by mrtextminer

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

Posted on September 26, 2007 by mrtextminer

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 (http://jdee.sunsite.dk/). However, we need to add … Continue reading →

Posted in Java, Linux | Leave a comment

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

Posted on September 20, 2007 by mrtextminer

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 →

Posted in Java | Leave a comment

Opera web browser: Slow browsing problem in Linux

Posted on September 19, 2007 by mrtextminer

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

Posted on September 18, 2007 by mrtextminer

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

Posted on September 17, 2007 by mrtextminer

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

Posted on September 17, 2007 by mrtextminer

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 →

Posted in text mining | Leave a comment

Mount Windows NTFS partition in Debian Etch

Posted on September 15, 2007 by mrtextminer

The situation is that you have a machine with a dual boot of Windows XP or Vista and Debian Etch, and you want to be able to access the Windows XP partition from the Debian partition. What you need to … Continue reading →

Posted in Linux | 7 Comments

Literature reading: Text mining: Generating hypotheses from MEDLINE

Posted on September 15, 2007 by mrtextminer

Title: Text Mining: Generating hypotheses from MEDLINE Author: Padmini Srinivasan. Publisher: Journal of the American Society for Information Science and Technology, 55(5): 396-413,  2004. In this paper, the author presents two literature-based discovery algorithms for hypothesis generation, termed open discovery and closed discovery algorithms. … Continue reading →

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Java Hashtable: Sorted by Values

Posted on September 14, 2007 by mrtextminer

When writing a program, we occasionally encounter a situation where we need to use Hashtable for storing data and then sort data in the Hashtable. In this blog, I demonstrate how to sort data in a Hashtable based on values. … Continue reading →

Posted in Java | 15 Comments